Automated Code Analysis Automated Code Analysis
./usr/share/pyshared/cogent/maths/period.py:268: invalid syntax
^
./usr/share/pyshared/cogent/__init__.py:4: 'os' imported but unused
./usr/share/pyshared/cogent/__init__.py:47: 'STANDARD_CODON' imported but unused
./usr/share/pyshared/cogent/__init__.py:47: 'PROTEIN' imported but unused
./usr/share/pyshared/cogent/__init__.py:47: 'DNA' imported but unused
./usr/share/pyshared/cogent/__init__.py:47: 'CodonAlphabet' imported but unused
./usr/share/pyshared/cogent/__init__.py:47: 'RNA' imported but unused
./usr/share/pyshared/cogent/maths/matrix_logarithm.py:7: 'transpose' imported but unused
./usr/share/pyshared/cogent/maths/matrix_exponentiation.py:17: 'LinAlgError' imported but unused
./usr/share/pyshared/cogent/maths/matrix_exponentiation.py:38: redefinition of function 'inv' from line 34
./usr/share/pyshared/cogent/maths/scipy_optimisers.py:5: 'fmin_bfgs' imported but unused
./usr/share/pyshared/cogent/maths/scipy_optimisers.py:81: local variable 'template' is assigned to but never used
./usr/share/pyshared/cogent/maths/optimiser.py:66: local variable 'detail' is assigned to but never used
./usr/share/pyshared/cogent/maths/geometry.py:4: redefinition of unused 'sqrt' from line 4
./usr/share/pyshared/cogent/maths/distance_transform.py:56: 'logical_or' imported but unused
./usr/share/pyshared/cogent/maths/distance_transform.py:56: 'logical_xor' imported but unused
./usr/share/pyshared/cogent/maths/distance_transform.py:56: 'geterr' imported but unused
./usr/share/pyshared/cogent/maths/distance_transform.py:56: 'logical_not' imported but unused
./usr/share/pyshared/cogent/maths/distance_transform.py:256: local variable 'dist' is assigned to but never used
./usr/share/pyshared/cogent/maths/distance_transform.py:465: local variable 'rowdiff' is assigned to but never used
./usr/share/pyshared/cogent/maths/distance_transform.py:723: local variable 'rowstds' is assigned to but never used
./usr/share/pyshared/cogent/maths/distance_transform.py:726: local variable 'n' is assigned to but never used
./usr/share/pyshared/cogent/maths/optimisers.py:9: 'DownhillSimplex' imported but unused
./usr/share/pyshared/cogent/maths/optimisers.py:51: undefined name 'wanings'
./usr/share/pyshared/cogent/maths/svd.py:6: 'expm' imported but unused
./usr/share/pyshared/cogent/maths/svd.py:7: 'logm' imported but unused
./usr/share/pyshared/cogent/maths/svd.py:9: 'reshape' imported but unused
./usr/share/pyshared/cogent/maths/svd.py:9: 'NewAxis' imported but unused
./usr/share/pyshared/cogent/maths/svd.py:9: 'product' imported but unused
./usr/share/pyshared/cogent/maths/svd.py:11: 'random' imported but unused
./usr/share/pyshared/cogent/maths/scipy_optimize.py:34: redefinition of unused 'linesearch' from line 32
./usr/share/pyshared/cogent/maths/scipy_optimize.py:320: local variable 'D' is assigned to but never used
./usr/share/pyshared/cogent/maths/scipy_optimize.py:487: redefinition of function 'phiprime' from line 477
./usr/share/pyshared/cogent/maths/scipy_optimize.py:892: local variable 'N' is assigned to but never used
./usr/share/pyshared/cogent/maths/scipy_optimize.py:899: local variable 'sk' is assigned to but never used
./usr/share/pyshared/cogent/maths/scipy_optimize.py:1393: local variable 'xmin' is assigned to but never used
./usr/share/pyshared/cogent/maths/scipy_optimize.py:1393: local variable 'fval' is assigned to but never used
./usr/share/pyshared/cogent/maths/stats/test.py:14: 'clip' imported but unused
./usr/share/pyshared/cogent/maths/stats/test.py:14: 'reshape' imported but unused
./usr/share/pyshared/cogent/maths/stats/test.py:14: 'nan' imported but unused
./usr/share/pyshared/cogent/maths/stats/test.py:20: 'add' imported but unused
./usr/share/pyshared/cogent/maths/stats/test.py:21: 'choice' imported but unused
./usr/share/pyshared/cogent/maths/stats/test.py:500: local variable 'e' is assigned to but never used
./usr/share/pyshared/cogent/maths/stats/test.py:604: local variable 'Syy' is assigned to but never used
./usr/share/pyshared/cogent/maths/stats/test.py:775: local variable 'e' is assigned to but never used
./usr/share/pyshared/cogent/maths/stats/test.py:1007: local variable 'total_obs' is assigned to but never used
./usr/share/pyshared/cogent/maths/stats/test.py:1008: local variable 'num_x' is assigned to but never used
./usr/share/pyshared/cogent/maths/stats/test.py:1042: local variable 'sample' is assigned to but never used
./usr/share/pyshared/cogent/maths/stats/test.py:1048: local variable 'ties' is assigned to but never used
./usr/share/pyshared/cogent/maths/stats/test.py:1089: local variable 'total_obs' is assigned to but never used
./usr/share/pyshared/cogent/maths/stats/test.py:1090: local variable 'num_x' is assigned to but never used
./usr/share/pyshared/cogent/maths/stats/period.py:2: 'shuffle' imported but unused
./usr/share/pyshared/cogent/maths/stats/period.py:2: 'random' imported but unused
./usr/share/pyshared/cogent/maths/stats/period.py:9: redefinition of unused 'factorial' from line 6
./usr/share/pyshared/cogent/maths/stats/period.py:87: redefinition of unused 'seq_to_symbols' from line 84
./usr/share/pyshared/cogent/maths/stats/special.py:485: local variable 'sgngam' is assigned to but never used
./usr/share/pyshared/cogent/maths/stats/special.py:1087: local variable 'i' is assigned to but never used
./usr/share/pyshared/cogent/maths/stats/__init__.py:13: 'chisqprob' imported but unused
./usr/share/pyshared/cogent/maths/stats/distribution.py:6: 'ndtri' imported but unused
./usr/share/pyshared/cogent/maths/stats/util.py:111: 'e' imported but unused
./usr/share/pyshared/cogent/maths/stats/util.py:524: redefinition of function '_get_mode' from line 447
./usr/share/pyshared/cogent/maths/stats/util.py:676: local variable 'r' is assigned to but never used
./usr/share/pyshared/cogent/maths/stats/util.py:723: local variable 'v' is assigned to but never used
./usr/share/pyshared/cogent/maths/stats/util.py:746: local variable 'i' is assigned to but never used
./usr/share/pyshared/cogent/maths/stats/alpha_diversity.py:152: local variable 'alpha' is assigned to but never used
./usr/share/pyshared/cogent/maths/stats/cai/get_by_cai.py:3: 'CutgParser' imported but unused
./usr/share/pyshared/cogent/maths/stats/cai/get_by_cai.py:5: 'CodonUsage' imported but unused
./usr/share/pyshared/cogent/maths/stats/cai/util.py:76: local variable 'result' is assigned to but never used
./usr/share/pyshared/cogent/maths/stats/cai/util.py:104: local variable 'k' is assigned to but never used
./usr/share/pyshared/cogent/maths/stats/cai/util.py:105: local variable 'v' is assigned to but never used
./usr/share/pyshared/cogent/maths/stats/cai/util.py:106: local variable 'n' is assigned to but never used
./usr/share/pyshared/cogent/maths/stats/cai/util.py:257: undefined name 'arithmetic_meani'
./usr/share/pyshared/cogent/maths/stats/cai/adaptor.py:5: 'Info' imported but unused
./usr/share/pyshared/cogent/maths/stats/cai/adaptor.py:8: 'GeneticCode' imported but unused
./usr/share/pyshared/cogent/maths/stats/cai/adaptor.py:9: 'sort' imported but unused
./usr/share/pyshared/cogent/maths/stats/cai/adaptor.py:9: 'concatenate' imported but unused
./usr/share/pyshared/cogent/maths/stats/cai/adaptor.py:9: 'sqrt' imported but unused
./usr/share/pyshared/cogent/maths/stats/cai/adaptor.py:9: 'zeros' imported but unused
./usr/share/pyshared/cogent/maths/stats/cai/adaptor.py:11: 'argv' imported but unused
./usr/share/pyshared/cogent/maths/stats/cai/adaptor.py:80: undefined name 'UnsafeCodonsFromString'
./usr/share/pyshared/cogent/maths/unifrac/fast_tree.py:582: local variable 'row_result' is assigned to but never used
./usr/share/pyshared/cogent/maths/unifrac/fast_unifrac.py:7: 'from cogent.maths.unifrac.fast_tree import *' used; unable to detect undefined names
./usr/share/pyshared/cogent/maths/unifrac/fast_unifrac.py:11: 'from cogent.cluster.metric_scaling import *' used; unable to detect undefined names
./usr/share/pyshared/cogent/maths/unifrac/fast_unifrac.py:527: local variable 'result' is assigned to but never used
./usr/share/pyshared/cogent/maths/unifrac/fast_unifrac.py:958: redefinition of unused 'StringIO' from line 15
./usr/share/pyshared/cogent/maths/matrix/distance.py:91: redefinition of function 'Pow' from line 85
./usr/share/pyshared/cogent/app/knetfold.py:3: 'CommandLineAppResult' imported but unused
./usr/share/pyshared/cogent/app/knetfold.py:5: '_find_synonym' imported but unused
./usr/share/pyshared/cogent/app/knetfold.py:5: 'Parameters' imported but unused
./usr/share/pyshared/cogent/app/knetfold.py:5: 'MixedParameter' imported but unused
./usr/share/pyshared/cogent/app/knetfold.py:5: 'FlagParameter' imported but unused
./usr/share/pyshared/cogent/app/knetfold.py:5: 'Parameter' imported but unused
./usr/share/pyshared/cogent/app/ilm.py:3: 'CommandLineAppResult' imported but unused
./usr/share/pyshared/cogent/app/ilm.py:3: 'ResultPath' imported but unused
./usr/share/pyshared/cogent/app/ilm.py:5: 'Parameters' imported but unused
./usr/share/pyshared/cogent/app/ilm.py:5: 'Parameter' imported but unused
./usr/share/pyshared/cogent/app/raxml.py:12: 'choice' imported but unused
./usr/share/pyshared/cogent/app/raxml.py:300: local variable 'e' is assigned to but never used
./usr/share/pyshared/cogent/app/uclust.py:22: 'makedirs' imported but unused
./usr/share/pyshared/cogent/app/uclust.py:22: 'remove' imported but unused
./usr/share/pyshared/cogent/app/uclust.py:23: 'splitext' imported but unused
./usr/share/pyshared/cogent/app/uclust.py:23: 'isfile' imported but unused
./usr/share/pyshared/cogent/app/uclust.py:23: 'isdir' imported but unused
./usr/share/pyshared/cogent/app/uclust.py:23: 'abspath' imported but unused
./usr/share/pyshared/cogent/app/uclust.py:483: local variable 'uc_output_filepath' is assigned to but never used
./usr/share/pyshared/cogent/app/uclust.py:484: local variable 'cd_hit_filepath' is assigned to but never used
./usr/share/pyshared/cogent/app/uclust.py:496: local variable 'uc_filepath' is assigned to but never used
./usr/share/pyshared/cogent/app/uclust.py:497: local variable 'clstr_filepath' is assigned to but never used
./usr/share/pyshared/cogent/app/infernal.py:8: 'MinimalFastaParser' imported but unused
./usr/share/pyshared/cogent/app/infernal.py:15: 'ViennaStructure' imported but unused
./usr/share/pyshared/cogent/app/infernal.py:15: 'wuss_to_vienna' imported but unused
./usr/share/pyshared/cogent/app/vienna_package.py:3: 'CommandLineAppResult' imported but unused
./usr/share/pyshared/cogent/app/vienna_package.py:5: 'Parameters' imported but unused
./usr/share/pyshared/cogent/app/vienna_package.py:5: 'Parameter' imported but unused
./usr/share/pyshared/cogent/app/vienna_package.py:5: 'is_not_None' imported but unused
./usr/share/pyshared/cogent/app/vienna_package.py:5: '_find_synonym' imported but unused
./usr/share/pyshared/cogent/app/vienna_package.py:268: undefined name 'FILETYPE_TO_EXTENSION'
./usr/share/pyshared/cogent/app/rnaforester.py:3: 'mkdir' imported but unused
./usr/share/pyshared/cogent/app/rnaforester.py:3: 'close' imported but unused
./usr/share/pyshared/cogent/app/rnaforester.py:3: 'getcwd' imported but unused
./usr/share/pyshared/cogent/app/rnaforester.py:4: 'choice' imported but unused
./usr/share/pyshared/cogent/app/rnaforester.py:6: 'ResultPath' imported but unused
./usr/share/pyshared/cogent/app/rnaforester.py:8: 'Parameters' imported but unused
./usr/share/pyshared/cogent/app/rnaforester.py:8: 'Parameter' imported but unused
./usr/share/pyshared/cogent/app/rnaforester.py:8: 'ValuedParameter' imported but unused
./usr/share/pyshared/cogent/app/rnaforester.py:8: 'MixedParameter' imported but unused
./usr/share/pyshared/cogent/app/rnaforester.py:8: 'is_not_None' imported but unused
./usr/share/pyshared/cogent/app/rnaforester.py:8: '_find_synonym' imported but unused
./usr/share/pyshared/cogent/app/rnaforester.py:105: undefined name 'ApplicationError'
./usr/share/pyshared/cogent/app/rnaforester.py:145: undefined name 'ApplicationError'
./usr/share/pyshared/cogent/app/rnaforester.py:148: local variable 'synonyms' is assigned to but never used
./usr/share/pyshared/cogent/app/rnashapes.py:13: 'CommandLineAppResult' imported but unused
./usr/share/pyshared/cogent/app/rnashapes.py:13: 'ResultPath' imported but unused
./usr/share/pyshared/cogent/app/rnashapes.py:15: 'is_not_None' imported but unused
./usr/share/pyshared/cogent/app/rnashapes.py:15: '_find_synonym' imported but unused
./usr/share/pyshared/cogent/app/rnashapes.py:15: 'Parameters' imported but unused
./usr/share/pyshared/cogent/app/rnashapes.py:15: 'MixedParameter' imported but unused
./usr/share/pyshared/cogent/app/rnashapes.py:15: 'Parameter' imported but unused
./usr/share/pyshared/cogent/app/gctmpca.py:26: 'FilePath' imported but unused
./usr/share/pyshared/cogent/app/gctmpca.py:27: 'DSO78_matrix' imported but unused
./usr/share/pyshared/cogent/app/unafold.py:8: 'CommandLineAppResult' imported but unused
./usr/share/pyshared/cogent/app/unafold.py:10: 'Parameters' imported but unused
./usr/share/pyshared/cogent/app/unafold.py:10: 'Parameter' imported but unused
./usr/share/pyshared/cogent/app/cove.py:3: 'CommandLineAppResult' imported but unused
./usr/share/pyshared/cogent/app/cove.py:5: 'Parameters' imported but unused
./usr/share/pyshared/cogent/app/cove.py:5: 'Parameter' imported but unused
./usr/share/pyshared/cogent/app/cove.py:5: 'MixedParameter' imported but unused
./usr/share/pyshared/cogent/app/cove.py:5: 'is_not_None' imported but unused
./usr/share/pyshared/cogent/app/cove.py:5: '_find_synonym' imported but unused
./usr/share/pyshared/cogent/app/rnaview.py:5: 'MixedParameter' imported but unused
./usr/share/pyshared/cogent/app/cmfinder.py:7: 'CommandLineAppResult' imported but unused
./usr/share/pyshared/cogent/app/cmfinder.py:9: 'MixedParameter' imported but unused
./usr/share/pyshared/cogent/app/cmfinder.py:9: 'Parameters' imported but unused
./usr/share/pyshared/cogent/app/cmfinder.py:9: 'Parameter' imported but unused
./usr/share/pyshared/cogent/app/cmfinder.py:133: local variable 'motifList' is assigned to but never used
./usr/share/pyshared/cogent/app/cmfinder.py:138: local variable 'inputPath' is assigned to but never used
./usr/share/pyshared/cogent/app/dialign.py:17: 'guess_input_handler' imported but unused
./usr/share/pyshared/cogent/app/dialign.py:17: 'get_tmp_filename' imported but unused
./usr/share/pyshared/cogent/app/dialign.py:19: 'choice' imported but unused
./usr/share/pyshared/cogent/app/dialign.py:20: 'DndParser' imported but unused
./usr/share/pyshared/cogent/app/dialign.py:21: 'PhyloNode' imported but unused
./usr/share/pyshared/cogent/app/dialign.py:22: 'MinimalFastaParser' imported but unused
./usr/share/pyshared/cogent/app/comrna.py:3: 'CommandLineAppResult' imported but unused
./usr/share/pyshared/cogent/app/comrna.py:3: 'ResultPath' imported but unused
./usr/share/pyshared/cogent/app/comrna.py:5: 'is_not_None' imported but unused
./usr/share/pyshared/cogent/app/comrna.py:5: '_find_synonym' imported but unused
./usr/share/pyshared/cogent/app/comrna.py:5: 'Parameters' imported but unused
./usr/share/pyshared/cogent/app/comrna.py:5: 'MixedParameter' imported but unused
./usr/share/pyshared/cogent/app/comrna.py:5: 'FlagParameter' imported but unused
./usr/share/pyshared/cogent/app/comrna.py:5: 'Parameter' imported but unused
./usr/share/pyshared/cogent/app/stride.py:7: redefinition of unused 'StringIO' from line 5
./usr/share/pyshared/cogent/app/dynalign.py:5: 'Parameters' imported but unused
./usr/share/pyshared/cogent/app/dynalign.py:5: 'FlagParameter' imported but unused
./usr/share/pyshared/cogent/app/dynalign.py:5: 'Parameter' imported but unused
./usr/share/pyshared/cogent/app/dynalign.py:5: 'MixedParameter' imported but unused
./usr/share/pyshared/cogent/app/dynalign.py:7: 'commands' imported but unused
./usr/share/pyshared/cogent/app/dynalign.py:8: 'platform' imported but unused
./usr/share/pyshared/cogent/app/dynalign.py:9: 'mkdir' imported but unused
./usr/share/pyshared/cogent/app/dynalign.py:9: 'close' imported but unused
./usr/share/pyshared/cogent/app/dynalign.py:9: 'getcwd' imported but unused
./usr/share/pyshared/cogent/app/dynalign.py:168: undefined name 'ApplicationError'
./usr/share/pyshared/cogent/app/dynalign.py:208: undefined name 'ApplicationError'
./usr/share/pyshared/cogent/app/dynalign.py:210: local variable 'parameters' is assigned to but never used
./usr/share/pyshared/cogent/app/dynalign.py:211: local variable 'synonyms' is assigned to but never used
./usr/share/pyshared/cogent/app/sffinfo.py:4: 'ResultPath' imported but unused
./usr/share/pyshared/cogent/app/sffinfo.py:114: undefined name 'ApplicationError'
./usr/share/pyshared/cogent/app/sffinfo.py:119: local variable 'synonyms' is assigned to but never used
./usr/share/pyshared/cogent/app/consan.py:4: 'ResultPath' imported but unused
./usr/share/pyshared/cogent/app/consan.py:6: 'Parameters' imported but unused
./usr/share/pyshared/cogent/app/consan.py:6: 'Parameter' imported but unused
./usr/share/pyshared/cogent/app/consan.py:6: 'MixedParameter' imported but unused
./usr/share/pyshared/cogent/app/consan.py:6: 'is_not_None' imported but unused
./usr/share/pyshared/cogent/app/consan.py:6: '_find_synonym' imported but unused
./usr/share/pyshared/cogent/app/consan.py:123: undefined name 'ApplicationError'
./usr/share/pyshared/cogent/app/pfold.py:10: 'CommandLineAppResult' imported but unused
./usr/share/pyshared/cogent/app/pfold.py:10: 'ResultPath' imported but unused
./usr/share/pyshared/cogent/app/dotur.py:6: 'MixedParameter' imported but unused
./usr/share/pyshared/cogent/app/dotur.py:10: 'SequenceCollection' imported but unused
./usr/share/pyshared/cogent/app/dotur.py:11: 'PROTEIN' imported but unused
./usr/share/pyshared/cogent/app/dotur.py:11: 'DNA' imported but unused
./usr/share/pyshared/cogent/app/dotur.py:11: 'RNA' imported but unused
./usr/share/pyshared/cogent/app/contrafold.py:3: 'CommandLineAppResult' imported but unused
./usr/share/pyshared/cogent/app/contrafold.py:3: 'ResultPath' imported but unused
./usr/share/pyshared/cogent/app/contrafold.py:5: 'is_not_None' imported but unused
./usr/share/pyshared/cogent/app/contrafold.py:5: '_find_synonym' imported but unused
./usr/share/pyshared/cogent/app/contrafold.py:5: 'Parameters' imported but unused
./usr/share/pyshared/cogent/app/contrafold.py:5: 'MixedParameter' imported but unused
./usr/share/pyshared/cogent/app/contrafold.py:5: 'ValuedParameter' imported but unused
./usr/share/pyshared/cogent/app/contrafold.py:5: 'Parameter' imported but unused
./usr/share/pyshared/cogent/app/clearcut.py:5: 'MixedParameter' imported but unused
./usr/share/pyshared/cogent/app/clearcut.py:8: 'SequenceCollection' imported but unused
./usr/share/pyshared/cogent/app/clearcut.py:9: 'PROTEIN' imported but unused
./usr/share/pyshared/cogent/app/fasttree_v1.py:64: local variable 'suppress_stdout' is assigned to but never used
./usr/share/pyshared/cogent/app/fasttree_v1.py:95: undefined name 'ApplicationError'
./usr/share/pyshared/cogent/app/mfold.py:9: 'CommandLineAppResult' imported but unused
./usr/share/pyshared/cogent/app/mfold.py:11: 'Parameters' imported but unused
./usr/share/pyshared/cogent/app/mfold.py:11: 'Parameter' imported but unused
./usr/share/pyshared/cogent/app/sfold.py:10: 'CommandLineAppResult' imported but unused
./usr/share/pyshared/cogent/app/sfold.py:12: 'Parameters' imported but unused
./usr/share/pyshared/cogent/app/sfold.py:12: 'MixedParameter' imported but unused
./usr/share/pyshared/cogent/app/sfold.py:12: 'FlagParameter' imported but unused
./usr/share/pyshared/cogent/app/sfold.py:12: 'Parameter' imported but unused
./usr/share/pyshared/cogent/app/pknotsrg.py:3: 'CommandLineAppResult' imported but unused
./usr/share/pyshared/cogent/app/pknotsrg.py:3: 'ResultPath' imported but unused
./usr/share/pyshared/cogent/app/pknotsrg.py:5: 'Parameters' imported but unused
./usr/share/pyshared/cogent/app/pknotsrg.py:5: 'MixedParameter' imported but unused
./usr/share/pyshared/cogent/app/pknotsrg.py:5: 'Parameter' imported but unused
./usr/share/pyshared/cogent/app/formatdb.py:65: local variable 'input_filepath' is assigned to but never used
./usr/share/pyshared/cogent/app/fasttree.py:71: local variable 'suppress_stdout' is assigned to but never used
./usr/share/pyshared/cogent/app/fasttree.py:102: undefined name 'ApplicationError'
./usr/share/pyshared/cogent/app/rdp_classifier.py:20: 'Parameter' imported but unused
./usr/share/pyshared/cogent/app/rdp_classifier.py:22: 'guess_input_handler' imported but unused
./usr/share/pyshared/cogent/app/nupack.py:11: 'Parameters' imported but unused
./usr/share/pyshared/cogent/app/nupack.py:11: 'FlagParameter' imported but unused
./usr/share/pyshared/cogent/app/nupack.py:11: 'Parameter' imported but unused
./usr/share/pyshared/cogent/app/nupack.py:11: 'ValuedParameter' imported but unused
./usr/share/pyshared/cogent/app/nupack.py:11: 'MixedParameter' imported but unused
./usr/share/pyshared/cogent/app/nupack.py:11: 'is_not_None' imported but unused
./usr/share/pyshared/cogent/app/nupack.py:11: '_find_synonym' imported but unused
./usr/share/pyshared/cogent/app/nupack.py:143: undefined name 'ApplicationError'
./usr/share/pyshared/cogent/app/blast.py:6: 'MixedParameter' imported but unused
./usr/share/pyshared/cogent/app/blast.py:7: 'get_tmp_filename' imported but unused
./usr/share/pyshared/cogent/app/blast.py:10: 'QMEBlast9' imported but unused
./usr/share/pyshared/cogent/app/blast.py:913: local variable 'last_num_ids' is assigned to but never used
./usr/share/pyshared/cogent/app/blast.py:997: local variable 'seq_file' is assigned to but never used
./usr/share/pyshared/cogent/app/util.py:2: 'commands' imported but unused
./usr/share/pyshared/cogent/app/util.py:3: 'platform' imported but unused
./usr/share/pyshared/cogent/app/util.py:4: 'sep' imported but unused
./usr/share/pyshared/cogent/app/util.py:4: 'close' imported but unused
./usr/share/pyshared/cogent/app/util.py:7: 'array' imported but unused
./usr/share/pyshared/cogent/app/util.py:7: 'nonzero' imported but unused
./usr/share/pyshared/cogent/app/util.py:7: 'zeros' imported but unused
./usr/share/pyshared/cogent/app/util.py:7: 'max' imported but unused
./usr/share/pyshared/cogent/app/util.py:8: 'Parameter' imported but unused
./usr/share/pyshared/cogent/app/util.py:8: 'FlagParameter' imported but unused
./usr/share/pyshared/cogent/app/util.py:8: 'ValuedParameter' imported but unused
./usr/share/pyshared/cogent/app/util.py:8: 'MixedParameter' imported but unused
./usr/share/pyshared/cogent/app/util.py:8: 'is_not_None' imported but unused
./usr/share/pyshared/cogent/app/util.py:8: '_find_synonym' imported but unused
./usr/share/pyshared/cogent/app/util.py:10: 'if_' imported but unused
./usr/share/pyshared/cogent/app/util.py:366: local variable 'synonyms' is assigned to but never used
./usr/share/pyshared/cogent/app/carnac.py:3: 'CommandLineAppResult' imported but unused
./usr/share/pyshared/cogent/app/carnac.py:5: 'Parameters' imported but unused
./usr/share/pyshared/cogent/app/carnac.py:5: 'Parameter' imported but unused
./usr/share/pyshared/cogent/app/carnac.py:58: local variable 'seq_counter' is assigned to but never used
./usr/share/pyshared/cogent/app/rnaalifold.py:3: 'CommandLineAppResult' imported but unused
./usr/share/pyshared/cogent/app/rnaalifold.py:5: 'Parameters' imported but unused
./usr/share/pyshared/cogent/app/rnaalifold.py:5: 'Parameter' imported but unused
./usr/share/pyshared/cogent/app/rnaalifold.py:5: '_find_synonym' imported but unused
./usr/share/pyshared/cogent/app/rnaalifold.py:10: 'rnaalifold_parser' imported but unused
./usr/share/pyshared/cogent/app/rnaalifold.py:12: 'ViennaStructure' imported but unused
./usr/share/pyshared/cogent/app/foldalign.py:11: 'CommandLineAppResult' imported but unused
./usr/share/pyshared/cogent/app/foldalign.py:11: 'ResultPath' imported but unused
./usr/share/pyshared/cogent/app/foldalign.py:13: 'is_not_None' imported but unused
./usr/share/pyshared/cogent/app/foldalign.py:13: '_find_synonym' imported but unused
./usr/share/pyshared/cogent/app/foldalign.py:13: 'Parameters' imported but unused
./usr/share/pyshared/cogent/app/foldalign.py:13: 'MixedParameter' imported but unused
./usr/share/pyshared/cogent/app/foldalign.py:13: 'Parameter' imported but unused
./usr/share/pyshared/cogent/app/muscle.py:8: 'choice' imported but unused
./usr/share/pyshared/cogent/app/mafft.py:7: 'get_tmp_filename' imported but unused
./usr/share/pyshared/cogent/app/mafft.py:9: 'choice' imported but unused
./usr/share/pyshared/cogent/app/mafft.py:11: 'PROTEIN' imported but unused
./usr/share/pyshared/cogent/app/mafft.py:11: 'DNA' imported but unused
./usr/share/pyshared/cogent/app/mafft.py:11: 'RNA' imported but unused
./usr/share/pyshared/cogent/app/mafft.py:13: 'PhyloNode' imported but unused
./usr/share/pyshared/cogent/app/mafft.py:14: 'DndParser' imported but unused
./usr/share/pyshared/cogent/recalculation/calculation.py:5: 'warnings' imported but unused
./usr/share/pyshared/cogent/recalculation/calculation.py:209: local variable 'detail' is assigned to but never used
./usr/share/pyshared/cogent/recalculation/definition.py:67: 'warnings' imported but unused
./usr/share/pyshared/cogent/recalculation/definition.py:80: 'chdtri' imported but unused
./usr/share/pyshared/cogent/recalculation/definition.py:81: 'parallel' imported but unused
./usr/share/pyshared/cogent/recalculation/definition.py:418: local variable 'N' is assigned to but never used
./usr/share/pyshared/cogent/recalculation/scope.py:663: redefinition of function 'callback' from line 659
./usr/share/pyshared/cogent/util/terminal.py:19: redefinition of unused 'curses' from line 17
./usr/share/pyshared/cogent/util/table.py:538: local variable 'is_reversed' is assigned to but never used
./usr/share/pyshared/cogent/util/table.py:548: local variable 'cast' is assigned to but never used
./usr/share/pyshared/cogent/util/misc.py:12: 'maxint' imported but unused
./usr/share/pyshared/cogent/util/misc.py:13: 'popen' imported but unused
./usr/share/pyshared/cogent/util/misc.py:15: 'sum' imported but unused
./usr/share/pyshared/cogent/util/misc.py:15: 'logical_not' imported but unused
./usr/share/pyshared/cogent/util/misc.py:204: local variable 'e' is assigned to but never used
./usr/share/pyshared/cogent/util/misc.py:1098: local variable 'ValueError' is assigned to but never used
./usr/share/pyshared/cogent/util/progress_display.py:24: 'contextlib' imported but unused
./usr/share/pyshared/cogent/util/progress_display.py:24: 'warnings' imported but unused
./usr/share/pyshared/cogent/util/progress_display.py:25: 'atexit' imported but unused
./usr/share/pyshared/cogent/util/progress_display.py:25: 'os' imported but unused
./usr/share/pyshared/cogent/util/update_version.py:273: local variable 'found_version_line' is assigned to but never used
./usr/share/pyshared/cogent/util/update_version.py:292: local variable 'found_version_line' is assigned to but never used
./usr/share/pyshared/cogent/util/update_version.py:311: local variable 'found_version_line' is assigned to but never used
./usr/share/pyshared/cogent/util/dict2d.py:234: local variable 'constructor' is assigned to but never used
./usr/share/pyshared/cogent/util/dict2d.py:543: local variable 'item_lookup' is assigned to but never used
./usr/share/pyshared/cogent/util/organizer.py:74: local variable 'results' is assigned to but never used
./usr/share/pyshared/cogent/util/trie.py:148: local variable 'labels' is assigned to but never used
./usr/share/pyshared/cogent/util/transform.py:16: 'and_' imported but unused
./usr/share/pyshared/cogent/util/transform.py:16: 'or_' imported but unused
./usr/share/pyshared/cogent/util/transform.py:17: 'logical_or' imported but unused
./usr/share/pyshared/cogent/util/transform.py:17: 'logical_and' imported but unused
./usr/share/pyshared/cogent/util/transform.py:17: 'logical_not' imported but unused
./usr/share/pyshared/cogent/util/transform.py:224: redefinition of function 'result' from line 220
./usr/share/pyshared/cogent/util/transform.py:499: redefinition of function 'result' from line 494
./usr/share/pyshared/cogent/util/unit_test.py:36: 'TestSuite' imported but unused
./usr/share/pyshared/cogent/util/unit_test.py:36: 'main' imported but unused
./usr/share/pyshared/cogent/util/unit_test.py:36: 'findTestCases' imported but unused
./usr/share/pyshared/cogent/util/unit_test.py:37: 'recursive_flatten' imported but unused
./usr/share/pyshared/cogent/util/unit_test.py:317: local variable 'e' is assigned to but never used
./usr/share/pyshared/cogent/util/parallel.py:51: redefinition of unused 'MPI' from line 48
./usr/share/pyshared/cogent/util/recode_alignment.py:41: 'OptionParser' imported but unused
./usr/share/pyshared/cogent/util/recode_alignment.py:43: 'Alignment' imported but unused
./usr/share/pyshared/cogent/util/recode_alignment.py:45: 'PROTEIN' imported but unused
./usr/share/pyshared/cogent/util/array.py:4: 'mul' imported but unused
./usr/share/pyshared/cogent/util/array.py:4: 'getitem' imported but unused
./usr/share/pyshared/cogent/seqsim/analysis.py:2: 'RangeNode' imported but unused
./usr/share/pyshared/cogent/seqsim/analysis.py:2: 'balanced_breakpoints' imported but unused
./usr/share/pyshared/cogent/seqsim/analysis.py:103: local variable 'rates' is assigned to but never used
./usr/share/pyshared/cogent/seqsim/analysis.py:291: undefined name 'BalancedTree'
./usr/share/pyshared/cogent/seqsim/analysis.py:294: undefined name 'xxx'
./usr/share/pyshared/cogent/seqsim/analysis.py:296: undefined name 'Rates'
./usr/share/pyshared/cogent/seqsim/analysis.py:297: undefined name 'scale_trace'
./usr/share/pyshared/cogent/seqsim/analysis.py:302: undefined name 'random_q_matrix'
./usr/share/pyshared/cogent/seqsim/analysis.py:303: undefined name 'scale_trace'
./usr/share/pyshared/cogent/seqsim/analysis.py:307: undefined name 'rand_rna'
./usr/share/pyshared/cogent/seqsim/analysis.py:319: undefined name 'BalancedTree'
./usr/share/pyshared/cogent/seqsim/analysis.py:324: undefined name 'random_q_matrix'
./usr/share/pyshared/cogent/seqsim/analysis.py:325: undefined name 'scale_trace'
./usr/share/pyshared/cogent/seqsim/analysis.py:329: undefined name 'rand_rna'
./usr/share/pyshared/cogent/seqsim/analysis.py:336: undefined name 'flatten_q_matrices'
./usr/share/pyshared/cogent/seqsim/analysis.py:338: undefined name 'scale_trace'
./usr/share/pyshared/cogent/seqsim/analysis.py:339: undefined name 'flatten_q_matrices'
./usr/share/pyshared/cogent/seqsim/analysis.py:341: undefined name 'cov'
./usr/share/pyshared/cogent/seqsim/analysis.py:342: undefined name 'corrcoef'
./usr/share/pyshared/cogent/seqsim/analysis.py:343: undefined name 'euclidean_norm'
./usr/share/pyshared/cogent/seqsim/analysis.py:344: undefined name 'euclidean_norm'
./usr/share/pyshared/cogent/seqsim/analysis.py:345: undefined name 'eigenvalues'
./usr/share/pyshared/cogent/seqsim/analysis.py:348: undefined name 'eigenvalues'
./usr/share/pyshared/cogent/seqsim/analysis.py:351: undefined name 'ratio_two_best'
./usr/share/pyshared/cogent/seqsim/analysis.py:352: undefined name 'ratio_two_best'
./usr/share/pyshared/cogent/seqsim/analysis.py:353: undefined name 'ratio_best_to_sum'
./usr/share/pyshared/cogent/seqsim/analysis.py:354: undefined name 'ratio_best_to_sum'
./usr/share/pyshared/cogent/seqsim/analysis.py:355: undefined name 'weiss'
./usr/share/pyshared/cogent/seqsim/analysis.py:357: undefined name 'dists_from_mean'
./usr/share/pyshared/cogent/seqsim/analysis.py:359: undefined name 'var'
./usr/share/pyshared/cogent/seqsim/analysis.py:361: undefined name 'mean'
./usr/share/pyshared/cogent/seqsim/analysis.py:362: undefined name 'euclidean_distance'
./usr/share/pyshared/cogent/seqsim/analysis.py:365: undefined name 'euclidean_norm'
./usr/share/pyshared/cogent/seqsim/analysis.py:365: undefined name 'cov'
./usr/share/pyshared/cogent/seqsim/analysis.py:378: undefined name 'all_p_from_tree'
./usr/share/pyshared/cogent/seqsim/analysis.py:379: undefined name 'pair_p_from_tree'
./usr/share/pyshared/cogent/seqsim/analysis.py:380: undefined name 'get_qs'
./usr/share/pyshared/cogent/seqsim/analysis.py:381: undefined name 'get_qs'
./usr/share/pyshared/cogent/seqsim/analysis.py:382: undefined name 'take_off_diag'
./usr/share/pyshared/cogent/seqsim/analysis.py:384: undefined name 'scale_trace'
./usr/share/pyshared/cogent/seqsim/analysis.py:385: undefined name 'flatten_q_matrices'
./usr/share/pyshared/cogent/seqsim/analysis.py:386: undefined name 'flatten_q_matrices'
./usr/share/pyshared/cogent/seqsim/analysis.py:387: undefined name 'dists_from_mean'
./usr/share/pyshared/cogent/seqsim/analysis.py:389: undefined name 'var'
./usr/share/pyshared/cogent/seqsim/analysis.py:390: undefined name 'dists_from_mean'
./usr/share/pyshared/cogent/seqsim/analysis.py:392: undefined name 'var'
./usr/share/pyshared/cogent/seqsim/analysis.py:394: undefined name 'flatten_q_matrices'
./usr/share/pyshared/cogent/seqsim/analysis.py:395: undefined name 'corrcoef'
./usr/share/pyshared/cogent/seqsim/analysis.py:396: undefined name 'ratio_two_best'
./usr/share/pyshared/cogent/seqsim/analysis.py:396: undefined name 'eigenvalues'
./usr/share/pyshared/cogent/seqsim/analysis.py:398: undefined name 'cov'
./usr/share/pyshared/cogent/seqsim/analysis.py:399: undefined name 'eigenvalues'
./usr/share/pyshared/cogent/seqsim/analysis.py:402: undefined name 'ratio_two_best'
./usr/share/pyshared/cogent/seqsim/analysis.py:403: undefined name 'weiss'
./usr/share/pyshared/cogent/seqsim/analysis.py:413: undefined name 'all_p_from_tree'
./usr/share/pyshared/cogent/seqsim/analysis.py:414: undefined name 'get_qs'
./usr/share/pyshared/cogent/seqsim/analysis.py:416: undefined name 'scale_trace'
./usr/share/pyshared/cogent/seqsim/analysis.py:417: undefined name 'flatten_q_matrices'
./usr/share/pyshared/cogent/seqsim/analysis.py:418: undefined name 'dists_from_mean'
./usr/share/pyshared/cogent/seqsim/analysis.py:420: undefined name 'var'
./usr/share/pyshared/cogent/seqsim/analysis.py:422: undefined name 'flatten_q_matrices'
./usr/share/pyshared/cogent/seqsim/analysis.py:423: undefined name 'corrcoef'
./usr/share/pyshared/cogent/seqsim/analysis.py:424: undefined name 'ratio_two_best'
./usr/share/pyshared/cogent/seqsim/analysis.py:424: undefined name 'eigenvalues'
./usr/share/pyshared/cogent/seqsim/analysis.py:434: undefined name 'random_mats'
./usr/share/pyshared/cogent/seqsim/analysis.py:434: undefined name 'random_q_mats'
./usr/share/pyshared/cogent/seqsim/analysis.py:435: undefined name 'scale_one_q'
./usr/share/pyshared/cogent/seqsim/analysis.py:435: undefined name 'scale_many_q'
./usr/share/pyshared/cogent/seqsim/analysis.py:437: undefined name 'svd_q'
./usr/share/pyshared/cogent/seqsim/analysis.py:444: undefined name 'balanced_one_q_tree'
./usr/share/pyshared/cogent/seqsim/analysis.py:445: undefined name 'all_p_from_tree'
./usr/share/pyshared/cogent/seqsim/analysis.py:446: undefined name 'svd_q'
./usr/share/pyshared/cogent/seqsim/analysis.py:446: undefined name 'get_qs'
./usr/share/pyshared/cogent/seqsim/analysis.py:451: undefined name 'all_p_from_tree'
./usr/share/pyshared/cogent/seqsim/analysis.py:452: undefined name 'svd_q'
./usr/share/pyshared/cogent/seqsim/analysis.py:452: undefined name 'get_qs'
./usr/share/pyshared/cogent/seqsim/analysis.py:452: undefined name 'all_p_from_tree'
./usr/share/pyshared/cogent/seqsim/analysis.py:455: undefined name 'all_p_from_tree'
./usr/share/pyshared/cogent/seqsim/analysis.py:457: undefined name 'svd_q'
./usr/share/pyshared/cogent/seqsim/analysis.py:457: undefined name 'get_qs'
./usr/share/pyshared/cogent/seqsim/analysis.py:457: undefined name 'all_p_from_tree'
./usr/share/pyshared/cogent/seqsim/analysis.py:460: undefined name 'all_p_from_tree'
./usr/share/pyshared/cogent/seqsim/analysis.py:461: undefined name 'get_qs'
./usr/share/pyshared/cogent/seqsim/analysis.py:470: undefined name 'header'
./usr/share/pyshared/cogent/seqsim/analysis.py:474: undefined name 'header'
./usr/share/pyshared/cogent/seqsim/analysis.py:476: undefined name 'header'
./usr/share/pyshared/cogent/seqsim/analysis.py:477: undefined name 'header'
./usr/share/pyshared/cogent/seqsim/analysis.py:493: undefined name 'random'
./usr/share/pyshared/cogent/seqsim/analysis.py:500: undefined name 'balanced_one_q_tree'
./usr/share/pyshared/cogent/seqsim/analysis.py:513: undefined name 'balanced_one_q_tree'
./usr/share/pyshared/cogent/seqsim/analysis.py:520: undefined name 'lengths'
./usr/share/pyshared/cogent/seqsim/analysis.py:546: undefined name 'tree_controller'
./usr/share/pyshared/cogent/seqsim/birth_death.py:404: local variable 'max_taxa' is assigned to but never used
./usr/share/pyshared/cogent/seqsim/birth_death.py:405: undefined name 'num_taxa'
./usr/share/pyshared/cogent/seqsim/birth_death.py:408: undefined name 'num_taxa'
./usr/share/pyshared/cogent/seqsim/microarray_normalize.py:31: './usr/share/pyshared/cogent/draw/linear.py:1127: invalid syntax
^
zeros' imported but unused
./usr/share/pyshared/cogent/seqsim/microarray_normalize.py:31: 'transpose' imported but unused
./usr/share/pyshared/cogent/seqsim/microarray_normalize.py:31: 'ceil' imported but unused
./usr/share/pyshared/cogent/seqsim/microarray_normalize.py:97: local variable 'gmean' is assigned to but never used
./usr/share/pyshared/cogent/seqsim/microarray_normalize.py:125: undefined name 'rank_row_by_variance'
./usr/share/pyshared/cogent/seqsim/microarray_normalize.py:135: local variable 'constant_rank_indices' (defined in enclosing scope on line 127) referenced before assignment
./usr/share/pyshared/cogent/seqsim/microarray_normalize.py:146: undefined name 'nonzero'
./usr/share/pyshared/cogent/seqsim/microarray_normalize.py:188: undefined name 'NormalizationError'
./usr/share/pyshared/cogent/seqsim/tree.py:6: 'array' imported but unused
./usr/share/pyshared/cogent/seqsim/tree.py:494: local variable 'result' is assigned to but never used
./usr/share/pyshared/cogent/seqsim/tree.py:516: local variable 'new_nodes' is assigned to but never used
./usr/share/pyshared/cogent/seqsim/usage.py:25: 'mul' imported but unused
./usr/share/pyshared/cogent/seqsim/usage.py:25: 'div' imported but unused
./usr/share/pyshared/cogent/seqsim/usage.py:29: redefinition of unused 'log' from line 29
./usr/share/pyshared/cogent/seqsim/usage.py:29: 'identity' imported but unused
./usr/share/pyshared/cogent/seqsim/usage.py:822: redefinition of function 'similarity_f' from line 819
./usr/share/pyshared/cogent/seqsim/usage.py:851: redefinition of function 'similarity_f' from line 847
./usr/share/pyshared/cogent/seqsim/usage.py:858: redefinition of function 'similarity_f' from line 851
./usr/share/pyshared/cogent/seqsim/usage.py:861: redefinition of function 'similarity_f' from line 858
./usr/share/pyshared/cogent/seqsim/usage.py:934: local variable 'num_negs' is assigned to but never used
./usr/share/pyshared/cogent/seqsim/usage.py:1125: undefined name 'Float64'
./usr/share/pyshared/cogent/seqsim/markov.py:15: 'shuffle' imported but unused
./usr/share/pyshared/cogent/seqsim/markov.py:15: 'randrange' imported but unused
./usr/share/pyshared/cogent/seqsim/markov.py:19: 'copy' imported but unused
./usr/share/pyshared/cogent/seqsim/markov.py:20: 'rank' imported but unused
./usr/share/pyshared/cogent/seqsim/markov.py:20: 'searchsorted' imported but unused
./usr/share/pyshared/cogent/seqsim/markov.py:20: 'ones' imported but unused
./usr/share/pyshared/cogent/seqsim/markov.py:20: 'argsort' imported but unused
./usr/share/pyshared/cogent/seqsim/markov.py:318: undefined name 'KwordError'
./usr/share/pyshared/cogent/seqsim/markov.py:413: local variable 'total' is assigned to but never used
./usr/share/pyshared/cogent/seqsim/sequence_generators.py:23: 'path' imported but unused
./usr/share/pyshared/cogent/seqsim/sequence_generators.py:24: 'choice' imported but unused
./usr/share/pyshared/cogent/draw/arrow_rates.py:4: redefinition of unused 'rc' from line 2
./usr/share/pyshared/cogent/draw/arrow_rates.py:4: 'show' imported but unused
./usr/share/pyshared/cogent/draw/arrow_rates.py:4: 'draw' imported but unused
./usr/share/pyshared/cogent/draw/arrow_rates.py:118: local variable 'A' is assigned to but never used
./usr/share/pyshared/cogent/draw/arrow_rates.py:119: local variable 'T' is assigned to but never used
./usr/share/pyshared/cogent/draw/arrow_rates.py:120: local variable 'G' is assigned to but never used
./usr/share/pyshared/cogent/draw/arrow_rates.py:121: local variable 'C' is assigned to but never used
./usr/share/pyshared/cogent/draw/arrow_rates.py:202: local variable 'arrow_label_offset' is assigned to but never used
./usr/share/pyshared/cogent/draw/multivariate_plot.py:4: 'plot' imported but unused
./usr/share/pyshared/cogent/draw/multivariate_plot.py:8: 'set_trace' imported but unused
./usr/share/pyshared/cogent/draw/rlg2mpl.py:8: 'Line2D' imported but unused
./usr/share/pyshared/cogent/draw/rlg2mpl.py:14: 'numpy' imported but unused
./usr/share/pyshared/cogent/draw/rlg2mpl.py:47: local variable 'fontname' is assigned to but never used./usr/share/pyshared/cogent/parse/infernal.py:50: invalid syntax
^
./usr/share/pyshared/cogent/draw/rlg2mpl.py:48: local variable 'fontsize' is assigned to but never used
./usr/share/pyshared/cogent/draw/rlg2mpl.py:49: local variable 'color' is assigned to but never used
./usr/share/pyshared/cogent/draw/rlg2mpl.py:50: local variable 'ha' is assigned to but never used
./usr/share/pyshared/cogent/draw/rlg2mpl.py:51: local variable 'va' is assigned to but never used
./usr/share/pyshared/cogent/draw/codon_usage.py:43: redefinition of unused 'standard_series_colors' from line 11
./usr/share/pyshared/cogent/draw/codon_usage.py:80: local variable 'colors' is assigned to but never used
./usr/share/pyshared/cogent/draw/__init__.py:15: 'TrackDefn' imported but unused
./usr/share/pyshared/cogent/draw/__init__.py:15: 'Diamond' imported but unused
./usr/share/pyshared/cogent/draw/__init__.py:15: 'Area' imported but unused
./usr/share/pyshared/cogent/draw/__init__.py:15: 'DisplayPolicy' imported but unused
./usr/share/pyshared/cogent/draw/__init__.py:15: 'colors' imported but unused
./usr/share/pyshared/cogent/draw/__init__.py:15: 'Arrow' imported but unused
./usr/share/pyshared/cogent/draw/__init__.py:15: 'BluntArrow' imported but unused
./usr/share/pyshared/cogent/draw/__init__.py:15: 'Box' imported but unused
./usr/share/pyshared/cogent/draw/__init__.py:15: 'Display' imported but unused
./usr/share/pyshared/cogent/draw/__init__.py:19: 'cogent' imported but unused
./usr/share/pyshared/cogent/draw/legend.py:6: 'PatchCollection' imported but unused
./usr/share/pyshared/cogent/draw/legend.py:7: 'Text' imported but unused
./usr/share/pyshared/cogent/draw/legend.py:8: 'Affine2D' imported but unused
./usr/share/pyshared/cogent/draw/legend.py:9: 'Group' imported but unused
./usr/share/pyshared/cogent/draw/legend.py:35: local variable 'v' is assigned to but never used
./usr/share/pyshared/cogent/draw/legend.py:47: local variable 'result' is assigned to but never used
./usr/share/pyshared/cogent/draw/legend.py:84: local variable 'g' is assigned to but never used
./usr/share/pyshared/cogent/draw/util.py:15: 'use' imported but unused
./usr/share/pyshared/cogent/draw/util.py:33: redefinition of unused 'ImageFilter' from line 31
./usr/share/pyshared/cogent/draw/util.py:33: redefinition of unused 'Image' from line 30
./usr/share/pyshared/cogent/draw/util.py:34: 'shape' imported but unused
./usr/share/pyshared/cogent/draw/util.py:34: 'array' imported but unused
./usr/share/pyshared/cogent/draw/util.py:35: 'CodonUsage' imported but unused
./usr/share/pyshared/cogent/draw/util.py:153: undefined name 'normalize'
./usr/share/pyshared/cogent/draw/util.py:158: undefined name 'amax'
./usr/share/pyshared/cogent/draw/util.py:158: undefined name 'amin'
./usr/share/pyshared/cogent/draw/util.py:260: local variable 'label_offset' is assigned to but never used
./usr/share/pyshared/cogent/draw/util.py:343: local variable 'x' is assigned to but never used
./usr/share/pyshared/cogent/draw/util.py:344: local variable 'y' is assigned to but never used
./usr/share/pyshared/cogent/draw/util.py:590: undefined name 'reshape'
./usr/share/pyshared/cogent/draw/util.py:599: undefined name 'clabel'
./usr/share/pyshared/cogent/draw/util.py:758: undefined name 'xlabel'
./usr/share/pyshared/cogent/parse/record.py:79: redefinition of function 'parser' from line 76
./usr/share/pyshared/cogent/parse/record.py:100: redefinition of function 'parser' from line 79
./usr/share/pyshared/cogent/parse/record.py:307: redefinition of function 'setter' from line 304
./usr/share/pyshared/cogent/parse/record.py:445: redefinition of function 'parser' from line 442
./usr/share/pyshared/cogent/parse/record.py:473: redefinition of function 'parser' from line 466
./usr/share/pyshared/cogent/parse/cigar.py:20: '_LostSpan' imported but unused
./usr/share/pyshared/cogent/parse/aaindex.py:48: local variable 'result' is assigned to but never used
./usr/share/pyshared/cogent/parse/cutg.py:20: 'DbRef' imported but unused
./usr/share/pyshared/cogent/parse/cutg.py:158: local variable 'count' is assigned to but never used
./usr/share/pyshared/cogent/parse/pdb.py:7: 'AA_NAMES' imported but unused
./usr/share/pyshared/cogent/parse/pdb.py:199: local variable 'current_res_id' is assigned to but never used
./usr/share/pyshared/cogent/parse/blast_xml.py:204: undefined name 'MinimalPsiBlastParser9'
./usr/share/pyshared/cogent/parse/blast_xml.py:206: undefined name 'MinimalBlastParser9'
./usr/share/pyshared/cogent/parse/blast_xml.py:215: local variable 'iteration' is assigned to but never used
./usr/share/pyshared/cogent/parse/fasta.py:6: 'DbRef' imported but unused
./usr/share/pyshared/cogent/parse/fasta.py:139: local variable 'e' is assigned to but never used
./usr/share/pyshared/cogent/parse/rnaforester.py:3: 'split' imported but unused
./usr/share/pyshared/cogent/parse/rnaforester.py:3: 'strip' imported but unused
./usr/share/pyshared/cogent/parse/rnaforester.py:4: 'Pairs' imported but unused
./usr/share/pyshared/cogent/parse/rnaforester.py:80: local variable 'result' is assigned to but never used
./usr/share/pyshared/cogent/parse/rnashapes.py:15: 'split' imported but unused
./usr/share/pyshared/cogent/parse/rnashapes.py:15: 'strip' imported but unused
./usr/share/pyshared/cogent/parse/rnashapes.py:16: 'make_trans' imported but unused
./usr/share/pyshared/cogent/parse/rnashapes.py:17: 'Pairs' imported but unused
./usr/share/pyshared/cogent/parse/rnashapes.py:56: local variable 'name' is assigned to but never used
./usr/share/pyshared/cogent/parse/table.py:3: 'cPickle' imported but unused
./usr/share/pyshared/cogent/parse/table.py:83: local variable 'cast' is assigned to but never used
./usr/share/pyshared/cogent/parse/table.py:89: local variable 'v' is assigned to but never used
./usr/share/pyshared/cogent/parse/rfam.py:4: 'strip' imported but unused
./usr/share/pyshared/cogent/parse/rfam.py:14: 'keep_chars' imported but unused
./usr/share/pyshared/cogent/parse/rfam.py:14: 'trans_all' imported but unused
./usr/share/pyshared/cogent/parse/rfam.py:39: redefinition of unused 'Sequence' from line 10
./usr/share/pyshared/cogent/parse/tree.py:22: 'strip' imported but unused
./usr/share/pyshared/cogent/parse/flowgram_parser.py:18: 'DelimitedRecordFinder' imported but unused
./usr/share/pyshared/cogent/parse/cove.py:3: 'split' imported but unused
./usr/share/pyshared/cogent/parse/cove.py:3: 'strip' imported but unused
./usr/share/pyshared/cogent/parse/cove.py:5: 'wuss_to_vienna' imported but unused
./usr/share/pyshared/cogent/parse/mage.py:5: 'SimplexHeader' imported but unused
./usr/share/pyshared/cogent/parse/cmfinder.py:3: 'make_trans' imported but unused
./usr/share/pyshared/cogent/parse/cmfinder.py:4: 'Pairs' imported but unused
./usr/share/pyshared/cogent/parse/comrna.py:12: 'make_trans' imported but unused
./usr/share/pyshared/cogent/parse/flowgram_collection.py:19: 'Sequence' imported but unused
./usr/share/pyshared/cogent/parse/flowgram_collection.py:323: local variable 'e' is assigned to but never used
./usr/share/pyshared/cogent/parse/flowgram_collection.py:374: undefined name 'DataError'
./usr/share/pyshared/cogent/parse/flowgram_collection.py:403: undefined name 'flows'
./usr/share/pyshared/cogent/parse/flowgram_collection.py:426: undefined name 'flows'
./usr/share/pyshared/cogent/parse/flowgram_collection.py:451: undefined name 'flows'
./usr/share/pyshared/cogent/parse/flowgram_collection.py:537: local variable 'result' is assigned to but never used
./usr/share/pyshared/cogent/parse/bpseq.py:35: 'Vienna' imported but unused
./usr/share/pyshared/cogent/parse/meme.py:8: 'DelimitedSplitter' imported but unused
./usr/share/pyshared/cogent/parse/meme.py:42: local variable 'protein_order' is assigned to but never used
./usr/share/pyshared/cogent/parse/meme.py:96: local variable 'data_dict' is assigned to but never used
./usr/share/pyshared/cogent/parse/kegg_ko.py:5: 'listdir' imported but unused
./usr/share/pyshared/cogent/parse/kegg_ko.py:5: 'path' imported but unused
./usr/share/pyshared/cogent/parse/kegg_ko.py:6: 'OptionParser' imported but unused
./usr/share/pyshared/cogent/parse/kegg_ko.py:7: 'datetime' imported but unused
./usr/share/pyshared/cogent/parse/kegg_ko.py:8: 'tarfile' importe./usr/share/pyshared/cogent/parse/dotur.py:51: invalid syntax
^
d but unused
./usr/share/pyshared/cogent/parse/kegg_ko.py:355: redefinition of unused 'argv' from line 3
./usr/share/pyshared/cogent/parse/ct.py:26: 'split' imported but unused
./usr/share/pyshared/cogent/parse/ct.py:49: local variable 'length' is assigned to but never used
./usr/share/pyshared/cogent/parse/ct.py:67: undefined name 'pairs'
./usr/share/pyshared/cogent/parse/consan.py:3: 'wuss_to_vienna' imported but unused
./usr/share/pyshared/cogent/parse/consan.py:24: local variable 'seqs' is assigned to but never used
./usr/share/pyshared/cogent/parse/pfold.py:3: 'split' imported but unused
./usr/share/pyshared/cogent/parse/pfold.py:3: 'strip' imported but unused
./usr/share/pyshared/cogent/parse/pfold.py:4: 'Pairs' imported but unused
./usr/share/pyshared/cogent/parse/pfold.py:4: 'ViennaStructure' imported but unused
./usr/share/pyshared/cogent/parse/gcg.py:16: local variable 'alignmentdict' is assigned to but never used
./usr/share/pyshared/cogent/parse/paml_matrix.py:7: 'substitution_model' imported but unused
./usr/share/pyshared/cogent/parse/mothur.py:46: local variable 'num_otus' is assigned to but never used
./usr/share/pyshared/cogent/parse/rdb.py:6: 'strip' imported but unused
./usr/share/pyshared/cogent/parse/rdb.py:9: 'Sequence' imported but unused
./usr/share/pyshared/cogent/parse/flowgram.py:280: local variable 'extra_shift' is assigned to but never used
./usr/share/pyshared/cogent/parse/pknotsrg.py:9: 'split' imported but unused
./usr/share/pyshared/cogent/parse/pknotsrg.py:9: 'strip' imported but unused
./usr/share/pyshared/cogent/parse/pknotsrg.py:11: 'Pairs' imported but unused
./usr/share/pyshared/cogent/parse/ebi.py:7: 'pformat' imported but unused
./usr/share/pyshared/cogent/parse/ebi.py:8: 'is_empty' imported but unused
./usr/share/pyshared/cogent/parse/ebi.py:11: 'identity' imported but unused
./usr/share/pyshared/cogent/parse/ebi.py:84: redefinition of function 'add_item' from line 78
./usr/share/pyshared/cogent/parse/ebi.py:97: redefinition of function 'add_item' from line 84
./usr/share/pyshared/cogent/parse/ebi.py:104: redefinition of function 'add_item' from line 97
./usr/share/pyshared/cogent/parse/ebi.py:206: local variable 'e' is assigned to but never used
./usr/share/pyshared/cogent/parse/ebi.py:747: local variable 'e' is assigned to but never used
./usr/share/pyshared/cogent/parse/ebi.py:1376: local variable 'e' is assigned to but never used
./usr/share/pyshared/cogent/parse/locuslink.py:46: 'strip' imported but unused
./usr/share/pyshared/cogent/parse/locuslink.py:46: 'maketrans' imported but unused
./usr/share/pyshared/cogent/parse/locuslink.py:259: 'stdout' imported but unused
./usr/share/pyshared/cogent/parse/nupack.py:3: 'split' imported but unused
./usr/share/pyshared/cogent/parse/nupack.py:3: 'strip' imported but unused
./usr/share/pyshared/cogent/parse/macsim.py:3: 'annotation' imported but unused
./usr/share/pyshared/cogent/parse/blast.py:6: 'RecordError' imported but unused
./usr/share/pyshared/cogent/parse/blast.py:390: local variable 'iteration' is assigned to but never used
./usr/share/pyshared/cogent/parse/unigene.py:7: 'strip' imported but unused
./usr/share/pyshared/cogent/parse/unigene.py:7: 'maketrans' imported but unused
./usr/share/pyshared/cogent/parse/gibbs.py:147: local variable 'motif_num' is assigned to but never used
./usr/share/pyshared/cogent/parse/gibbs.py:153: local variable 'cur_key' is assigned to but never used
./usr/share/pyshared/cogent/parse/clustal.py:22: 'strip' imported but unused
./usr/share/pyshared/cogent/parse/column.py:16: 'split' imported but unused
./usr/share/pyshared/cogent/parse/rnaalifold.py:3: 'split' imported but unused
./usr/share/pyshared/cogent/parse/rnaalifold.py:3: 'strip' imported but unused
./usr/share/pyshared/cogent/parse/rnaalifold.py:4: 'Pairs' imported but unused
./usr/share/pyshared/cogent/parse/foldalign.py:3: 'split' imported but unused
./usr/share/pyshared/cogent/parse/foldalign.py:4: 'Pairs' imported but unused
./usr/share/pyshared/cogent/parse/foldalign.py:5: 'adjust_base' imported but unused
./usr/share/pyshared/cogent/parse/kegg_taxonomy.py:14: 'listdir' imported but unused
./usr/share/pyshared/cogent/parse/kegg_taxonomy.py:14: 'path' imported but unused
./usr/share/pyshared/cogent/parse/kegg_taxonomy.py:15: 'OptionParser' imported but unused
./usr/share/pyshared/cogent/parse/kegg_taxonomy.py:16: 'datetime' imported but unused
./usr/share/pyshared/cogent/parse/kegg_taxonomy.py:87: redefinition of unused 'argv' from line 12
./usr/share/pyshared/cogent/parse/record_finder.py:16: 'FieldError' imported but unused
./usr/share/pyshared/cogent/parse/sprinzl.py:5: 'maketrans' imported but unused
./usr/share/pyshared/cogent/cluster/nmds.py:9: 'size' imported but unused
./usr/share/pyshared/cogent/cluster/nmds.py:9: 'trace' imported but unused
./usr/share/pyshared/cogent/cluster/nmds.py:9: 'transpose' imported but unused
./usr/share/pyshared/cogent/cluster/nmds.py:9: 'multiply' imported but unused
./usr/share/pyshared/cogent/cluster/nmds.py:259: redefinition of unused 'size' from line 9
./usr/share/pyshared/cogent/cluster/nmds.py:265: redefinition of unused 'size' from line 9
./usr/share/pyshared/cogent/cluster/UPGMA.py:13: 'sum' imported but unused
./usr/share/pyshared/cogent/cluster/UPGMA.py:13: 'ma' imported but unused
./usr/share/pyshared/cogent/cluster/UPGMA.py:155: local variable 'row_order' is assigned to but never used
./usr/share/pyshared/cogent/cluster/procrustes.py:9: 'divide' imported but unused
./usr/share/pyshared/cogent/cluster/procrustes.py:9: 'subtract' imported but unused
./usr/share/pyshared/cogent/cluster/approximate_mds.py:90: 'floor' imported but unused
./usr/share/pyshared/cogent/cluster/approximate_mds.py:92: 'argwhere' imported but unused
./usr/share/pyshared/cogent/struct/pairs_util.py:16: 'searchsorted' imported but unused
./usr/share/pyshared/cogent/struct/pairs_util.py:452: local variable 'pred_dict' is assigned to but never used
./usr/share/pyshared/cogent/struct/dihedral.py:35: 'cos' imported but unused
./usr/share/pyshared/cogent/struct/rna2d.py:443: local variable 'num_bases' is assigned to but never used
./usr/share/pyshared/cogent/struct/asa.py:73: undefined name 'lattice_structures'
./usr/share/pyshared/cogent/struct/asa.py:200: local variable 'models' is assigned to but never used
./usr/share/pyshared/cogent/struct/annotation.py:3: 'HIERARCHY' imported but unused
./usr/share/pyshared/cogent/struct/manipulation.py:6: 'HIERARCHY' imported but unused
./usr/share/pyshared/cogent/motif/k_word.py:8: 'combinations' imported but unused
./usr/share/pyshared/cogent/evolve/discrete_markov.py:4: 'CalcDefn' imported but unused
./usr/share/pyshared/cogent/evolve/discrete_markov.py:4: 'ConstDefn' imported but unused
./usr/share/pyshared/cogent/evolve/discrete_markov.py:4: 'NonParamDefn' imported but unused
./usr/share/pyshared/cogent/evolve/models.py:77: local variable 'preds' is assigned to but never used
./usr/share/pyshared/cogent/evolve/motif_prob_model.py:217: local variable 'positions' is assigned to but never used
./usr/share/pyshared/cogent/evolve/bootstrap.py:26: 'optimisers' imported but unused
./usr/share/pyshared/cogent/evolve/substitution_model.py:39: 'RateDefn' imported but unused
./usr/share/pyshared/cogent/evolve/substitution_model.py:636: local variable 'const_param' is assigned to but never used
./usr/share/pyshared/cogent/evolve/substitution_model.py:668: local variable 'const_param' is assigned to but never used
./usr/share/pyshared/cogent/evolve/substitution_calculation.py:8: 'CallDefn' imported but unused
./usr/share/pyshared/cogent/evolve/substitution_calculation.py:8: 'ConstDefn' imported but unused
./usr/share/pyshared/cogent/evolve/substitution_calculation.py:8: 'PartitionDefn' imported but unused
./usr/share/pyshared/cogent/evolve/substitution_calculation.py:8: 'NonParamDefn' imported but unused
./usr/share/pyshared/cogent/evolve/substitution_calculation.py:8: 'GammaDefn' imported but unused
./usr/share/pyshared/cogent/evolve/substitution_calculation.py:8: 'CalcDefn' imported but unused
./usr/share/pyshared/cogent/evolve/substitution_calculation.py:8: 'ProductDefn' imported but unused
./usr/sha./usr/share/pyshared/cogent/phylo/least_squares.py:82: invalid syntax
^
re/pyshared/cogent/evolve/substitution_calculation.py:8: 'WeightedPartitionDefn' imported but unused
./usr/share/pyshared/cogent/evolve/substitution_calculation.py:8: 'SelectForDimension' imported but unused
./usr/share/pyshared/cogent/evolve/substitution_calculation.py:8: 'MonotonicDefn' imported but unused
./usr/share/pyshared/cogent/evolve/substitution_calculation.py:12: 'chooseFastExponentiators' imported but unused
./usr/share/pyshared/cogent/evolve/substitution_calculation.py:12: 'FastExponentiator' imported but unused
./usr/share/pyshared/cogent/evolve/likelihood_calculation.py:15: '_FuncDefn' imported but unused
./usr/share/pyshared/cogent/evolve/coevolution.py:56: 'splitext' imported but unused
./usr/share/pyshared/cogent/evolve/coevolution.py:58: 'sqrt' imported but unused
./usr/share/pyshared/cogent/evolve/coevolution.py:58: 'mean' imported but unused
./usr/share/pyshared/cogent/evolve/coevolution.py:58: 'abs' imported but unused
./usr/share/pyshared/cogent/evolve/coevolution.py:58: 'transpose' imported but unused
./usr/share/pyshared/cogent/evolve/coevolution.py:58: 'put' imported but unused
./usr/share/pyshared/cogent/evolve/coevolution.py:58: 'float64' imported but unused
./usr/share/pyshared/cogent/evolve/coevolution.py:58: 'tril' imported but unused
./usr/share/pyshared/cogent/evolve/coevolution.py:58: 'reshape' imported but unused
./usr/share/pyshared/cogent/evolve/coevolution.py:58: 'take' imported but unused
./usr/share/pyshared/cogent/evolve/coevolution.py:58: 'exp' imported but unused
./usr/share/pyshared/cogent/evolve/coevolution.py:66: 'Profile' imported but unused
./usr/share/pyshared/cogent/evolve/coevolution.py:67: 'Alphabet' imported but unused
./usr/share/pyshared/cogent/evolve/coevolution.py:73: 'TreeError' imported but unused
./usr/share/pyshared/cogent/evolve/coevolution.py:74: 'seqs_from_fasta' imported but unused
./usr/share/pyshared/cogent/evolve/coevolution.py:509: redefinition of unused 'e' from line 58
./usr/share/pyshared/cogent/evolve/coevolution.py:509: local variable 'e' is assigned to but never used
./usr/share/pyshared/cogent/evolve/coevolution.py:643: local variable 'num_positions' is assigned to but never used
./usr/share/pyshared/cogent/evolve/coevolution.py:644: local variable 'num_seqs' is assigned to but never used
./usr/share/pyshared/cogent/evolve/coevolution.py:758: local variable 'num_seqs' is assigned to but never used
./usr/share/pyshared/cogent/evolve/coevolution.py:824: local variable 'num_seqs' is assigned to but never used
./usr/share/pyshared/cogent/evolve/coevolution.py:1448: local variable 'e' is assigned to but never used
./usr/share/pyshared/cogent/evolve/coevolution.py:2095: redefinition of function 'is_not_null_value' from line 2092
./usr/share/pyshared/cogent/evolve/coevolution.py:2196: local variable 'aln' is assigned to but never used
./usr/share/pyshared/cogent/evolve/coevolution.py:2209: local variable 'tree' is assigned to but never used
./usr/share/pyshared/cogent/evolve/coevolution.py:2317: local variable 'extension' is assigned to but never used
./usr/share/pyshared/cogent/phylo/distance.py:4: 'warning' imported but unused
./usr/share/pyshared/cogent/phylo/distance.py:6: 'LoadSeqs' imported but unused
./usr/share/pyshared/cogent/phylo/compatibility.py:466: 'sys' imported but unused
./usr/share/pyshared/cogent/phylo/maximum_likelihood.py:4: 'exp' imported but unused
./usr/share/pyshared/cogent/phylo/maximum_likelihood.py:6: 'LoadTrees' imported but unused
./usr/share/pyshared/cogent/phylo/tree_collection.py:65: undefined name 'exp'
./usr/share/pyshared/cogent/db/ncbi.py:8: 'urlopen' imported but unused
./usr/share/pyshared/cogent/db/ncbi.py:8: 'urlretrieve' imported but unused
./usr/share/pyshared/cogent/db/ncbi.py:13: 'never_ignore' imported but unused
./usr/share/pyshared/cogent/db/ensembl/compara.py:7: 'get_latest_release' imported but unused
./usr/share/pyshared/cogent/db/ensembl/compara.py:9: 'Coordinate' imported but unused
./usr/share/pyshared/cogent/db/ensembl/region.py:10: 'location_query' imported but unused
./usr/share/pyshared/cogent/db/ensembl/__init__.py:5: 'NoItemError' imported but unused
./usr/share/pyshared/cogent/db/ensembl/host.py:5: 'Table' imported but unused
./usr/share/pyshared/cogent/db/ensembl/host.py:8: 'asserted_one' imported but unused
./usr/share/pyshared/cogent/db/ensembl/related_region.py:1: 'pprint' imported but unused
./usr/share/pyshared/cogent/db/ensembl/related_region.py:8: 'NoItemError' imported but unused
./usr/share/pyshared/cogent/db/ensembl/related_region.py:9: 'location_query' imported but unused
./usr/share/pyshared/cogent/db/ensembl/related_region.py:10: 'Species' imported but unused
./usr/share/pyshared/cogent/db/ensembl/genome.py:319: undefined name 'coord'
./usr/share/pyshared/cogent/db/ensembl/genome.py:319: local variable 'coord' is assigned to but never used
./usr/share/pyshared/cogent/db/ensembl/genome.py:354: local variable 'feature_coord_levels' is assigned to but never used
./usr/share/pyshared/cogent/db/ensembl/util.py:1: 're' imported but unused
./usr/share/pyshared/cogent/db/ensembl/util.py:2: 'create_engine' imported but unused
./usr/share/pyshared/cogent/db/ensembl/util.py:2: 'Table' imported but unused
./usr/share/pyshared/cogent/db/ensembl/util.py:2: 'MetaData' imported but unused
./usr/share/pyshared/cogent/db/ensembl/sequence.py:4: 'Map' imported but unused
./usr/share/pyshared/cogent/db/ensembl/sequence.py:6: 'Species' imported but unused
./usr/share/pyshared/cogent/db/ensembl/assembly.py:3: 'Map' imported but unused
./usr/share/pyshared/cogent/db/ensembl/assembly.py:6: 'DbConnection' imported but unused
./usr/share/pyshared/cogent/core/entity.py:22: 'gt' imported but unused
./usr/share/pyshared/cogent/core/entity.py:22: 'ne' imported but unused
./usr/share/pyshared/cogent/core/entity.py:22: 'ge' imported but unused
./usr/share/pyshared/cogent/core/entity.py:22: 'le' imported but unused
./usr/share/pyshared/cogent/core/entity.py:22: 'lt' imported but unused
./usr/share/pyshared/cogent/core/entity.py:22: 'is_' imported but unused
./usr/share/pyshared/cogent/core/entity.py:22: 'or_' imported but unused
./usr/share/pyshared/cogent/core/entity.py:22: 'is_not' imported but unused
./usr/share/pyshared/cogent/core/entity.py:22: 'and_' imported but unused
./usr/share/pyshared/cogent/core/tree.py:34: 'InverseDict' imported but unused
./usr/share/pyshared/cogent/core/usage.py:14: 'mean' imported but unused
./usr/share/pyshared/cogent/core/alignment.py:35: 'logical_or' imported but unused
./usr/share/pyshared/cogent/core/alignment.py:35: 'zeros' imported but unused
./usr/share/pyshared/cogent/core/alignment.py:350: local variable 'result' is assigned to but never used
./usr/share/pyshared/cogent/core/alignment.py:520: local variable 'e' is assigned to but never used
./usr/share/pyshared/cogent/core/alignment.py:654: local variable 'item_lookup' is assigned to but never used
./usr/share/pyshared/cogent/core/alignment.py:721: redefinition of function 'f' from line 717
./usr/share/pyshared/cogent/core/alignment.py:1246: local variable 'max_run' is assigned to but never used
./usr/share/pyshared/cogent/core/alignment.py:2020: local variable 'max_label_length' is assigned to but never used
./usr/share/pyshared/cogent/core/alignment.py:2176: undefined name 'CodonSequenceGap'
./usr/share/pyshared/cogent/core/alignment.py:2180: undefined name 'random'
./usr/share/pyshared/cogent/core/moltype.py:27: 'if_' imported but unused
./usr/share/pyshared/cogent/core/moltype.py:30: 'ModelNucleicAcidSequence' imported but unused
./usr/share/pyshared/cogent/core/moltype.py:46: 'uint16' imported but unused
./usr/share/pyshared/cogent/core/moltype.py:46: 'arange' imported but unused
./usr/share/pyshared/cogent/core/moltype.py:46: 'asarray' imported but unused
./usr/share/pyshared/cogent/core/moltype.py:46: 'uint32' imported but unused
./usr/share/pyshared/cogent/core/moltype.py:46: 'transpose' imported but unused
./usr/share/pyshared/cogent/core/moltype.py:46: 'remainder' imported but unused
./usr/share/pyshared/cogent/core/moltype.py:46: 'newaxis' imported but unused
./usr/share/pyshared/cogent/core/moltype.py:46: 'array' imported b./usr/share/pyshared/cogent/format/rna_struct.py:449: invalid syntax
^
./usr/share/pyshared/cogent/format/stockholm.py:93: unexpected indent
^
./usr/share/pyshared/cogent/format/clustal.py:69: unexpected indent
^
ut unused
./usr/share/pyshared/cogent/core/moltype.py:46: 'zeros' imported but unused
./usr/share/pyshared/cogent/core/moltype.py:46: 'uint8' imported but unused
./usr/share/pyshared/cogent/core/moltype.py:46: 'ravel' imported but unused
./usr/share/pyshared/cogent/core/moltype.py:46: 'take' imported but unused
./usr/share/pyshared/cogent/core/moltype.py:46: 'fromstring' imported but unused
./usr/share/pyshared/cogent/core/moltype.py:46: 'sum' imported but unused
./usr/share/pyshared/cogent/core/moltype.py:52: 'translate' imported but unused
./usr/share/pyshared/cogent/core/moltype.py:637: local variable 'curr' is assigned to but never used
./usr/share/pyshared/cogent/core/moltype.py:724: undefined name 'first_index_in_set'
./usr/share/pyshared/cogent/core/moltype.py:733: undefined name 'first_index_in_set'
./usr/share/pyshared/cogent/core/alphabet.py:22: 're' imported but unused
./usr/share/pyshared/cogent/core/alphabet.py:23: 'string' imported but unused
./usr/share/pyshared/cogent/core/alphabet.py:24: redefinition of unused 'take' from line 24
./usr/share/pyshared/cogent/core/alphabet.py:24: 'remainder' imported but unused
./usr/share/pyshared/cogent/core/alphabet.py:546: local variable 'result' is assigned to but never used
./usr/share/pyshared/cogent/core/profile.py:11: 'concatenate' imported but unused
./usr/share/pyshared/cogent/core/profile.py:11: 'log' imported but unused
./usr/share/pyshared/cogent/core/profile.py:11: 'asarray' imported but unused
./usr/share/pyshared/cogent/core/profile.py:11: 'reshape' imported but unused
./usr/share/pyshared/cogent/core/profile.py:11: 'alltrue' imported but unused
./usr/share/pyshared/cogent/core/profile.py:11: 'ravel' imported but unused
./usr/share/pyshared/cogent/core/profile.py:11: 'sort' imported but unused
./usr/share/pyshared/cogent/core/profile.py:11: 'uint8' imported but unused
./usr/share/pyshared/cogent/core/profile.py:11: 'put' imported but unused
./usr/share/pyshared/cogent/core/profile.py:11: 'isfinite' imported but unused
./usr/share/pyshared/cogent/core/profile.py:89: local variable 'sums' is assigned to but never used
./usr/share/pyshared/cogent/core/profile.py:92: local variable 'tfs' is assigned to but never used
./usr/share/pyshared/cogent/core/profile.py:207: local variable 'max_col_idx' is assigned to but never used
./usr/share/pyshared/cogent/core/profile.py:397: local variable 'sl' is assigned to but never used
./usr/share/pyshared/cogent/core/sequence.py:15: 'Feature' imported but unused
./usr/share/pyshared/cogent/core/sequence.py:16: 'keep_chars' imported but unused
./usr/share/pyshared/cogent/core/sequence.py:16: 'per_longest' imported but unused
./usr/share/pyshared/cogent/core/sequence.py:1008: undefined name 'm'
./usr/share/pyshared/cogent/core/bitvector.py:254: local variable 'bits' is assigned to but never used
./usr/share/pyshared/cogent/core/bitvector.py:642: local variable 'TypeError' is assigned to but never used
./usr/share/pyshared/cogent/format/table.py:91: local variable 'th' is assigned to but never used
./usr/share/pyshared/cogent/format/table.py:96: local variable 'td' is assigned to but never used
./usr/share/pyshared/cogent/format/table.py:445: local variable 'num_row' is assigned to but never used
./usr/share/pyshared/cogent/format/mage.py:19: 'fabs' imported but unused
./usr/share/pyshared/cogent/format/mage.py:22: 'extract_delimited' imported but unused
./usr/share/pyshared/cogent/format/alignment.py:33: undefined name 'FileFormatError'
./usr/share/pyshared/cogent/format/alignment.py:141: undefined name 'warnings'
./usr/share/pyshared/cogent/format/pdb_color.py:54: undefined name 'chain'
./usr/share/pyshared/cogent/format/pdb_color.py:195: undefined name 'cmd'
./usr/share/pyshared/cogent/format/pdb_color.py:203: undefined name 'cmd'
./usr/share/pyshared/cogent/format/pdb_color.py:210: undefined name 'cmd'
./usr/share/pyshared/cogent/format/motif.py:13: 'DNA' imported but unused
./usr/share/pyshared/cogent/format/motif.py:14: 'Alignment' imported but unused
./usr/share/pyshared/cogent/format/motif.py:944: local variable 'e' is ./usr/share/pyshared/cogent/align/partial_order_graph.py:221: invalid syntax
^
./usr/lib/python2.6/dist-packages/cogent/maths/period.py:268: invalid syntax
^
assigned to but never used
./usr/share/pyshared/cogent/format/motif.py:1592: local variable 'mod_id_map' is assigned to but never used
./usr/share/pyshared/cogent/format/motif.py:1722: local variable 'mod_id_map' is assigned to but never used
./usr/share/pyshared/cogent/align/dp_calculation.py:4: 'PositiveParamDefn' imported but unused
./usr/share/pyshared/cogent/align/dp_calculation.py:8: 'numpy' imported but unused
./usr/share/pyshared/cogent/align/align.py:8: 'sys' imported but unused
./usr/share/pyshared/cogent/align/pairwise.py:202: undefined name 'seq'
./usr/share/pyshared/cogent/align/pairwise.py:601: local variable 'rr' is assigned to but never used
./usr/share/pyshared/cogent/align/indel_positions.py:14: local variable 'full_aligned_positions' is assigned to but never used
./usr/share/pyshared/cogent/align/indel_positions.py:98: local variable 'l' is assigned to but never used
./usr/share/pyshared/cogent/align/indel_positions.py:230: undefined name 'length'
./usr/share/pyshared/cogent/align/__init__.py:3: 'make_dna_scoring_dict' imported but unused
./usr/share/pyshared/cogent/align/__init__.py:3: '_align_pairwise' imported but unused
./usr/share/pyshared/cogent/align/__init__.py:3: 'local_pairwise' imported but unused
./usr/share/pyshared/cogent/align/__init__.py:3: 'global_pairwise' imported but unused
./usr/share/pyshared/cogent/align/__init__.py:3: 'classic_align_pairwise' imported but unused
./usr/share/pyshared/cogent/align/weights/methods.py:5: 'choice' imported but unused
./usr/share/pyshared/cogent/align/weights/methods.py:12: 'DndParser' imported but unused
./usr/share/pyshared/cogent/align/weights/methods.py:14: 'RNA_ORDER' imported but unused
./usr/share/pyshared/cogent/align/weights/methods.py:432: redefinition of unused 'Alignment' from line 11
./usr/share/pyshared/cogent/align/weights/util.py:7: 'asarray' imported but unused
./usr/share/pyshared/cogent/align/weights/util.py:7: 'sqrt' imported but unused
./usr/share/pyshared/cogent/align/weights/util.py:7: 'take' imported but unused
./usr/share/pyshared/cogent/align/weights/util.py:13: 'Alignment' imported but unused
./usr/lib/python2.6/dist-packages/cogent/__init__.py:4: 'os' imported but unused
./usr/lib/python2.6/dist-packages/cogent/__init__.py:47: 'STANDARD_CODON' imported but unused
./usr/lib/python2.6/dist-packages/cogent/__init__.py:47: 'PROTEIN' imported but unused
./usr/lib/python2.6/dist-packages/cogent/__init__.py:47: 'DNA' imported but unused
./usr/lib/python2.6/dist-packages/cogent/__init__.py:47: 'CodonAlphabet' imported but unused
./usr/lib/python2.6/dist-packages/cogent/__init__.py:47: 'RNA' imported but unused
./usr/lib/python2.6/dist-packages/cogent/maths/matrix_logarithm.py:7: 'transpose' imported but unused
./usr/lib/python2.6/dist-packages/cogent/maths/matrix_exponentiation.py:17: 'LinAlgError' imported but unused
./usr/lib/python2.6/dist-packages/cogent/maths/matrix_exponentiation.py:38: redefinition of function 'inv' from line 34
./usr/lib/python2.6/dist-packages/cogent/maths/scipy_optimisers.py:5: 'fmin_bfgs' imported but unused
./usr/lib/python2.6/dist-packages/cogent/maths/scipy_optimisers.py:81: local variable 'template' is assigned to but never used
./usr/lib/python2.6/dist-packages/cogent/maths/optimiser.py:66: local variable 'detail' is assigned to but never used
./usr/lib/python2.6/dist-packages/cogent/maths/geometry.py:4: redefinition of unused 'sqrt' from line 4
./usr/lib/python2.6/dist-packages/cogent/maths/distance_transform.py:56: 'logical_or' imported but unused
./usr/lib/python2.6/dist-packages/cogent/maths/distance_transform.py:56: 'logical_xor' imported but unused
./usr/lib/python2.6/dist-packages/cogent/maths/distance_transform.py:56: 'geterr' imported but unused
./usr/lib/python2.6/dist-packages/cogent/maths/distance_transform.py:56: 'logical_not' imported but unused
./usr/lib/python2.6/dist-packages/cogent/maths/distance_transform.py:256: local variable 'dist' is assigned to but never used
./usr/lib/python2.6/dist-packages/cogent/maths/distance_transform.py:465: local variable 'rowdiff' is assigned to but never used
./usr/lib/python2.6/dist-packages/cogent/maths/distance_transform.py:723: local variable 'rowstds' is assigned to but never used
./usr/lib/python2.6/dist-packages/cogent/maths/distance_transform.py:726: local variable 'n' is assigned to but never used
./usr/lib/python2.6/dist-packages/cogent/maths/optimisers.py:9: 'DownhillSimplex' imported but unused
./usr/lib/python2.6/dist-packages/cogent/maths/optimisers.py:51: undefined name 'wanings'
./usr/lib/python2.6/dist-packages/cogent/maths/svd.py:6: 'expm' imported but unused
./usr/lib/python2.6/dist-packages/cogent/maths/svd.py:7: 'logm' imported but unused
./usr/lib/python2.6/dist-packages/cogent/maths/svd.py:9: 'reshape' imported but unused
./usr/lib/python2.6/dist-packages/cogent/maths/svd.py:9: 'NewAxis' imported but unused
./usr/lib/python2.6/dist-packages/cogent/maths/svd.py:9: 'product' imported but unused
./usr/lib/python2.6/dist-packages/cogent/maths/svd.py:11: 'random' imported but unused
./usr/lib/python2.6/dist-packages/cogent/maths/scipy_optimize.py:34: redefinition of unused 'linesearch' from line 32
./usr/lib/python2.6/dist-packages/cogent/maths/scipy_optimize.py:320: local variable 'D' is assigned to but never used
./usr/lib/python2.6/dist-packages/cogent/maths/scipy_optimize.py:487: redefinition of function 'phiprime' from line 477
./usr/lib/python2.6/dist-packages/cogent/maths/scipy_optimize.py:892: local variable 'N' is assigned to but never used
./usr/lib/python2.6/dist-packages/cogent/maths/scipy_optimize.py:899: local variable 'sk' is assigned to but never used
./usr/lib/python2.6/dist-packages/cogent/maths/scipy_optimize.py:1393: local variable 'xmin' is assigned to but never used
./usr/lib/python2.6/dist-packages/cogent/maths/scipy_optimize.py:1393: local variable 'fval' is assigned to but never used
./usr/lib/python2.6/dist-packages/cogent/maths/stats/test.py:14: 'clip' imported but unused
./usr/lib/python2.6/dist-packages/cogent/maths/stats/test.py:14: 'reshape' imported but unused
./usr/lib/python2.6/dist-packages/cogent/maths/stats/test.py:14: 'nan' imported but unused
./usr/lib/python2.6/dist-packages/cogent/maths/stats/test.py:20: 'add' imported but unused
./usr/lib/python2.6/dist-packages/cogent/maths/stats/test.py:21: 'choice' imported but unused
./usr/lib/python2.6/dist-packages/cogent/maths/stats/test.py:500: local variable 'e' is assigned to but never used
./usr/lib/python2.6/dist-packages/cogent/maths/stats/test.py:604: local variable 'Syy' is assigned to but never used
./usr/lib/python2.6/dist-packages/cogent/maths/stats/test.py:775: local variable 'e' is assigned to but never used
./usr/lib/python2.6/dist-packages/cogent/maths/stats/test.py:1007: local variable 'total_obs' is assigned to but never used
./usr/lib/python2.6/dist-packages/cogent/maths/stats/test.py:1008: local variable 'num_x' is assigned to but never used
./usr/lib/python2.6/dist-packages/cogent/maths/stats/test.py:1042: local variable 'sample' is assigned to but never used
./usr/lib/python2.6/dist-packages/cogent/maths/stats/test.py:1048: local variable 'ties' is assigned to but never used
./usr/lib/python2.6/dist-packages/cogent/maths/stats/test.py:1089: local variable 'total_obs' is assigned to but never used
./usr/lib/python2.6/dist-packages/cogent/maths/stats/test.py:1090: local variable 'num_x' is assigned to but never used
./usr/lib/python2.6/dist-packages/cogent/maths/stats/period.py:2: 'shuffle' imported but unused
./usr/lib/python2.6/dist-packages/cogent/maths/stats/period.py:2: 'random' imported but unused
./usr/lib/python2.6/dist-packages/cogent/maths/stats/period.py:9: redefinition of unused 'factorial' from line 6
./usr/lib/python2.6/dist-packages/cogent/maths/stats/period.py:87: redefinition of unused 'seq_to_symbols' from line 84
./usr/lib/python2.6/dist-packages/cogent/maths/stats/special.py:485: local variable 'sgngam' is assigned to but never used
./usr/lib/python2.6/dist-packages/cogent/maths/stats/special.py:1087: local variable 'i' is assigned to but never used
./usr/lib/python2.6/dist-packages/cogent/maths/stats/__init__.py:13: 'chisqprob' imported but unused
./usr/lib/python2.6/dist-packages/cogent/maths/stats/distribution.py:6: 'ndtri' imported but unused
./usr/lib/python2.6/dist-packages/cogent/maths/stats/util.py:111: 'e' imported but unused
./usr/lib/python2.6/dist-packages/cogent/maths/stats/util.py:524: redefinition of function '_get_mode' from line 447
./usr/lib/python2.6/dist-packages/cogent/maths/stats/util.py:676: local variable 'r' is assigned to but never used
./usr/lib/python2.6/dist-packages/cogent/maths/stats/util.py:723: local variable 'v' is assigned to but never used
./usr/lib/python2.6/dist-packages/cogent/maths/stats/util.py:746: local variable 'i' is assigned to but never used
./usr/lib/python2.6/dist-packages/cogent/maths/stats/alpha_diversity.py:152: local variable 'alpha' is assigned to but never used
./usr/lib/python2.6/dist-packages/cogent/maths/stats/cai/get_by_cai.py:3: 'CutgParser' imported but unused
./usr/lib/python2.6/dist-packages/cogent/maths/stats/cai/get_by_cai.py:5: 'CodonUsage' imported but unused
./usr/lib/python2.6/dist-packages/cogent/maths/stats/cai/util.py:76: local variable 'result' is assigned to but never used
./usr/lib/python2.6/dist-packages/cogent/maths/stats/cai/util.py:104: local variable 'k' is assigned to but never used
./usr/lib/python2.6/dist-packages/cogent/maths/stats/cai/util.py:105: local variable 'v' is assigned to but never used
./usr/lib/python2.6/dist-packages/cogent/maths/stats/cai/util.py:106: local variable 'n' is assigned to but never used
./usr/lib/python2.6/dist-packages/cogent/maths/stats/cai/util.py:257: undefined name 'arithmetic_meani'
./usr/lib/python2.6/dist-packages/cogent/maths/stats/cai/adaptor.py:5: 'Info' imported but unused
./usr/lib/python2.6/dist-packages/cogent/maths/stats/cai/adaptor.py:8: 'GeneticCode' imported but unused
./usr/lib/python2.6/dist-packages/cogent/maths/stats/cai/adaptor.py:9: 'sort' imported but unused
./usr/lib/python2.6/dist-packages/cogent/maths/stats/cai/adaptor.py:9: 'concatenate' imported but unused
./usr/lib/python2.6/dist-packages/cogent/maths/stats/cai/adaptor.py:9: 'sqrt' imported but unused
./usr/lib/python2.6/dist-packages/cogent/maths/stats/cai/adaptor.py:9: 'zeros' imported but unused
./usr/lib/python2.6/dist-packages/cogent/maths/stats/cai/adaptor.py:11: 'argv' imported but unused
./usr/lib/python2.6/dist-packages/cogent/maths/stats/cai/adaptor.py:80: undefined name 'UnsafeCodonsFromString'
./usr/lib/python2.6/dist-packages/cogent/maths/unifrac/fast_tree.py:582: local variable 'row_result' is assigned to but never used
./usr/lib/python2.6/dist-packages/cogent/maths/unifrac/fast_unifrac.py:7: 'from cogent.maths.unifrac.fast_tree import *' used; unable to detect undefined names
./usr/lib/python2.6/dist-packages/cogent/maths/unifrac/fast_unifrac.py:11: 'from cogent.cluster.metric_scaling import *' used; unable to detect undefined names
./usr/lib/python2.6/dist-packages/cogent/maths/unifrac/fast_unifrac.py:527: local variable 'result' is assigned to but never used
./usr/lib/python2.6/dist-packages/cogent/maths/unifrac/fast_unifrac.py:958: redefinition of unused 'StringIO' from line 15
./usr/lib/python2.6/dist-packages/cogent/maths/matrix/distance.py:91: redefinition of function 'Pow' from line 85
./usr/lib/python2.6/dist-packages/cogent/app/knetfold.py:3: 'CommandLineAppResult' imported but unused
./usr/lib/python2.6/dist-packages/cogent/app/knetfold.py:5: '_find_synonym' imported but unused
./usr/lib/python2.6/dist-packages/cogent/app/knetfold.py:5: 'Parameters' imported but unused
./usr/lib/python2.6/dist-packages/cogent/app/knetfold.py:5: 'MixedParameter' imported but unused
./usr/lib/python2.6/dist-packages/cogent/app/knetfold.py:5: 'FlagParameter' imported but unused
./usr/lib/python2.6/dist-packages/cogent/app/knetfold.py:5: 'Parameter' imported but unused
./usr/lib/python2.6/dist-packages/cogent/app/ilm.py:3: 'CommandLineAppResult' imported but unused
./usr/lib/python2.6/dist-packages/cogent/app/ilm.py:3: 'ResultPath' imported but unused
./usr/lib/python2.6/dist-packages/cogent/app/ilm.py:5: 'Parameters' imported but unused
./usr/lib/python2.6/dist-packages/cogent/app/ilm.py:5: 'Parameter' imported but unused
./usr/lib/python2.6/dist-packages/cogent/app/raxml.py:12: 'choice' imported but unused
./usr/lib/python2.6/dist-packages/cogent/app/raxml.py:300: local variable 'e' is assigned to but never used
./usr/lib/python2.6/dist-packages/cogent/app/uclust.py:22: 'makedirs' imported but unused
./usr/lib/python2.6/dist-packages/cogent/app/uclust.py:22: 'remove' imported but unused
./usr/lib/python2.6/dist-packages/cogent/app/uclust.py:23: 'splitext' imported but unused
./usr/lib/python2.6/dist-packages/cogent/app/uclust.py:23: 'isfile' imported but unused
./usr/lib/python2.6/dist-packages/cogent/app/uclust.py:23: 'isdir' imported but unused
./usr/lib/python2.6/dist-packages/cogent/app/uclust.py:23: 'abspath' imported but unused
./usr/lib/python2.6/dist-packages/cogent/app/uclust.py:483: local variable 'uc_output_filepath' is assigned to but never used
./usr/lib/python2.6/dist-packages/cogent/app/uclust.py:484: local variable 'cd_hit_filepath' is assigned to but never used
./usr/lib/python2.6/dist-packages/cogent/app/uclust.py:496: local variable 'uc_filepath' is assigned to but never used
./usr/lib/python2.6/dist-packages/cogent/app/uclust.py:497: local variable 'clstr_filepath' is assigned to but never used
./usr/lib/python2.6/dist-packages/cogent/app/infernal.py:8: 'MinimalFastaParser' imported but unused
./usr/lib/python2.6/dist-packages/cogent/app/infernal.py:15: 'ViennaStructure' imported but unused
./usr/lib/python2.6/dist-packages/cogent/app/infernal.py:15: 'wuss_to_vienna' imported but unused
./usr/lib/python2.6/dist-packages/cogent/app/vienna_package.py:3: 'CommandLineAppResult' imported but unused
./usr/lib/python2.6/dist-packages/cogent/app/vienna_package.py:5: 'Parameters' imported but unused
./usr/lib/python2.6/dist-packages/cogent/app/vienna_package.py:5: 'Parameter' imported but unused
./usr/lib/python2.6/dist-packages/cogent/app/vienna_package.py:5: 'is_not_None' imported but unused
./usr/lib/python2.6/dist-packages/cogent/app/vienna_package.py:5: '_find_synonym' imported but unused
./usr/lib/python2.6/dist-packages/cogent/app/vienna_package.py:268: undefined name 'FILETYPE_TO_EXTENSION'
./usr/lib/python2.6/dist-packages/cogent/app/rnaforester.py:3: 'mkdir' imported but unused
./usr/lib/python2.6/dist-packages/cogent/app/rnaforester.py:3: 'close' imported but unused
./usr/lib/python2.6/dist-packages/cogent/app/rnaforester.py:3: 'getcwd' imported but unused
./usr/lib/python2.6/dist-packages/cogent/app/rnaforester.py:4: 'choice' imported but unused
./usr/lib/python2.6/dist-packages/cogent/app/rnaforester.py:6: 'ResultPath' imported but unused
./usr/lib/python2.6/dist-packages/cogent/app/rnaforester.py:8: 'Parameters' imported but unused
./usr/lib/python2.6/dist-packages/cogent/app/rnaforester.py:8: 'Parameter' imported but unused
./usr/lib/python2.6/dist-packages/cogent/app/rnaforester.py:8: 'ValuedParameter' imported but unused
./usr/lib/python2.6/dist-packages/cogent/app/rnaforester.py:8: 'MixedParameter' imported but unused
./usr/lib/python2.6/dist-packages/cogent/app/rnaforester.py:8: 'is_not_None' imported but unused
./usr/lib/python2.6/dist-packages/cogent/app/rnaforester.py:8: '_find_synonym' imported but unused
./usr/lib/python2.6/dist-packages/cogent/app/rnaforester.py:105: undefined name 'ApplicationError'
./usr/lib/python2.6/dist-packages/cogent/app/rnaforester.py:145: undefined name 'ApplicationError'
./usr/lib/python2.6/dist-packages/cogent/app/rnaforester.py:148: local variable 'synonyms' is assigned to but never used
./usr/lib/python2.6/dist-packages/cogent/app/rnashapes.py:13: 'CommandLineAppResult' imported but unused
./usr/lib/python2.6/dist-packages/cogent/app/rnashapes.py:13: 'ResultPath' imported but unused
./usr/lib/python2.6/dist-packages/cogent/app/rnashapes.py:15: 'is_not_None' imported but unused
./usr/lib/python2.6/dist-packages/cogent/app/rnashapes.py:15: '_find_synonym' imported but unused
./usr/lib/python2.6/dist-packages/cogent/app/rnashapes.py:15: 'Parameters' imported but unused
./usr/lib/python2.6/dist-packages/cogent/app/rnashapes.py:15: 'MixedParameter' imported but unused
./usr/lib/python2.6/dist-packages/cogent/app/rnashapes.py:15: 'Parameter' imported but unused
./usr/lib/python2.6/dist-packages/cogent/app/gctmpca.py:26: 'FilePath' imported but unused
./usr/lib/python2.6/dist-packages/cogent/app/gctmpca.py:27: 'DSO78_matrix' imported but unused
./usr/lib/python2.6/dist-packages/cogent/app/unafold.py:8: 'CommandLineAppResult' imported but unused
./usr/lib/python2.6/dist-packages/cogent/app/unafold.py:10: 'Parameters' imported but unused
./usr/lib/python2.6/dist-packages/cogent/app/unafold.py:10: 'Parameter' imported but unused
./usr/lib/python2.6/dist-packages/cogent/app/cove.py:3: 'CommandLineAppResult' imported but unused
./usr/lib/python2.6/dist-packages/cogent/app/cove.py:5: 'Parameters' imported but unused
./usr/lib/python2.6/dist-packages/cogent/app/cove.py:5: 'Parameter' imported but unused
./usr/lib/python2.6/dist-packages/cogent/app/cove.py:5: 'MixedParameter' imported but unused
./usr/lib/python2.6/dist-packages/cogent/app/cove.py:5: 'is_not_None' imported but unused
./usr/lib/python2.6/dist-packages/cogent/app/cove.py:5: '_find_synonym' imported but unused
./usr/lib/python2.6/dist-packages/cogent/app/rnaview.py:5: 'MixedParameter' imported but unused
./usr/lib/python2.6/dist-packages/cogent/app/cmfinder.py:7: 'CommandLineAppResult' imported but unused
./usr/lib/python2.6/dist-packages/cogent/app/cmfinder.py:9: 'MixedParameter' imported but unused
./usr/lib/python2.6/dist-packages/cogent/app/cmfinder.py:9: 'Parameters' imported but unused
./usr/lib/python2.6/dist-packages/cogent/app/cmfinder.py:9: 'Parameter' imported but unused
./usr/lib/python2.6/dist-packages/cogent/app/cmfinder.py:133: local variable 'motifList' is assigned to but never used
./usr/lib/python2.6/dist-packages/cogent/app/cmfinder.py:138: local variable 'inputPath' is assigned to but never used
./usr/lib/python2.6/dist-packages/cogent/app/dialign.py:17: 'guess_input_handler' imported but unused
./usr/lib/python2.6/dist-packages/cogent/app/dialign.py:17: 'get_tmp_filename' imported but unused
./usr/lib/python2.6/dist-packages/cogent/app/dialign.py:19: 'choice' imported but unused
./usr/lib/python2.6/dist-packages/cogent/app/dialign.py:20: 'DndParser' imported but unused
./usr/lib/python2.6/dist-packages/cogent/app/dialign.py:21: 'PhyloNode' imported but unused
./usr/lib/python2.6/dist-packages/cogent/app/dialign.py:22: 'MinimalFastaParser' imported but unused
./usr/lib/python2.6/dist-packages/cogent/app/comrna.py:3: 'CommandLineAppResult' imported but unused
./usr/lib/python2.6/dist-packages/cogent/app/comrna.py:3: 'ResultPath' imported but unused
./usr/lib/python2.6/dist-packages/cogent/app/comrna.py:5: 'is_not_None' imported but unused
./usr/lib/python2.6/dist-packages/cogent/app/comrna.py:5: '_find_synonym' imported but unused
./usr/lib/python2.6/dist-packages/cogent/app/comrna.py:5: 'Parameters' imported but unused
./usr/lib/python2.6/dist-packages/cogent/app/comrna.py:5: 'MixedParameter' imported but unused
./usr/lib/python2.6/dist-packages/cogent/app/comrna.py:5: 'FlagParameter' imported but unused
./usr/lib/python2.6/dist-packages/cogent/app/comrna.py:5: 'Parameter' imported but unused
./usr/lib/python2.6/dist-packages/cogent/app/stride.py:7: redefinition of unused 'StringIO' from line 5
./usr/lib/python2.6/dist-packages/cogent/app/dynalign.py:5: 'Parameters' imported but unused
./usr/lib/python2.6/dist-packages/cogent/app/dynalign.py:5: 'FlagParameter' imported but unused
./usr/lib/python2.6/dist-packages/cogent/app/dynalign.py:5: 'Parameter' imported but unused
./usr/lib/python2.6/dist-packages/cogent/app/dynalign.py:5: 'MixedParameter' imported but unused
./usr/lib/python2.6/dist-packages/cogent/app/dynalign.py:7: 'commands' imported but unused
./usr/lib/python2.6/dist-packages/cogent/app/dynalign.py:8: 'platform' imported but unused
./usr/lib/python2.6/dist-packages/cogent/app/dynalign.py:9: 'mkdir' imported but unused
./usr/lib/python2.6/dist-packages/cogent/app/dynalign.py:9: 'close' imported but unused
./usr/lib/python2.6/dist-packages/cogent/app/dynalign.py:9: 'getcwd' imported but unused
./usr/lib/python2.6/dist-packages/cogent/app/dynalign.py:168: undefined name 'ApplicationError'
./usr/lib/python2.6/dist-packages/cogent/app/dynalign.py:208: undefined name 'ApplicationError'
./usr/lib/python2.6/dist-packages/cogent/app/dynalign.py:210: local variable 'parameters' is assigned to but never used
./usr/lib/python2.6/dist-packages/cogent/app/dynalign.py:211: local variable 'synonyms' is assigned to but never used
./usr/lib/python2.6/dist-packages/cogent/app/sffinfo.py:4: 'ResultPath' imported but unused
./usr/lib/python2.6/dist-packages/cogent/app/sffinfo.py:114: undefined name 'ApplicationError'
./usr/lib/python2.6/dist-packages/cogent/app/sffinfo.py:119: local variable 'synonyms' is assigned to but never used
./usr/lib/python2.6/dist-packages/cogent/app/consan.py:4: 'ResultPath' imported but unused
./usr/lib/python2.6/dist-packages/cogent/app/consan.py:6: 'Parameters' imported but unused
./usr/lib/python2.6/dist-packages/cogent/app/consan.py:6: 'Parameter' imported but unused
./usr/lib/python2.6/dist-packages/cogent/app/consan.py:6: 'MixedParameter' imported but unused
./usr/lib/python2.6/dist-packages/cogent/app/consan.py:6: 'is_not_None' imported but unused
./usr/lib/python2.6/dist-packages/cogent/app/consan.py:6: '_find_synonym' imported but unused
./usr/lib/python2.6/dist-packages/cogent/app/consan.py:123: undefined name 'ApplicationError'
./usr/lib/python2.6/dist-packages/cogent/app/pfold.py:10: 'CommandLineAppResult' imported but unused
./usr/lib/python2.6/dist-packages/cogent/app/pfold.py:10: 'ResultPath' imported but unused
./usr/lib/python2.6/dist-packages/cogent/app/dotur.py:6: 'MixedParameter' imported but unused
./usr/lib/python2.6/dist-packages/cogent/app/dotur.py:10: 'SequenceCollection' imported but unused
./usr/lib/python2.6/dist-packages/cogent/app/dotur.py:11: 'PROTEIN' imported but unused
./usr/lib/python2.6/dist-packages/cogent/app/dotur.py:11: 'DNA' imported but unused
./usr/lib/python2.6/dist-packages/cogent/app/dotur.py:11: 'RNA' imported but unused
./usr/lib/python2.6/dist-packages/cogent/app/contrafold.py:3: 'CommandLineAppResult' imported but unused
./usr/lib/python2.6/dist-packages/cogent/app/contrafold.py:3: 'ResultPath' imported but unused
./usr/lib/python2.6/dist-packages/cogent/app/contrafold.py:5: 'is_not_None' imported but unused
./usr/lib/python2.6/dist-packages/cogent/app/contrafold.py:5: '_find_synonym' imported but unused
./usr/lib/python2.6/dist-packages/cogent/app/contrafold.py:5: 'Parameters' imported but unused
./usr/lib/python2.6/dist-packages/cogent/app/contrafold.py:5: 'MixedParameter' imported but unused
./usr/lib/python2.6/dist-packages/cogent/app/contrafold.py:5: 'ValuedParameter' imported but unused
./usr/lib/python2.6/dist-packages/cogent/app/contrafold.py:5: 'Parameter' imported but unused
./usr/lib/python2.6/dist-packages/cogent/app/clearcut.py:5: 'MixedParameter' imported but unused
./usr/lib/python2.6/dist-packages/cogent/app/clearcut.py:8: 'SequenceCollection' imported but unused
./usr/lib/python2.6/dist-packages/cogent/app/clearcut.py:9: 'PROTEIN' imported but unused
./usr/lib/python2.6/dist-packages/cogent/app/fasttree_v1.py:64: local variable 'suppress_stdout' is assigned to but never used
./usr/lib/python2.6/dist-packages/cogent/app/fasttree_v1.py:95: undefined name 'ApplicationError'
./usr/lib/python2.6/dist-packages/cogent/app/mfold.py:9: 'CommandLineAppResult' imported but unused
./usr/lib/python2.6/dist-packages/cogent/app/mfold.py:11: 'Parameters' imported but unused
./usr/lib/python2.6/dist-packages/cogent/app/mfold.py:11: 'Parameter' imported but unused
./usr/lib/python2.6/dist-packages/cogent/app/sfold.py:10: 'CommandLineAppResult' imported but unused
./usr/lib/python2.6/dist-packages/cogent/app/sfold.py:12: 'Parameters' imported but unused
./usr/lib/python2.6/dist-packages/cogent/app/sfold.py:12: 'MixedParameter' imported but unused
./usr/lib/python2.6/dist-packages/cogent/app/sfold.py:12: 'FlagParameter' imported but unused
./usr/lib/python2.6/dist-packages/cogent/app/sfold.py:12: 'Parameter' imported but unused
./usr/lib/python2.6/dist-packages/cogent/app/pknotsrg.py:3: 'CommandLineAppResult' imported but unused
./usr/lib/python2.6/dist-packages/cogent/app/pknotsrg.py:3: 'ResultPath' imported but unused
./usr/lib/python2.6/dist-packages/cogent/app/pknotsrg.py:5: 'Parameters' imported but unused
./usr/lib/python2.6/dist-packages/cogent/app/pknotsrg.py:5: 'MixedParameter' imported but unused
./usr/lib/python2.6/dist-packages/cogent/app/pknotsrg.py:5: 'Parameter' imported but unused
./usr/lib/python2.6/dist-packages/cogent/app/formatdb.py:65: local variable 'input_filepath' is assigned to but never used
./usr/lib/python2.6/dist-packages/cogent/app/fasttree.py:71: local variable 'suppress_stdout' is assigned to but never used
./usr/lib/python2.6/dist-packages/cogent/app/fasttree.py:102: undefined name 'ApplicationError'
./usr/lib/python2.6/dist-packages/cogent/app/rdp_classifier.py:20: 'Parameter' imported but unused
./usr/lib/python2.6/dist-packages/cogent/app/rdp_classifier.py:22: 'guess_input_handler' imported but unused
./usr/lib/python2.6/dist-packages/cogent/app/nupack.py:11: 'Parameters' imported but unused
./usr/lib/python2.6/dist-packages/cogent/app/nupack.py:11: 'FlagParameter' imported but unused
./usr/lib/python2.6/dist-packages/cogent/app/nupack.py:11: 'Parameter' imported but unused
./usr/lib/python2.6/dist-packages/cogent/app/nupack.py:11: 'ValuedParameter' imported but unused
./usr/lib/python2.6/dist-packages/cogent/app/nupack.py:11: 'MixedParameter' imported but unused
./usr/lib/python2.6/dist-packages/cogent/app/nupack.py:11: 'is_not_None' imported but unused
./usr/lib/python2.6/dist-packages/cogent/app/nupack.py:11: '_find_synonym' imported but unused
./usr/lib/python2.6/dist-packages/cogent/app/nupack.py:143: undefined name 'ApplicationError'
./usr/lib/python2.6/dist-packages/cogent/app/blast.py:6: 'MixedParameter' imported but unused
./usr/lib/python2.6/dist-packages/cogent/app/blast.py:7: 'get_tmp_filename' imported but unused
./usr/lib/python2.6/dist-packages/cogent/app/blast.py:10: 'QMEBlast9' imported but unused
./usr/lib/python2.6/dist-packages/cogent/app/blast.py:913: local variable 'last_num_ids' is assigned to but never used
./usr/lib/python2.6/dist-packages/cogent/app/blast.py:997: local variable 'seq_file' is assigned to but never used
./usr/lib/python2.6/dist-packages/cogent/app/util.py:2: 'commands' imported but unused
./usr/lib/python2.6/dist-packages/cogent/app/util.py:3: 'platform' imported but unused
./usr/lib/python2.6/dist-packages/cogent/app/util.py:4: 'sep' imported but unused
./usr/lib/python2.6/dist-packages/cogent/app/util.py:4: 'close' imported but unused
./usr/lib/python2.6/dist-packages/cogent/app/util.py:7: 'array' imported but unused
./usr/lib/python2.6/dist-packages/cogent/app/util.py:7: 'nonzero' imported but unused
./usr/lib/python2.6/dist-packages/cogent/app/util.py:7: 'zeros' imported but unused
./usr/lib/python2.6/dist-packages/cogent/app/util.py:7: 'max' imported but unused
./usr/lib/python2.6/dist-packages/cogent/app/util.py:8: 'Parameter' imported but unused
./usr/lib/python2.6/dist-packages/cogent/app/util.py:8: 'FlagParameter' imported but unused
./usr/lib/python2.6/dist-packages/cogent/app/util.py:8: 'ValuedParameter' imported but unused
./usr/lib/python2.6/dist-packages/cogent/app/util.py:8: 'MixedParameter' imported but unused
./usr/lib/python2.6/dist-packages/cogent/app/util.py:8: 'is_not_None' imported but unused
./usr/lib/python2.6/dist-packages/cogent/app/util.py:8: '_find_synonym' imported but unused
./usr/lib/python2.6/dist-packages/cogent/app/util.py:10: 'if_' imported but unused
./usr/lib/python2.6/dist-packages/cogent/app/util.py:366: local variable 'synonyms' is assigned to but never used
./usr/lib/python2.6/dist-packages/cogent/app/carnac.py:3: 'CommandLineAppResult' imported but unused
./usr/lib/python2.6/dist-packages/cogent/app/carnac.py:5: 'Parameters' imported but unused
./usr/lib/python2.6/dist-packages/cogent/app/carnac.py:5: 'Parameter' imported but unused
./usr/lib/python2.6/dist-packages/cogent/app/carnac.py:58: local variable 'seq_counter' is assigned to but never used
./usr/lib/python2.6/dist-packages/cogent/app/rnaalifold.py:3: 'CommandLineAppResult' imported but unused
./usr/lib/python2.6/dist-packages/cogent/app/rnaalifold.py:5: 'Parameters' imported but unused
./usr/lib/python2.6/dist-packages/cogent/app/rnaalifold.py:5: 'Parameter' imported but unused
./usr/lib/python2.6/dist-packages/cogent/app/rnaalifold.py:5: '_find_synonym' imported but unused
./usr/lib/python2.6/dist-packages/cogent/app/rnaalifold.py:10: 'rnaalifold_parser' imported but unused
./usr/lib/python2.6/dist-packages/cogent/app/rnaalifold.py:12: 'ViennaStructure' imported but unused
./usr/lib/python2.6/dist-packages/cogent/app/foldalign.py:11: 'CommandLineAppResult' imported but unused
./usr/lib/python2.6/dist-packages/cogent/app/foldalign.py:11: 'ResultPath' imported but unused
./usr/lib/python2.6/dist-packages/cogent/app/foldalign.py:13: 'is_not_None' imported but unused
./usr/lib/python2.6/dist-packages/cogent/app/foldalign.py:13: '_find_synonym' imported but unused
./usr/lib/python2.6/dist-packages/cogent/app/foldalign.py:13: 'Parameters' imported but unused
./usr/lib/python2.6/dist-packages/cogent/app/foldalign.py:13: 'MixedParameter' imported but unused
./usr/lib/python2.6/dist-packages/cogent/app/foldalign.py:13: 'Parameter' imported but unused
./usr/lib/python2.6/dist-packages/cogent/app/muscle.py:8: 'choice' imported but unused
./usr/lib/python2.6/dist-packages/cogent/app/mafft.py:7: 'get_tmp_filename' imported but unused
./usr/lib/python2.6/dist-packages/cogent/app/mafft.py:9: 'choice' imported but unused
./usr/lib/python2.6/dist-packages/cogent/app/mafft.py:11: 'PROTEIN' imported but unused
./usr/lib/python2.6/dist-packages/cogent/app/mafft.py:11: 'DNA' imported but unused
./usr/lib/python2.6/dist-packages/cogent/app/mafft.py:11: 'RNA' imported but unused
./usr/lib/python2.6/dist-packages/cogent/app/mafft.py:13: 'PhyloNode' imported but unused
./usr/lib/python2.6/dist-packages/cogent/app/mafft.py:14: 'DndParser' imported but unused
./usr/lib/python2.6/dist-packages/cogent/recalculation/calculation.py:5: 'warnings' imported but unused
./usr/lib/python2.6/dist-packages/cogent/recalculation/calculation.py:209: local variable 'detail' is assigned to but never used
./usr/lib/python2.6/dist-packages/cogent/recalculation/definition.py:67: 'warnings' imported but unused
./usr/lib/python2.6/dist-packages/cogent/recalculation/definition.py:80: 'chdtri' imported but unused
./usr/lib/python2.6/dist-packages/cogent/recalculation/definition.py:81: 'parallel' imported but unused
./usr/lib/python2.6/dist-packages/cogent/recalculation/definition.py:418: local variable 'N' is assigned to but never used
./usr/lib/python2.6/dist-packages/cogent/recalculation/scope.py:663: redefinition of function 'callback' from line 659
./usr/lib/python2.6/dist-packages/cogent/util/terminal.py:19: redefinition of unused 'curses' from line 17
./usr/lib/python2.6/dist-packages/cogent/util/table.py:538: local variable 'is_reversed' is assigned to but never used
./usr/lib/python2.6/dist-packages/cogent/util/table.py:548: local variable 'cast' is assigned to but never used
./usr/lib/python2.6/dist-packages/cogent/util/misc.py:12: 'maxint' imported but unused
./usr/lib/python2.6/dist-packages/cogent/util/misc.py:13: 'popen' imported but unused
./usr/lib/python2.6/dist-packages/cogent/util/misc.py:15: 'sum' imported but unused
./usr/lib/python2.6/dist-packages/cogent/util/misc.py:15: 'logical_not' imported but unused
./usr/lib/python2.6/dist-packages/cogent/util/misc.py:204: local variable 'e' is assigned to but never used
./usr/lib/python2.6/dist-packages/cogent/util/misc.py:1098: local variable 'ValueError' is assigned to but never used
./usr/lib/python2.6/dist-packages/cogent/util/progress_display.py:24: 'contextlib' imported but unused
./usr/lib/python2.6/dist-packages/cogent/util/progress_display.py:24: 'warnings' imported but unused
./usr/lib/python2.6/dist-packages/cogent/util/progress_display.py:25: 'atexit' imported but unused
./usr/lib/python2.6/dist-packages/cogent/util/progress_display.py:25: 'os' imported but unused
./usr/lib/python2.6/dist-packages/cogent/util/update_version.py:273: local variable 'found_version_line' is assigned to but never used
./usr/lib/python2.6/dist-packages/cogent/util/update_version.py:292: local variable 'found_version_line' is assigned to but never used
./usr/lib/python2.6/dist-packages/cogent/util/update_version.py:311: local variable 'found_version_line' is assigned to but never used
./usr/lib/python2.6/dist-packages/cogent/util/dict2d.py:234: local variable 'constructor' is assigned to but never used
./usr/lib/python2.6/dist-packages/cogent/util/dict2d.py:543: local variable 'item_lookup' is assigned to but never used
./usr/lib/python2.6/dist-packages/cogent/util/organizer.py:74: local variable 'results' is assigned to but never used
./usr/lib/python2.6/dist-packages/cogent/util/trie.py:148: local variable 'labels' is assigned to but never used
./usr/lib/python2.6/dist-packages/cogent/util/transform.py:16: 'and_' imported but unused
./usr/lib/python2.6/dist-packages/cogent/util/transform.py:16: 'or_' imported but unused
./usr/lib/python2.6/dist-packages/cogent/util/transform.py:17: 'logical_or' imported but unused
./usr/lib/python2.6/dist-packages/cogent/util/transform.py:17: 'logical_and' imported but unused
./usr/lib/python2.6/dist-packages/cogent/util/transform.py:17: 'logical_not' imported but unused
./usr/lib/python2.6/dist-packages/cogent/util/transform.py:224: redefinition of function 'result' from line 220
./usr/lib/python2.6/dist-packages/cogent/util/transform.py:499: redefinition of function 'result' from line 494
./usr/lib/python2.6/dist-packages/cogent/util/unit_test.py:36: 'TestSuite' imported but unused
./usr/lib/python2.6/dist-packages/cogent/util/unit_test.py:36: 'main' imported but unused
./usr/lib/python2.6/dist-packages/cogent/util/unit_test.py:36: 'findTestCases' imported but unused
./usr/lib/python2.6/dist-packages/cogent/util/unit_test.py:37: 'recursive_flatten' imported but unused
./usr/lib/python2.6/dist-packages/cogent/util/unit_test.py:317: local variable 'e' is assigned to but never used
./usr/lib/python2.6/dist-packages/cogent/util/parallel.py:51: redefinition of unused 'MPI' from line 48
./usr/lib/python2.6/dist-packages/cogent/util/recode_alignment.py:41: 'OptionParser' imported but unused
./usr/lib/python2.6/dist-packages/cogent/util/recode_alignment.py:43: 'Alignment' imported but unused
./usr/lib/python2.6/dist-packages/cogent/util/recode_alignment.py:45: 'PROTEIN' imported but unused
./usr/lib/python2.6/dist-packages/cogent/util/array.py:4: 'mul' imported but unused
./usr/lib/python2.6/dist-packages/cogent/util/array.py:4: 'getitem' imported but unused
./usr/lib/python2.6/dist-packages/cogent/seqsim/analysis.py:2: 'RangeNode' imported but unused
./usr/lib/python2.6/dist-packages/cogent/seqsim/analysis.py:2: 'balanced_breakpoints' imported but unused
./usr/lib/python2.6/dist-packages/cogent/seqsim/analysis.py:103: local variable 'rates' is assigned to but never used
./usr/lib/python2.6/dist-packages/cogent/seqsim/analysis.py:291: undefined name 'BalancedTree'
./usr/lib/python2.6/dist-packages/cogent/seqsim/analysis.py:294: undefined name 'xxx'
./usr/lib/python2.6/dist-packages/cogent/seqsim/analysis.py:296: undefined name 'Rates'
./usr/lib/python2.6/dist-packages/cogent/seqsim/analysis.py:297: undefined name 'scale_trace'
./usr/lib/python2.6/dist-packages/cogent/seqsim/analysis.py:302: undefined name 'random_q_matrix'
./usr/lib/python2.6/dist-packages/cogent/seqsim/analysis.py:303: undefined name 'scale_trace'
./usr/lib/python2.6/dist-packages/cogent/seqsim/analysis.py:307: undefined name 'rand_rna'
./usr/lib/python2.6/dist-packages/cogent/seqsim/analysis.py:319: undefined name 'BalancedTree'
./usr/lib/python2.6/dist-packages/cogent/seqsim/analysis.py:324: undefined name 'random_q_matrix'
./usr/lib/python2.6/dist-packages/cogent/seqsim/analysis.py:325: undefined name 'scale_trace'
./usr/lib/python2.6/dist-packages/cogent/seqsim/analysis.py:329: undefined name 'rand_rna'
./usr/lib/python2.6/dist-packages/cogent/seqsim/analysis.py:336: undefined name 'flatten_q_matrices'
./usr/lib/python2.6/dist-packages/cogent/seqsim/analysis.py:338: undefined name 'scale_trace'
./usr/lib/python2.6/dist-packages/cogent/seqsim/analysis.py:339: undefined name 'flatten_q_matrices'
./usr/lib/python2.6/dist-packages/cogent/seqsim/analysis.py:341: undefined name 'cov'
./usr/lib/python2.6/dist-packages/cogent/seqsim/analysis.py:342: undefined name 'corrcoef'
./usr/lib/python2.6/dist-packages/cogent/seqsim/analysis.py:343: undefined name 'euclidean_norm'
./usr/lib/python2.6/dist-packages/cogent/seqsim/analysis.py:344: undefined name 'euclidean_norm'
./usr/lib/python2.6/dist-packages/cogent/seqsim/analysis.py:345: undefined name 'eigenvalues'
./usr/lib/python2.6/dist-packages/cogent/seqsim/analysis.py:348: undefined name 'eigenvalues'
./usr/lib/python2.6/dist-packages/cogent/seqsim/analysis.py:351: undefined name 'ratio_two_best'
./usr/lib/python2.6/dist-packages/cogent/seqsim/analysis.py:352: undefined name 'ratio_two_best'
./usr/lib/python2.6/dist-packages/cogent/seqsim/analysis.py:353: undefined name 'ratio_best_to_sum'
./usr/lib/python2.6/dist-packages/cogent/seqsim/analysis.py:354: undefined name 'ratio_best_to_sum'
./usr/lib/python2.6/dist-packages/cogent/seqsim/analysis.py:355: undefined name 'weiss'
./usr/lib/python2.6/dist-packages/cogent/seqsim/analysis.py:357: undefined name 'dists_from_mean'
./usr/lib/python2.6/dist-packages/cogent/seqsim/analysis.py:359: undefined name 'var'
./usr/lib/python2.6/dist-packages/cogent/seqsim/analysis.py:361: undefined name 'mean'
./usr/lib/python2.6/dist-packages/cogent/seqsim/analysis.py:362: undefined name 'euclidean_distance'
./usr/lib/python2.6/dist-packages/cogent/seqsim/analysis.py:365: undefined name 'euclidean_norm'
./usr/lib/python2.6/dist-packages/cogent/seqsim/analysis.py:365: undefined name 'cov'
./usr/lib/python2.6/dist-packages/cogent/seqsim/analysis.py:378: undefined name 'all_p_from_tree'
./usr/lib/python2.6/dist-packages/cogent/seqsim/analysis.py:379: undefined name 'pair_p_from_tree'
./usr/lib/python2.6/dist-packages/cogent/seqsim/analysis.py:380: undefined name 'get_qs'
./usr/lib/python2.6/dist-packages/cogent/seqsim/analysis.py:381: undefined name 'get_qs'
./usr/lib/python2.6/dist-packages/cogent/seqsim/analysis.py:382: undefined name 'take_off_diag'
./usr/lib/python2.6/dist-packages/cogent/seqsim/analysis.py:384: undefined name 'scale_trace'
./usr/lib/python2.6/dist-packages/cogent/seqsim/analysis.py:385: undefined name 'flatten_q_matrices'
./usr/lib/python2.6/dist-packages/cogent/seqsim/analysis.py:386: undefined name 'flatten_q_matrices'
./usr/lib/python2.6/dist-packages/cogent/seqsim/analysis.py:387: undefined name 'dists_from_mean'
./usr/lib/python2.6/dist-packages/cogent/seqsim/analysis.py:389: undefined name 'var'
./usr/lib/python2.6/dist-packages/cogent/seqsim/analysis.py:390: undefined name 'dists_from_mean'
./usr/lib/python2.6/dist-packages/cogent/seqsim/analysis.py:392: undefined name 'var'
./usr/lib/python2.6/dist-packages/cogent/seqsim/analysis.py:394: undefined name 'flatten_q_matrices'
./usr/lib/python2.6/dist-packages/cogent/seqsim/analysis.py:395: undefined name 'corrcoef'
./usr/lib/python2.6/dist-packages/cogent/seqsim/analysis.py:396: undefined name 'ratio_two_best'
./usr/lib/python2.6/dist-packages/cogent/seqsim/analysis.py:396: undefined name 'eigenvalues'
./usr/lib/python2.6/dist-packages/cogent/seqsim/analysis.py:398: undefined name 'cov'
./usr/lib/python2.6/dist-packages/cogent/seqsim/analysis.py:399: undefined name 'eigenvalues'
./usr/lib/python2.6/dist-packages/cogent/seqsim/analysis.py:402: undefined name 'ratio_two_best'
./usr/lib/python2.6/dist-packages/cogent/seqsim/analysis.py:403: undefined name 'weiss'
./usr/lib/python2.6/dist-packages/cogent/seqsim/analysis.py:413: undefined name 'all_p_from_tree'
./usr/lib/python2.6/dist-packages/cogent/seqsim/analysis.py:414: undefined name 'get_qs'
./usr/lib/python2.6/dist-packages/cogent/seqsim/analysis.py:416: undefined name 'scale_trace'
./usr/lib/python2.6/dist-packages/cogent/seqsim/analysis.py:417: undefined name 'flatten_q_matrices'
./usr/lib/python2.6/dist-packages/cogent/seqsim/analysis.py:418: undefined name 'dists_from_mean'
./usr/lib/python2.6/dist-packages/cogent/seqsim/analysis.py:420: undefined name 'var'
./usr/lib/python2.6/dist-packages/cogent/seqsim/analysis.py:422: undefined name 'flatten_q_matrices'
./usr/lib/python2.6/dist-packages/cogent/seqsim/analysis.py:423: undefined name 'corrcoef'
./usr/lib/python2.6/dist-packages/cogent/seqsim/analysis.py:424: undefined name 'ratio_two_best'
./usr/lib/python2.6/dist-packages/cogent/seqsim/analysis.py:424: undefined name 'eigenvalues'
./usr/lib/python2.6/dist-packages/cogent/seqsim/analysis.py:434: undefined name 'random_mats'
./usr/lib/python2.6/dist-packages/cogent/seqsim/analysis.py:434: undefined name 'random_q_mats'
./usr/lib/python2.6/dist-packages/cogent/seqsim/analysis.py:435: undefined name 'scale_one_q'
./usr/lib/python2.6/dist-packages/cogent/seqsim/analysis.py:435: undefined name 'scale_many_q'
./usr/lib/python2.6/dist-packages/cogent/seqsim/analysis.py:437: undefined name 'svd_q'
./usr/lib/python2.6/dist-packages/cogent/seqsim/analysis.py:444: undefined name 'balanced_one_q_tree'
./usr/lib/python2.6/dist-packages/cogent/seqsim/analysis.py:445: undefined name 'all_p_from_tree'
./usr/lib/python2.6/dist-packages/cogent/seqsim/analysis.py:446: undefined name 'svd_q'
./usr/lib/python2.6/dist-packages/cogent/seqsim/analysis.py:446: undefined name 'get_qs'
./usr/lib/python2.6/dist-packages/cogent/seqsim/analysis.py:451: undefined name 'all_p_from_tree'
./usr/lib/python2.6/dist-packages/cogent/seqsim/analysis.py:452: undefined name 'svd_q'
./usr/lib/python2.6/dist-packages/cogent/seqsim/analysis.py:452: undefined name 'get_qs'
./usr/lib/python2.6/dist-packages/cogent/seqsim/analysis.py:452: undefined name 'all_p_from_tree'
./usr/lib/python2.6/dist-packages/cogent/seqsim/analysis.py:455: undefined name 'all_p_from_tree'
./usr/lib/python2.6/dist-packages/cogent/seqsim/analysis.py:457: undefined name 'svd_q'
./usr/lib/python2.6/dist-packages/cogent/seqsim/analysis.py:457: undefined name 'get_qs'
./usr/lib/python2.6/dist-packages/cogent/seqsim/analysis.py:457: undefined name 'all_p_from_tree'
./usr/lib/python2.6/dist-packages/cogent/seqsim/analysis.py:460: undefined name 'all_p_from_tree'
./usr/lib/python2.6/dist-packages/cogent/seqsim/analysis.py:461: undefined name 'get_qs'
./usr/lib/python2.6/dist-packages/cogent/seqsim/analysis.py:470: undefined name 'header'
./usr/lib/python2.6/dist-packages/cogent/seqsim/analysis.py:474: undefined name 'header'
./usr/lib/python2.6/dist-packages/cogent/seqsim/analysis.py:476: undefined name 'header'
./usr/lib/python2.6/dist-packages/cogent/seqsim/analysis.py:477: undefined name 'header'
./usr/lib/python2.6/dist-packages/cogent/seqsim/analysis.py:493: undefined name 'random'
./usr/lib/python2.6/dist-packages/cogent/seqsim/analysis.py:500: undefined name 'balanced_one_q_tree'
./usr/lib/python2.6/dist-packages/cogent/seqsim/analysis.py:513: undefined name 'balanced_one_q_tree'
./usr/lib/python2.6/dist-packages/cogent/seqsim/analysis.py:520: undefined name 'lengths'
./usr/lib/python2.6/dist-packages/cogent/seqsim/analysis.py:546: undefined name 'tree_controller'
./usr/lib/python2.6/dist-packages/cogent/seqsim/birth_death.py:404: local variable 'max_taxa' is assigned to but never used
./usr/lib/python2.6/dist-packages/cogent/seqsim/birth_death.py:405: undefined name 'num_taxa'
./usr/lib/python2.6/dist-packages/cogent/seqsim/birth_death.py:408: undefined name 'num_taxa'
./usr/lib/python2.6/dist-packages/cogent/seqsim/microarray_normalize.py:31: 'zeros' imported but unused
./usr/lib/python2.6/dist-packages/cogent/seqsim/microarray_normalize.py:31: 'transpose' imported but unused
./usr/lib/python2.6/dist-packages/cogent/seqsim/microarray_normalize.py:31: 'ceil' imported but unused
./usr/lib/python2.6/dist-packages/cogent/seqsim/microarray_normalize.py:97: local variable 'gmean' is assigned to but never used
./usr/lib/python2.6/dist-packages/cogent/seqsim/microarray_normalize.py:125: undefined name 'rank_row_by_variance'
./usr/lib/python2.6/dist-packages/cogent/seqsi./usr/lib/python2.6/dist-packages/cogent/draw/linear.py:1127: invalid syntax
^
m/microarray_normalize.py:135: local variable 'constant_rank_indices' (defined in enclosing scope on line 127) referenced before assignment
./usr/lib/python2.6/dist-packages/cogent/seqsim/microarray_normalize.py:146: undefined name 'nonzero'
./usr/lib/python2.6/dist-packages/cogent/seqsim/microarray_normalize.py:188: undefined name 'NormalizationError'
./usr/lib/python2.6/dist-packages/cogent/seqsim/tree.py:6: 'array' imported but unused
./usr/lib/python2.6/dist-packages/cogent/seqsim/tree.py:494: local variable 'result' is assigned to but never used
./usr/lib/python2.6/dist-packages/cogent/seqsim/tree.py:516: local variable 'new_nodes' is assigned to but never used
./usr/lib/python2.6/dist-packages/cogent/seqsim/usage.py:25: 'mul' imported but unused
./usr/lib/python2.6/dist-packages/cogent/seqsim/usage.py:25: 'div' imported but unused
./usr/lib/python2.6/dist-packages/cogent/seqsim/usage.py:29: redefinition of unused 'log' from line 29
./usr/lib/python2.6/dist-packages/cogent/seqsim/usage.py:29: 'identity' imported but unused
./usr/lib/python2.6/dist-packages/cogent/seqsim/usage.py:822: redefinition of function 'similarity_f' from line 819
./usr/lib/python2.6/dist-packages/cogent/seqsim/usage.py:851: redefinition of function 'similarity_f' from line 847
./usr/lib/python2.6/dist-packages/cogent/seqsim/usage.py:858: redefinition of function 'similarity_f' from line 851
./usr/lib/python2.6/dist-packages/cogent/seqsim/usage.py:861: redefinition of function 'similarity_f' from line 858
./usr/lib/python2.6/dist-packages/cogent/seqsim/usage.py:934: local variable 'num_negs' is assigned to but never used
./usr/lib/python2.6/dist-packages/cogent/seqsim/usage.py:1125: undefined name 'Float64'
./usr/lib/python2.6/dist-packages/cogent/seqsim/markov.py:15: 'shuffle' imported but unused
./usr/lib/python2.6/dist-packages/cogent/seqsim/markov.py:15: 'randrange' imported but unused
./usr/lib/python2.6/dist-packages/cogent/seqsim/markov.py:19: 'copy' imported but unused
./usr/lib/python2.6/dist-packages/cogent/seqsim/markov.py:20: 'rank' imported but unused
./usr/lib/python2.6/dist-packages/cogent/seqsim/markov.py:20: 'searchsorted' imported but unused
./usr/lib/python2.6/dist-packages/cogent/seqsim/markov.py:20: 'ones' imported but unused
./usr/lib/python2.6/dist-packages/cogent/seqsim/markov.py:20: 'argsort' imported but unused
./usr/lib/python2.6/dist-packages/cogent/seqsim/markov.py:318: undefined name 'KwordError'
./usr/lib/python2.6/dist-packages/cogent/seqsim/markov.py:413: local variable 'total' is assigned to but never used
./usr/lib/python2.6/dist-packages/cogent/seqsim/sequence_generators.py:23: 'path' imported but unused
./usr/lib/python2.6/dist-packages/cogent/seqsim/sequence_generators.py:24: 'choice' imported but unused
./usr/lib/python2.6/dist-packages/cogent/draw/arrow_rates.py:4: redefinition of unused 'rc' from line 2
./usr/lib/python2.6/dist-packages/cogent/draw/arrow_rates.py:4: 'show' imported but unused
./usr/lib/python2.6/dist-packages/cogent/draw/arrow_rates.py:4: 'draw' imported but unused
./usr/lib/python2.6/dist-packages/cogent/draw/arrow_rates.py:118: local variable 'A' is assigned to but never used
./usr/lib/python2.6/dist-packages/cogent/draw/arrow_rates.py:119: local variable 'T' is assigned to but never used
./usr/lib/python2.6/dist-packages/cogent/draw/arrow_rates.py:120: local variable 'G' is assigned to but never used
./usr/lib/python2.6/dist-packages/cogent/draw/arrow_rates.py:121: local variable 'C' is assigned to but never used
./usr/lib/python2.6/dist-packages/cogent/draw/arrow_rates.py:202: local variable 'arrow_label_offset' is assigned to but never used
./usr/lib/python2.6/dist-packages/cogent/draw/multivariate_plot.py:4: 'plot' imported but unused
./usr/lib/python2.6/dist-packages/cogent/draw/multivariate_plot.py:8: 'set_trace' imported but unused
./usr/lib/python2.6/dist-packages/cogent/draw/rlg2mpl.py:8: 'Line2D' imported but unused
./usr/lib/python2.6/dist-packages/cogent/draw/rlg2mpl.py:14: 'numpy' imported but unused
./usr/lib/python2.6/dist-packages/cogent/draw/rlg2mpl.py:47: local variable 'fontname' is assigned to but never used
./usr/lib/python2.6/dist-packages/cogent/draw/rlg2mpl.py:48: local variable 'fontsize' is assigned to but never used
./usr/lib/python2.6/dist-packages/cogent/draw/rlg2mpl.py:49: local variable 'color' is assigned to but never used
./usr/lib/python2.6/dist-packages/cogent/draw/rlg2mpl.py:50: local variable 'ha' is assigned to but never used
./usr/lib/python2.6/dist-packages/cogent/draw/rlg2mpl.py:51: local variable 'va' is assigned to but never used
./usr/lib/python2.6/dist-packages/cogent/draw/codon_usage.py:43: redefinition of unused 'standard_series_colors' from line 11
./usr/lib/python2.6/dist-packages/cogent/draw/codon_usage.py:80: local variable 'colors' is assigned to but never used
./usr/lib/python2.6/dist-packages/cogent/draw/__init__.py:15: 'TrackDefn' imported but unused
./usr/lib/python2.6/dist-packages/cogent/draw/__init__.py:15: 'Diamond' imported but unused
./usr/lib/python2.6/dist-packages/cogent/draw/__init__.py:15: 'Area' imported but unused
./usr/lib/python2.6/dist-packages/cogent/draw/__init__.py:15: 'DisplayPolicy' imported but unused
./usr/lib/python2.6/dist-packages/cogent/draw/__init__.py:15: 'colors' imported but unused
./usr/lib/python2.6/dist-packages/cogent/draw/__init__.py:15: 'Arrow' imported but unused
./usr/lib/python2.6/dist-packages/cogent/draw/__init__.py:15: 'BluntArrow' imported but unused
./usr/lib/python2.6/dist-packages/cogent/draw/__init__.py:15: 'Box' imported but unused
./usr/lib/python2.6/dist-packages/cogent/draw/__init__.py:15: 'Display' imported but unused
./usr/lib/python2.6/dist-packages/cogent/draw/__init__.py:19: 'cogent' imported but unused
./usr/lib/python2.6/dist-packages/cogent/draw/legend.py:6: 'PatchCollection' imported but unused
./usr/lib/python2.6/dist-packages/cogent/draw/legend.py:7: 'Text' imported but unused
./usr/lib/python2.6/dist-packages/cogent/draw/legend.py:8: 'Affine2D' imported but unused
./usr/lib/python2.6/dist-packages/cogent/draw/legend.py:9: 'Group' imported but unused
./usr/lib/python2.6/dist-packages/cogent/draw/legend.py:35: local variable 'v' is assigned to but never used
./usr/lib/python2.6/dist-packages/cogent/draw/legend.py:47: local variable 'result' is assigned to but never used
./usr/lib/python2.6/dist-packages/cogent/draw/legend.py:84: local variable 'g' is assigned to but never used
./usr/lib/python2.6/dist-packages/cogent/draw/util.py:15: 'use' imported but unused
./usr/lib/python2.6/dist-packages/cogent/draw/util.py:33: redefinition of unused 'ImageFilter' from line 31
./usr/lib/python2.6/dist-packages/cogent/draw/util.py:33: redefinition of unused 'Image' from line 30
./usr/lib/python2.6/dist-packages/cogent/draw/util.py:34: 'shape' imported but unused
./usr/lib/python2.6/dist-packages/cogent/draw/util.py:34: 'array' imported but unused
./usr/lib/python2.6/dist-packages/cogent/draw/util.py:35: 'CodonUsage' imported but unused
./usr/lib/python2.6/dist-packages/cogent/draw/util.py:153: undefined name 'normalize'
./usr/lib/python2.6/dist-packages/cogent/draw/util.py:158: undefined name 'amax'
./usr/lib/python2.6/dist-packages/cogent/draw/util.py:158: undefined name 'amin'
./usr/lib/python2.6/dist-packages/cogent/draw/util.py:260: local variable 'label_offset' is assigned to but never used
./usr/lib/python2.6/dist-packages/cogent/draw/util.py:343: local variable 'x' is assigned to but never used
./usr/lib/python2.6/dist-packages/cogent/draw/util.py:344: local variable 'y' is assigned to but never used
./usr/lib/python2.6/dist-packages/cogent/draw/util.py:590: undefined name 'reshape'
./usr/lib/python2.6/dist-packages/cogent/draw/util.py:599: undefined name 'clabel'
./usr/lib/python2.6/dist-packages/cogent/draw/util.py:758: undefined name 'xlabel'
./usr/lib/python2.6/dist-packages/cogent/parse/record.py:79: redefinition of function 'parser' from line 76
./usr/lib/python2.6/dist-packages/cogent/parse/record.py:100: redefinition of function 'parser' from line 79
./usr/lib/python2.6/dist-packages/cogent/parse/record.py:307: redefinition of function 'setter' from line 304
./usr/lib/python2.6/dist./usr/lib/python2.6/dist-packages/cogent/parse/infernal.py:50: invalid syntax
^
-packages/cogent/parse/record.py:445: redefinition of function 'parser' from line 442
./usr/lib/python2.6/dist-packages/cogent/parse/record.py:473: redefinition of function 'parser' from line 466
./usr/lib/python2.6/dist-packages/cogent/parse/cigar.py:20: '_LostSpan' imported but unused
./usr/lib/python2.6/dist-packages/cogent/parse/aaindex.py:48: local variable 'result' is assigned to but never used
./usr/lib/python2.6/dist-packages/cogent/parse/cutg.py:20: 'DbRef' imported but unused
./usr/lib/python2.6/dist-packages/cogent/parse/cutg.py:158: local variable 'count' is assigned to but never used
./usr/lib/python2.6/dist-packages/cogent/parse/pdb.py:7: 'AA_NAMES' imported but unused
./usr/lib/python2.6/dist-packages/cogent/parse/pdb.py:199: local variable 'current_res_id' is assigned to but never used
./usr/lib/python2.6/dist-packages/cogent/parse/blast_xml.py:204: undefined name 'MinimalPsiBlastParser9'
./usr/lib/python2.6/dist-packages/cogent/parse/blast_xml.py:206: undefined name 'MinimalBlastParser9'
./usr/lib/python2.6/dist-packages/cogent/parse/blast_xml.py:215: local variable 'iteration' is assigned to but never used
./usr/lib/python2.6/dist-packages/cogent/parse/fasta.py:6: 'DbRef' imported but unused
./usr/lib/python2.6/dist-packages/cogent/parse/fasta.py:139: local variable 'e' is assigned to but never used
./usr/lib/python2.6/dist-packages/cogent/parse/rnaforester.py:3: 'split' imported but unused
./usr/lib/python2.6/dist-packages/cogent/parse/rnaforester.py:3: 'strip' imported but unused
./usr/lib/python2.6/dist-packages/cogent/parse/rnaforester.py:4: 'Pairs' imported but unused
./usr/lib/python2.6/dist-packages/cogent/parse/rnaforester.py:80: local variable 'result' is assigned to but never used
./usr/lib/python2.6/dist-packages/cogent/parse/rnashapes.py:15: 'split' imported but unused
./usr/lib/python2.6/dist-packages/cogent/parse/rnashapes.py:15: 'strip' imported but unused
./usr/lib/python2.6/dist-packages/cogent/parse/rnashapes.py:16: 'make_trans' imported but unused
./usr/lib/python2.6/dist-packages/cogent/parse/rnashapes.py:17: 'Pairs' imported but unused
./usr/lib/python2.6/dist-packages/cogent/parse/rnashapes.py:56: local variable 'name' is assigned to but never used
./usr/lib/python2.6/dist-packages/cogent/parse/table.py:3: 'cPickle' imported but unused
./usr/lib/python2.6/dist-packages/cogent/parse/table.py:83: local variable 'cast' is assigned to but never used
./usr/lib/python2.6/dist-packages/cogent/parse/table.py:89: local variable 'v' is assigned to but never used
./usr/lib/python2.6/dist-packages/cogent/parse/rfam.py:4: 'strip' imported but unused
./usr/lib/python2.6/dist-packages/cogent/parse/rfam.py:14: 'keep_chars' imported but unused
./usr/lib/python2.6/dist-packages/cogent/parse/rfam.py:14: 'trans_all' imported but unused
./usr/lib/python2.6/dist-packages/cogent/parse/rfam.py:39: redefinition of unused 'Sequence' from line 10
./usr/lib/python2.6/dist-packages/cogent/parse/tree.py:22: 'strip' imported but unused
./usr/lib/python2.6/dist-packages/cogent/parse/flowgram_parser.py:18: 'DelimitedRecordFinder' imported but unused
./usr/lib/python2.6/dist-packages/cogent/parse/cove.py:3: 'split' imported but unused
./usr/lib/python2.6/dist-packages/cogent/parse/cove.py:3: 'strip' imported but unused
./usr/lib/python2.6/dist-packages/cogent/parse/cove.py:5: 'wuss_to_vienna' imported but unused
./usr/lib/python2.6/dist-packages/cogent/parse/mage.py:5: 'SimplexHeader' imported but unused
./usr/lib/python2.6/dist-packages/cogent/parse/cmfinder.py:3: 'make_trans' imported but unused
./usr/lib/python2.6/dist-packages/cogent/parse/cmfinder.py:4: 'Pairs' imported but unused
./usr/lib/python2.6/dist-packages/cogent/parse/comrna.py:12: 'make_trans' imported but unused
./usr/lib/python2.6/dist-packages/cogent/parse/flowgram_collection.py:19: 'Sequence' imported but unused
./usr/lib/python2.6/dist-packages/cogent/parse/flowgram_collection.py:323: local variable 'e' is assigned to but never used
./usr/lib/python2.6/dist-packages/cogent/parse/flowgram_collection.py:374: undefined name 'DataError'
./usr/lib/py./usr/lib/python2.6/dist-packages/cogent/parse/dotur.py:51: invalid syntax
^
thon2.6/dist-packages/cogent/parse/flowgram_collection.py:403: undefined name 'flows'
./usr/lib/python2.6/dist-packages/cogent/parse/flowgram_collection.py:426: undefined name 'flows'
./usr/lib/python2.6/dist-packages/cogent/parse/flowgram_collection.py:451: undefined name 'flows'
./usr/lib/python2.6/dist-packages/cogent/parse/flowgram_collection.py:537: local variable 'result' is assigned to but never used
./usr/lib/python2.6/dist-packages/cogent/parse/bpseq.py:35: 'Vienna' imported but unused
./usr/lib/python2.6/dist-packages/cogent/parse/meme.py:8: 'DelimitedSplitter' imported but unused
./usr/lib/python2.6/dist-packages/cogent/parse/meme.py:42: local variable 'protein_order' is assigned to but never used
./usr/lib/python2.6/dist-packages/cogent/parse/meme.py:96: local variable 'data_dict' is assigned to but never used
./usr/lib/python2.6/dist-packages/cogent/parse/kegg_ko.py:5: 'listdir' imported but unused
./usr/lib/python2.6/dist-packages/cogent/parse/kegg_ko.py:5: 'path' imported but unused
./usr/lib/python2.6/dist-packages/cogent/parse/kegg_ko.py:6: 'OptionParser' imported but unused
./usr/lib/python2.6/dist-packages/cogent/parse/kegg_ko.py:7: 'datetime' imported but unused
./usr/lib/python2.6/dist-packages/cogent/parse/kegg_ko.py:8: 'tarfile' imported but unused
./usr/lib/python2.6/dist-packages/cogent/parse/kegg_ko.py:355: redefinition of unused 'argv' from line 3
./usr/lib/python2.6/dist-packages/cogent/parse/ct.py:26: 'split' imported but unused
./usr/lib/python2.6/dist-packages/cogent/parse/ct.py:49: local variable 'length' is assigned to but never used
./usr/lib/python2.6/dist-packages/cogent/parse/ct.py:67: undefined name 'pairs'
./usr/lib/python2.6/dist-packages/cogent/parse/consan.py:3: 'wuss_to_vienna' imported but unused
./usr/lib/python2.6/dist-packages/cogent/parse/consan.py:24: local variable 'seqs' is assigned to but never used
./usr/lib/python2.6/dist-packages/cogent/parse/pfold.py:3: 'split' imported but unused
./usr/lib/python2.6/dist-packages/cogent/parse/pfold.py:3: 'strip' imported but unused
./usr/lib/python2.6/dist-packages/cogent/parse/pfold.py:4: 'Pairs' imported but unused
./usr/lib/python2.6/dist-packages/cogent/parse/pfold.py:4: 'ViennaStructure' imported but unused
./usr/lib/python2.6/dist-packages/cogent/parse/gcg.py:16: local variable 'alignmentdict' is assigned to but never used
./usr/lib/python2.6/dist-packages/cogent/parse/paml_matrix.py:7: 'substitution_model' imported but unused
./usr/lib/python2.6/dist-packages/cogent/parse/mothur.py:46: local variable 'num_otus' is assigned to but never used
./usr/lib/python2.6/dist-packages/cogent/parse/rdb.py:6: 'strip' imported but unused
./usr/lib/python2.6/dist-packages/cogent/parse/rdb.py:9: 'Sequence' imported but unused
./usr/lib/python2.6/dist-packages/cogent/parse/flowgram.py:280: local variable 'extra_shift' is assigned to but never used
./usr/lib/python2.6/dist-packages/cogent/parse/pknotsrg.py:9: 'split' imported but unused
./usr/lib/python2.6/dist-packages/cogent/parse/pknotsrg.py:9: 'strip' imported but unused
./usr/lib/python2.6/dist-packages/cogent/parse/pknotsrg.py:11: 'Pairs' imported but unused
./usr/lib/python2.6/dist-packages/cogent/parse/ebi.py:7: 'pformat' imported but unused
./usr/lib/python2.6/dist-packages/cogent/parse/ebi.py:8: 'is_empty' imported but unused
./usr/lib/python2.6/dist-packages/cogent/parse/ebi.py:11: 'identity' imported but unused
./usr/lib/python2.6/dist-packages/cogent/parse/ebi.py:84: redefinition of function 'add_item' from line 78
./usr/lib/python2.6/dist-packages/cogent/parse/ebi.py:97: redefinition of function 'add_item' from line 84
./usr/lib/python2.6/dist-packages/cogent/parse/ebi.py:104: redefinition of function 'add_item' from line 97
./usr/lib/python2.6/dist-packages/cogent/parse/ebi.py:206: local variable 'e' is assigned to but never used
./usr/lib/python2.6/dist-packages/cogent/parse/ebi.py:747: local variable 'e' is assigned to but never used
./usr/lib/python2.6/dist-packages/cogent/parse/ebi.py:1376: local variable 'e' is assigned to but never used
./usr/lib/python2.6/dist-packages/cogent/parse/locuslink.py:46: 'strip' imported but unused
./usr/lib/python2.6/dist-packages/cogent/parse/locuslink.py:46: 'maketrans' imported but unused
./usr/lib/python2.6/dist-packages/cogent/parse/locuslink.py:259: 'stdout' imported but unused
./usr/lib/python2.6/dist-packages/cogent/parse/nupack.py:3: 'split' imported but unused
./usr/lib/python2.6/dist-packages/cogent/parse/nupack.py:3: 'strip' imported but unused
./usr/lib/python2.6/dist-packages/cogent/parse/macsim.py:3: 'annotation' imported but unused
./usr/lib/python2.6/dist-packages/cogent/parse/blast.py:6: 'RecordError' imported but unused
./usr/lib/python2.6/dist-packages/cogent/parse/blast.py:390: local variable 'iteration' is assigned to but never used
./usr/lib/python2.6/dist-packages/cogent/parse/unigene.py:7: 'strip' imported but unused
./usr/lib/python2.6/dist-packages/cogent/parse/unigene.py:7: 'maketrans' imported but unused
./usr/lib/python2.6/dist-packages/cogent/parse/gibbs.py:147: local variable 'motif_num' is assigned to but never used
./usr/lib/python2.6/dist-packages/cogent/parse/gibbs.py:153: local variable 'cur_key' is assigned to but never used
./usr/lib/python2.6/dist-packages/cogent/parse/clustal.py:22: 'strip' imported but unused
./usr/lib/python2.6/dist-packages/cogent/parse/column.py:16: 'split' imported but unused
./usr/lib/python2.6/dist-packages/cogent/parse/rnaalifold.py:3: 'split' imported but unused
./usr/lib/python2.6/dist-packages/cogent/parse/rnaalifold.py:3: 'strip' imported but unused
./usr/lib/python2.6/dist-packages/cogent/parse/rnaalifold.py:4: 'Pairs' imported but unused
./usr/lib/python2.6/dist-packages/cogent/parse/foldalign.py:3: 'split' imported but unused
./usr/lib/python2.6/dist-packages/cogent/parse/foldalign.py:4: 'Pairs' imported but unused
./usr/lib/python2.6/dist-packages/cogent/parse/foldalign.py:5: 'adjust_base' imported but unused
./usr/lib/python2.6/dist-packages/cogent/parse/kegg_taxonomy.py:14: 'listdir' imported but unused
./usr/lib/python2.6/dist-packages/cogent/parse/kegg_taxonomy.py:14: 'path' imported but unused
./usr/lib/python2.6/dist-packages/cogent/parse/kegg_taxonomy.py:15: 'OptionParser' imported but unused
./usr/lib/python2.6/dist-packages/cogent/parse/kegg_taxonomy.py:16: 'datetime' imported but unused
./usr/lib/python2.6/dist-packages/cogent/parse/kegg_taxonomy.py:87: redefinition of unused 'argv' from line 12
./usr/lib/python2.6/dist-packages/cogent/parse/record_finder.py:16: 'FieldError' imported but unused
./usr/lib/python2.6/dist-packages/cogent/parse/sprinzl.py:5: 'maketrans' imported but unused
./usr/lib/python2.6/dist-packages/cogent/cluster/nmds.py:9: 'size' imported but unused
./usr/lib/python2.6/dist-packages/cogent/cluster/nmds.py:9: 'trace' imported but unused
./usr/lib/python2.6/dist-packages/cogent/cluster/nmds.py:9: 'transpose' imported but unused
./usr/lib/python2.6/dist-packages/cogent/cluster/nmds.py:9: 'multiply' imported but unused
./usr/lib/python2.6/dist-packages/cogent/cluster/nmds.py:259: redefinition of unused 'size' from line 9
./usr/lib/python2.6/dist-packages/cogent/cluster/nmds.py:265: redefinition of unused 'size' from line 9
./usr/lib/python2.6/dist-packages/cogent/cluster/UPGMA.py:13: 'sum' imported but unused
./usr/lib/python2.6/dist-packages/cogent/cluster/UPGMA.py:13: 'ma' imported but unused
./usr/lib/python2.6/dist-packages/cogent/cluster/UPGMA.py:155: local variable 'row_order' is assigned to but never used
./usr/lib/python2.6/dist-packages/cogent/cluster/procrustes.py:9: 'divide' imported but unused
./usr/lib/python2.6/dist-packages/cogent/cluster/procrustes.py:9: 'subtract' imported but unused
./usr/lib/python2.6/dist-packages/cogent/cluster/approximate_mds.py:90: 'floor' imported but unused
./usr/lib/python2.6/dist-packages/cogent/cluster/approximate_mds.py:92: 'argwhere' imported but unused
./usr/lib/python2.6/dist-packages/cogent/struct/pairs_util.py:16: 'searchsorted' imported but unused
./usr/lib/python2.6/dist-packages/cogent/struct/pairs_util.py:452: local variable 'pred_dict' is assigned to but never used
./usr/lib/python2.6/dist-packages/cogent/struct/dihedral.py:35: 'cos' imported but unused
./usr/lib/python2.6/dist-packages/cogent/struct/rna2d.py:443: local variable 'num_bases' is assigned to but never used
./usr/lib/python2.6/dist-packages/cogent/struct/asa.py:73: undefined name 'lattice_structures'
./usr/lib/python2.6/dist-packages/cogent/struct/asa.py:200: local variable 'models' is assigned to but never used
./usr/lib/python2.6/dist-packages/cogent/struct/annotation.py:3: 'HIERARCHY' imported but unused
./usr/lib/python2.6/dist-packages/cogent/struct/manipulation.py:6: 'HIERARCHY' imported but unused
./usr/lib/python2.6/dist-packages/cogent/motif/k_word.py:8: 'combinations' imported but unused
./usr/lib/python2.6/dist-packages/cogent/evolve/discrete_markov.py:4: 'CalcDefn' imported but unused
./usr/lib/python2.6/dist-packages/cogent/evolve/discrete_markov.py:4: 'ConstDefn' imported but unused
./usr/lib/python2.6/dist-packages/cogent/evolve/discrete_markov.py:4: 'NonParamDefn' imported but unused
./usr/lib/python2.6/dist-packages/cogent/evolve/models.py:77: local variable 'preds' is assigned to but never used
./usr/lib/python2.6/dist-packages/cogent/evolve/motif_prob_model.py:217: local variable 'positions' is assigned to but never used
./usr/lib/python2.6/dist-packages/cogent/evolve/bootstrap.py:26: 'optimisers' imported but unused
./usr/lib/python2.6/dist-packages/cogent/evolve/substitution_model.py:39: 'RateDefn' imported but unused
./usr/lib/python2.6/dist-packages/cogent/evolve/substitution_model.py:636: local variable 'const_param' is assigned to but never used
./usr/lib/python2.6/dist-packages/cogent/evolve/substitution_model.py:668: local variable 'const_param' is assigned to but never used
./usr/lib/python2.6/dist-packages/cogent/evolve/substitution_calculation.py:8: 'CallDefn' imported but unused
./usr/lib/python2.6/dist-packages/cogent/evolve/substitution_calculation.py:8: 'ConstDefn' imported but unused
./usr/lib/python2.6/dist-packages/cogent/evolve/substitution_calculation.py:8: 'PartitionDefn' imported but unused
./usr/lib/python2.6/dist-packages/cogent/evolve/substitution_calculation.py:8: 'NonParamDefn' imported but unused
./usr/lib/python2.6/dist-packages/cogent/evolve/substitution_calculation.py:8: 'GammaDefn' imported but unused
./usr/lib/python2.6/dist-packages/cogent/evolve/substitution_calculation.py:8: 'CalcDefn' imported but unused
./usr/lib/python2.6/dist-packages/cogent/evolve/substitution_calculation.py:8: 'ProductDefn' imported but unused
./usr/lib/python2.6/dist-packages/cogent/evolve/substitution_calculation.py:8: 'WeightedPartitionDefn' imported but unused
./usr/lib/python2.6/dist-packages/cogent/evolve/substitution_calculation.py:8: 'SelectForDimension' imported but unused
./usr/lib/python2.6/dist-packages/cogent/evolve/substitution_calculation.py:8: 'MonotonicDefn' imported but unused
./usr/lib/python2.6/dist-packages/cogent/evolve/substitution_calculation.py:12: 'chooseFastExponentiators' imported but unused
./usr/lib/python2.6/dist-packages/cogent/evolve/substitution_calculation.py:12: 'FastExponentiator' imported but unused
./usr/lib/python2.6/dist-packages/cogent/evolve/likelihood_calculation.py:15: '_FuncDefn' imported but unused
./usr/lib/python2.6/dist-packages/cogent/evolve/coevolution.py:56: 'splitext' imported but unused
./usr/lib/python2.6/dist-packages/cogent/evolve/coevolution.py:58: 'sqrt' imported but unused
./usr/lib/python2.6/dist-packages/cogent/evolve/coevolution.py:58: 'mean' imported but unused
./usr/lib/python2.6/dist-packages/cogent/evolve/coevolution.py:58: 'abs' imported but unused
./usr/lib/python2.6/dist-packages/cogent/evolve/coevolution.py:58: 'transpose' imported but unused
./usr/lib/python2.6/dist-packages/cogent/evolve/coevolution.py:58: 'put' imported but unused
./usr/lib/python2.6/dist-packages/cogent/evolve/coevolution.py:58: 'float64' imported but unused
./usr/lib/python2.6/dist-packages/cogent/evolve/coevolution.py:58: 'tril' imported but unused
./usr/lib/python2.6/dist-packages/cogent/evolve/coevolution.py:58: 'reshape' imported but unused
./usr/lib/python2.6/dist-packages/cogent/ev./usr/lib/python2.6/dist-packages/cogent/phylo/least_squares.py:82: invalid syntax
^
olve/coevolution.py:58: 'take' imported but unused
./usr/lib/python2.6/dist-packages/cogent/evolve/coevolution.py:58: 'exp' imported but unused
./usr/lib/python2.6/dist-packages/cogent/evolve/coevolution.py:66: 'Profile' imported but unused
./usr/lib/python2.6/dist-packages/cogent/evolve/coevolution.py:67: 'Alphabet' imported but unused
./usr/lib/python2.6/dist-packages/cogent/evolve/coevolution.py:73: 'TreeError' imported but unused
./usr/lib/python2.6/dist-packages/cogent/evolve/coevolution.py:74: 'seqs_from_fasta' imported but unused
./usr/lib/python2.6/dist-packages/cogent/evolve/coevolution.py:509: redefinition of unused 'e' from line 58
./usr/lib/python2.6/dist-packages/cogent/evolve/coevolution.py:509: local variable 'e' is assigned to but never used
./usr/lib/python2.6/dist-packages/cogent/evolve/coevolution.py:643: local variable 'num_positions' is assigned to but never used
./usr/lib/python2.6/dist-packages/cogent/evolve/coevolution.py:644: local variable 'num_seqs' is assigned to but never used
./usr/lib/python2.6/dist-packages/cogent/evolve/coevolution.py:758: local variable 'num_seqs' is assigned to but never used
./usr/lib/python2.6/dist-packages/cogent/evolve/coevolution.py:824: local variable 'num_seqs' is assigned to but never used
./usr/lib/python2.6/dist-packages/cogent/evolve/coevolution.py:1448: local variable 'e' is assigned to but never used
./usr/lib/python2.6/dist-packages/cogent/evolve/coevolution.py:2095: redefinition of function 'is_not_null_value' from line 2092
./usr/lib/python2.6/dist-packages/cogent/evolve/coevolution.py:2196: local variable 'aln' is assigned to but never used
./usr/lib/python2.6/dist-packages/cogent/evolve/coevolution.py:2209: local variable 'tree' is assigned to but never used
./usr/lib/python2.6/dist-packages/cogent/evolve/coevolution.py:2317: local variable 'extension' is assigned to but never used
./usr/lib/python2.6/dist-packages/cogent/phylo/distance.py:4: 'warning' imported but unused
./usr/lib/python2.6/dist-packages/cogent/phylo/distance.py:6: 'LoadSeqs' imported but unused
./usr/lib/python2.6/dist-packages/cogent/phylo/compatibility.py:466: 'sys' imported but unused
./usr/lib/python2.6/dist-packages/cogent/phylo/maximum_likelihood.py:4: 'exp' imported but unused
./usr/lib/python2.6/dist-packages/cogent/phylo/maximum_likelihood.py:6: 'LoadTrees' imported but unused
./usr/lib/python2.6/dist-packages/cogent/phylo/tree_collection.py:65: undefined name 'exp'
./usr/lib/python2.6/dist-packages/cogent/db/ncbi.py:8: 'urlopen' imported but unused
./usr/lib/python2.6/dist-packages/cogent/db/ncbi.py:8: 'urlretrieve' imported but unused
./usr/lib/python2.6/dist-packages/cogent/db/ncbi.py:13: 'never_ignore' imported but unused
./usr/lib/python2.6/dist-packages/cogent/db/ensembl/compara.py:7: 'get_latest_release' imported but unused
./usr/lib/python2.6/dist-packages/cogent/db/ensembl/compara.py:9: 'Coordinate' imported but unused
./usr/lib/python2.6/dist-packages/cogent/db/ensembl/region.py:10: 'location_query' imported but unused
./usr/lib/python2.6/dist-packages/cogent/db/ensembl/__init__.py:5: 'NoItemError' imported but unused
./usr/lib/python2.6/dist-packages/cogent/db/ensembl/host.py:5: 'Table' imported but unused
./usr/lib/python2.6/dist-packages/cogent/db/ensembl/host.py:8: 'asserted_one' imported but unused
./usr/lib/python2.6/dist-packages/cogent/db/ensembl/related_region.py:1: 'pprint' imported but unused
./usr/lib/python2.6/dist-packages/cogent/db/ensembl/related_region.py:8: 'NoItemError' imported but unused
./usr/lib/python2.6/dist-packages/cogent/db/ensembl/related_region.py:9: 'location_query' imported but unused
./usr/lib/python2.6/dist-packages/cogent/db/ensembl/related_region.py:10: 'Species' imported but unused
./usr/lib/python2.6/dist-packages/cogent/db/ensembl/genome.py:319: undefined name 'coord'
./usr/lib/python2.6/dist-packages/cogent/db/ensembl/genome.py:319: local variable 'coord' is assigned to but never used
./usr/lib/python2.6/dist-packages/cogent/db/ensembl/genome.py:354: local variable 'feature_coord_levels' is assigned to but never used
./usr/lib/python2.6/dist-packages/cogent/db/ensembl/util.py:1: 're' imported but unused
./usr/lib/python2.6/dist-packages/cogent/db/ensembl/util.py:2: 'create_engine' imported but unused
./usr/lib/python2.6/dist-packages/cogent/db/ensembl/util.py:2: 'Table' imported but unused
./usr/lib/python2.6/dist-packages/cogent/db/ensembl/util.py:2: 'MetaData' imported but unused
./usr/lib/python2.6/dist-packages/cogent/db/ensembl/sequence.py:4: 'Map' imported but unused
./usr/lib/python2.6/dist-packages/cogent/db/ensembl/sequence.py:6: 'Species' imported but unused
./usr/lib/python2.6/dist-packages/cogent/db/ensembl/assembly.py:3: 'Map' imported but unused
./usr/lib/python2.6/dist-packages/cogent/db/ensembl/assembly.py:6: 'DbConnection' imported but unused
./usr/lib/python2.6/dist-packages/cogent/core/entity.py:22: 'gt' imported but unused
./usr/lib/python2.6/dist-packages/cogent/core/entity.py:22: 'ne' imported but unused
./usr/lib/python2.6/dist-packages/cogent/core/entity.py:22: 'ge' imported but unused
./usr/lib/python2.6/dist-packages/cogent/core/entity.py:22: 'le' imported but unused
./usr/lib/python2.6/dist-packages/cogent/core/entity.py:22: 'lt' imported but unused
./usr/lib/python2.6/dist-packages/cogent/core/entity.py:22: 'is_' imported but unused
./usr/lib/python2.6/dist-packages/cogent/core/entity.py:22: 'or_' imported but unused
./usr/lib/python2.6/dist-packages/cogent/core/entity.py:22: 'is_not' imported but unused
./usr/lib/python2.6/dist-packages/cogent/core/entity.py:22: 'and_' imported but unused
./usr/lib/python2.6/dist-packages/cogent/core/tree.py:34: 'InverseDict' imported but unused
./usr/lib/python2.6/dist-packages/cogent/core/usage.py:14: 'mean' imported but unused
./usr/lib/python2.6/dist-packages/cogent/core/alignment.py:35: 'logical_or' imported but unused
./usr/lib/python2.6/dist-packages/cogent/core/alignment.py:35: 'zeros' imported but unused
./usr/lib/python2.6/dist-packages/cogent/core/alignment.py:350: local variable 'result' is assigned to but never used
./usr/lib/python2.6/dist-packages/cogent/core/alignment.py:520: local variable 'e' is assigned to but never used
./usr/lib/python2.6/dist-packages/cogent/core/alignment.py:654: local variable 'item_lookup' is assigned to but never used
./usr/lib/python2.6/dist-packages/cogent/core/alignment.py:721: redefinition of function 'f' from line 717
./usr/lib/python2.6/dist-packages/cogent/core/alignment.py:1246: local variable 'max_run' is assigned to but never used
./usr/lib/python2.6/dist-packages/cogent/core/alignment.py:2020: local variable 'max_label_length' is assigned to but never used
./usr/lib/python2.6/dist-packages/cogent/core/alignment.py:2176: undefined name 'CodonSequenceGap'
./usr/lib/python2.6/dist-packages/cogent/core/alignment.py:2180: undefined name 'random'
./usr/lib/python2.6/dist-packages/cogent/core/moltype.py:27: 'if_' imported but unused
./usr/lib/python2.6/dist-packages/cogent/core/moltype.py:30: 'ModelNucleicAcidSequence' imported but unused
./usr/lib/python2.6/dist-packages/cogent/core/moltype.py:46: 'uint16' imported but unused
./usr/lib/python2.6/dist-packages/cogent/core/moltype.py:46: 'arange' imported but unused
./usr/lib/python2.6/dist-packages/cogent/core/moltype.py:46: 'asarray' imported but unused
./usr/lib/python2.6/dist-packages/cogent/core/moltype.py:46: 'uint32' imported but unused
./usr/lib/python2.6/dist-packages/cogent/core/moltype.py:46: 'transpose' imported but unused
./usr/lib/python2.6/dist-packages/cogent/core/moltype.py:46: 'remainder' imported but unused
./usr/lib/python2.6/dist-packages/cogent/core/moltype.py:46: 'newaxis' imported but unused
./usr/lib/python2.6/dist-packages/cogent/core/moltype.py:46: 'array' imported but unused
./usr/lib/python2.6/dist-packages/cogent/core/moltype.py:46: 'zeros' imported but unused
./usr/lib/python2.6/dist-packages/cogent/core/moltype.py:46: 'uint8' imported but unused
./usr/lib/python2.6/dist-packages/cogent/core/moltype.py:46: 'ravel' imported but unused
./usr/lib/python2.6/dist-packages/cogent/core/moltype.py:46: 'take' imported but unused
./usr/lib/python2.6/dist-packages/./usr/lib/python2.6/dist-packages/cogent/format/rna_struct.py:449: invalid syntax
^
./usr/lib/python2.6/dist-packages/cogent/format/stockholm.py:93: unexpected indent
^
./usr/lib/python2.6/dist-packages/cogent/format/clustal.py:69: unexpected indent
^
cogent/core/moltype.py:46: 'fromstring' imported but unused
./usr/lib/python2.6/dist-packages/cogent/core/moltype.py:46: 'sum' imported but unused
./usr/lib/python2.6/dist-packages/cogent/core/moltype.py:52: 'translate' imported but unused
./usr/lib/python2.6/dist-packages/cogent/core/moltype.py:637: local variable 'curr' is assigned to but never used
./usr/lib/python2.6/dist-packages/cogent/core/moltype.py:724: undefined name 'first_index_in_set'
./usr/lib/python2.6/dist-packages/cogent/core/moltype.py:733: undefined name 'first_index_in_set'
./usr/lib/python2.6/dist-packages/cogent/core/alphabet.py:22: 're' imported but unused
./usr/lib/python2.6/dist-packages/cogent/core/alphabet.py:23: 'string' imported but unused
./usr/lib/python2.6/dist-packages/cogent/core/alphabet.py:24: redefinition of unused 'take' from line 24
./usr/lib/python2.6/dist-packages/cogent/core/alphabet.py:24: 'remainder' imported but unused
./usr/lib/python2.6/dist-packages/cogent/core/alphabet.py:546: local variable 'result' is assigned to but never used
./usr/lib/python2.6/dist-packages/cogent/core/profile.py:11: 'concatenate' imported but unused
./usr/lib/python2.6/dist-packages/cogent/core/profile.py:11: 'log' imported but unused
./usr/lib/python2.6/dist-packages/cogent/core/profile.py:11: 'asarray' imported but unused
./usr/lib/python2.6/dist-packages/cogent/core/profile.py:11: 'reshape' imported but unused
./usr/lib/python2.6/dist-packages/cogent/core/profile.py:11: 'alltrue' imported but unused
./usr/lib/python2.6/dist-packages/cogent/core/profile.py:11: 'ravel' imported but unused
./usr/lib/python2.6/dist-packages/cogent/core/profile.py:11: 'sort' imported but unused
./usr/lib/python2.6/dist-packages/cogent/core/profile.py:11: 'uint8' imported but unused
./usr/lib/python2.6/dist-packages/cogent/core/profile.py:11: 'put' imported but unused
./usr/lib/python2.6/dist-packages/cogent/core/profile.py:11: 'isfinite' imported but unused
./usr/lib/python2.6/dist-packages/cogent/core/profile.py:89: local variable 'sums' is assigned to but never used
./usr/lib/python2.6/dist-packages/cogent/core/profile.py:92: local variable 'tfs' is assigned to but never used
./usr/lib/python2.6/dist-packages/cogent/core/profile.py:207: local variable 'max_col_idx' is assigned to but never used
./usr/lib/python2.6/dist-packages/cogent/core/profile.py:397: local variable 'sl' is assigned to but never used
./usr/lib/python2.6/dist-packages/cogent/core/sequence.py:15: 'Feature' imported but unused
./usr/lib/python2.6/dist-packages/cogent/core/sequence.py:16: 'keep_chars' imported but unused
./usr/lib/python2.6/dist-packages/cogent/core/sequence.py:16: 'per_longest' imported but unused
./usr/lib/python2.6/dist-packages/cogent/core/sequence.py:1008: undefined name 'm'
./usr/lib/python2.6/dist-packages/cogent/core/bitvector.py:254: local variable 'bits' is assigned to but never used
./usr/lib/python2.6/dist-packages/cogent/core/bitvector.py:642: local variable 'TypeError' is assigned to but never used
./usr/lib/python2.6/dist-packages/cogent/format/table.py:91: local variable 'th' is assigned to but never used
./usr/lib/python2.6/dist-packages/cogent/format/table.py:96: local variable 'td' is assigned to but never used
./usr/lib/python2.6/dist-packages/cogent/format/table.py:445: local variable 'num_row' is assigned to but never used
./usr/lib/python2.6/dist-packages/cogent/format/mage.py:19: 'fabs' imported but unused
./usr/lib/python2.6/dist-packages/cogent/format/mage.py:22: 'extract_delimited' imported but unused
./usr/lib/python2.6/dist-packages/cogent/format/alignment.py:33: undefined name 'FileFormatError'
./usr/lib/python2.6/dist-packages/cogent/format/alignment.py:141: undefined name 'warnings'
./usr/lib/python2.6/dist-packages/cogent/format/pdb_color.py:54: undefined name 'chain'
./usr/lib/python2.6/dist-packages/cogent/format/pdb_color.py:195: undefined name 'cmd'
./usr/lib/python2.6/dist-packages/cogent/format/pdb_color.py:203: undefined name 'cmd'
./usr/lib/python2.6/dist-packages/cogent/format/pdb_color.py:210: undefined name 'cmd'
./usr/lib/python2.6/dist-p./usr/lib/python2.6/dist-packages/cogent/align/partial_order_graph.py:221: invalid syntax
^
./usr/lib/python2.7/dist-packages/cogent/maths/period.py:268: invalid syntax
^
ackages/cogent/format/motif.py:13: 'DNA' imported but unused
./usr/lib/python2.6/dist-packages/cogent/format/motif.py:14: 'Alignment' imported but unused
./usr/lib/python2.6/dist-packages/cogent/format/motif.py:944: local variable 'e' is assigned to but never used
./usr/lib/python2.6/dist-packages/cogent/format/motif.py:1592: local variable 'mod_id_map' is assigned to but never used
./usr/lib/python2.6/dist-packages/cogent/format/motif.py:1722: local variable 'mod_id_map' is assigned to but never used
./usr/lib/python2.6/dist-packages/cogent/align/dp_calculation.py:4: 'PositiveParamDefn' imported but unused
./usr/lib/python2.6/dist-packages/cogent/align/dp_calculation.py:8: 'numpy' imported but unused
./usr/lib/python2.6/dist-packages/cogent/align/align.py:8: 'sys' imported but unused
./usr/lib/python2.6/dist-packages/cogent/align/pairwise.py:202: undefined name 'seq'
./usr/lib/python2.6/dist-packages/cogent/align/pairwise.py:601: local variable 'rr' is assigned to but never used
./usr/lib/python2.6/dist-packages/cogent/align/indel_positions.py:14: local variable 'full_aligned_positions' is assigned to but never used
./usr/lib/python2.6/dist-packages/cogent/align/indel_positions.py:98: local variable 'l' is assigned to but never used
./usr/lib/python2.6/dist-packages/cogent/align/indel_positions.py:230: undefined name 'length'
./usr/lib/python2.6/dist-packages/cogent/align/__init__.py:3: 'make_dna_scoring_dict' imported but unused
./usr/lib/python2.6/dist-packages/cogent/align/__init__.py:3: '_align_pairwise' imported but unused
./usr/lib/python2.6/dist-packages/cogent/align/__init__.py:3: 'local_pairwise' imported but unused
./usr/lib/python2.6/dist-packages/cogent/align/__init__.py:3: 'global_pairwise' imported but unused
./usr/lib/python2.6/dist-packages/cogent/align/__init__.py:3: 'classic_align_pairwise' imported but unused
./usr/lib/python2.6/dist-packages/cogent/align/weights/methods.py:5: 'choice' imported but unused
./usr/lib/python2.6/dist-packages/cogent/align/weights/methods.py:12: 'DndParser' imported but unused
./usr/lib/python2.6/dist-packages/cogent/align/weights/methods.py:14: 'RNA_ORDER' imported but unused
./usr/lib/python2.6/dist-packages/cogent/align/weights/methods.py:432: redefinition of unused 'Alignment' from line 11
./usr/lib/python2.6/dist-packages/cogent/align/weights/util.py:7: 'asarray' imported but unused
./usr/lib/python2.6/dist-packages/cogent/align/weights/util.py:7: 'sqrt' imported but unused
./usr/lib/python2.6/dist-packages/cogent/align/weights/util.py:7: 'take' imported but unused
./usr/lib/python2.6/dist-packages/cogent/align/weights/util.py:13: 'Alignment' imported but unused
./usr/lib/python2.7/dist-packages/cogent/__init__.py:4: 'os' imported but unused
./usr/lib/python2.7/dist-packages/cogent/__init__.py:47: 'STANDARD_CODON' imported but unused
./usr/lib/python2.7/dist-packages/cogent/__init__.py:47: 'PROTEIN' imported but unused
./usr/lib/python2.7/dist-packages/cogent/__init__.py:47: 'DNA' imported but unused
./usr/lib/python2.7/dist-packages/cogent/__init__.py:47: 'CodonAlphabet' imported but unused
./usr/lib/python2.7/dist-packages/cogent/__init__.py:47: 'RNA' imported but unused
./usr/lib/python2.7/dist-packages/cogent/maths/matrix_logarithm.py:7: 'transpose' imported but unused
./usr/lib/python2.7/dist-packages/cogent/maths/matrix_exponentiation.py:17: 'LinAlgError' imported but unused
./usr/lib/python2.7/dist-packages/cogent/maths/matrix_exponentiation.py:38: redefinition of function 'inv' from line 34
./usr/lib/python2.7/dist-packages/cogent/maths/scipy_optimisers.py:5: 'fmin_bfgs' imported but unused
./usr/lib/python2.7/dist-packages/cogent/maths/scipy_optimisers.py:81: local variable 'template' is assigned to but never used
./usr/lib/python2.7/dist-packages/cogent/maths/optimiser.py:66: local variable 'detail' is assigned to but never used
./usr/lib/python2.7/dist-packages/cogent/maths/geometry.py:4: redefinition of unused 'sqrt' from line 4
./usr/lib/python2.7/dist-packages/cogent/maths/distance_transform.py:56: 'logical_or' imported but unused
./usr/lib/python2.7/dist-packages/cogent/maths/distance_transform.py:56: 'logical_xor' imported but unused
./usr/lib/python2.7/dist-packages/cogent/maths/distance_transform.py:56: 'geterr' imported but unused
./usr/lib/python2.7/dist-packages/cogent/maths/distance_transform.py:56: 'logical_not' imported but unused
./usr/lib/python2.7/dist-packages/cogent/maths/distance_transform.py:256: local variable 'dist' is assigned to but never used
./usr/lib/python2.7/dist-packages/cogent/maths/distance_transform.py:465: local variable 'rowdiff' is assigned to but never used
./usr/lib/python2.7/dist-packages/cogent/maths/distance_transform.py:723: local variable 'rowstds' is assigned to but never used
./usr/lib/python2.7/dist-packages/cogent/maths/distance_transform.py:726: local variable 'n' is assigned to but never used
./usr/lib/python2.7/dist-packages/cogent/maths/optimisers.py:9: 'DownhillSimplex' imported but unused
./usr/lib/python2.7/dist-packages/cogent/maths/optimisers.py:51: undefined name 'wanings'
./usr/lib/python2.7/dist-packages/cogent/maths/svd.py:6: 'expm' imported but unused
./usr/lib/python2.7/dist-packages/cogent/maths/svd.py:7: 'logm' imported but unused
./usr/lib/python2.7/dist-packages/cogent/maths/svd.py:9: 'reshape' imported but unused
./usr/lib/python2.7/dist-packages/cogent/maths/svd.py:9: 'NewAxis' imported but unused
./usr/lib/python2.7/dist-packages/cogent/maths/svd.py:9: 'product' imported but unused
./usr/lib/python2.7/dist-packages/cogent/maths/svd.py:11: 'random' imported but unused
./usr/lib/python2.7/dist-packages/cogent/maths/scipy_optimize.py:34: redefinition of unused 'linesearch' from line 32
./usr/lib/python2.7/dist-packages/cogent/maths/scipy_optimize.py:320: local variable 'D' is assigned to but never used
./usr/lib/python2.7/dist-packages/cogent/maths/scipy_optimize.py:487: redefinition of function 'phiprime' from line 477
./usr/lib/python2.7/dist-packages/cogent/maths/scipy_optimize.py:892: local variable 'N' is assigned to but never used
./usr/lib/python2.7/dist-packages/cogent/maths/scipy_optimize.py:899: local variable 'sk' is assigned to but never used
./usr/lib/python2.7/dist-packages/cogent/maths/scipy_optimize.py:1393: local variable 'xmin' is assigned to but never used
./usr/lib/python2.7/dist-packages/cogent/maths/scipy_optimize.py:1393: local variable 'fval' is assigned to but never used
./usr/lib/python2.7/dist-packages/cogent/maths/stats/test.py:14: 'clip' imported but unused
./usr/lib/python2.7/dist-packages/cogent/maths/stats/test.py:14: 'reshape' imported but unused
./usr/lib/python2.7/dist-packages/cogent/maths/stats/test.py:14: 'nan' imported but unused
./usr/lib/python2.7/dist-packages/cogent/maths/stats/test.py:20: 'add' imported but unused
./usr/lib/python2.7/dist-packages/cogent/maths/stats/test.py:21: 'choice' imported but unused
./usr/lib/python2.7/dist-packages/cogent/maths/stats/test.py:500: local variable 'e' is assigned to but never used
./usr/lib/python2.7/dist-packages/cogent/maths/stats/test.py:604: local variable 'Syy' is assigned to but never used
./usr/lib/python2.7/dist-packages/cogent/maths/stats/test.py:775: local variable 'e' is assigned to but never used
./usr/lib/python2.7/dist-packages/cogent/maths/stats/test.py:1007: local variable 'total_obs' is assigned to but never used
./usr/lib/python2.7/dist-packages/cogent/maths/stats/test.py:1008: local variable 'num_x' is assigned to but never used
./usr/lib/python2.7/dist-packages/cogent/maths/stats/test.py:1042: local variable 'sample' is assigned to but never used
./usr/lib/python2.7/dist-packages/cogent/maths/stats/test.py:1048: local variable 'ties' is assigned to but never used
./usr/lib/python2.7/dist-packages/cogent/maths/stats/test.py:1089: local variable 'total_obs' is assigned to but never used
./usr/lib/python2.7/dist-packages/cogent/maths/stats/test.py:1090: local variable 'num_x' is assigned to but never used
./usr/lib/python2.7/dist-packages/cogent/maths/stats/period.py:2: 'shuffle' imported but unused
./usr/lib/python2.7/dist-packages/cogent/maths/stats/period.py:2: 'random' imported but unused
./usr/lib/python2.7/dist-packages/cogent/maths/stats/period.py:9: redefinition of unused 'factorial' from line 6
./usr/lib/python2.7/dist-packages/cogent/maths/stats/period.py:87: redefinition of unused 'seq_to_symbols' from line 84
./usr/lib/python2.7/dist-packages/cogent/maths/stats/special.py:485: local variable 'sgngam' is assigned to but never used
./usr/lib/python2.7/dist-packages/cogent/maths/stats/special.py:1087: local variable 'i' is assigned to but never used
./usr/lib/python2.7/dist-packages/cogent/maths/stats/__init__.py:13: 'chisqprob' imported but unused
./usr/lib/python2.7/dist-packages/cogent/maths/stats/distribution.py:6: 'ndtri' imported but unused
./usr/lib/python2.7/dist-packages/cogent/maths/stats/util.py:111: 'e' imported but unused
./usr/lib/python2.7/dist-packages/cogent/maths/stats/util.py:524: redefinition of function '_get_mode' from line 447
./usr/lib/python2.7/dist-packages/cogent/maths/stats/util.py:676: local variable 'r' is assigned to but never used
./usr/lib/python2.7/dist-packages/cogent/maths/stats/util.py:723: local variable 'v' is assigned to but never used
./usr/lib/python2.7/dist-packages/cogent/maths/stats/util.py:746: local variable 'i' is assigned to but never used
./usr/lib/python2.7/dist-packages/cogent/maths/stats/alpha_diversity.py:152: local variable 'alpha' is assigned to but never used
./usr/lib/python2.7/dist-packages/cogent/maths/stats/cai/get_by_cai.py:3: 'CutgParser' imported but unused
./usr/lib/python2.7/dist-packages/cogent/maths/stats/cai/get_by_cai.py:5: 'CodonUsage' imported but unused
./usr/lib/python2.7/dist-packages/cogent/maths/stats/cai/util.py:76: local variable 'result' is assigned to but never used
./usr/lib/python2.7/dist-packages/cogent/maths/stats/cai/util.py:104: local variable 'k' is assigned to but never used
./usr/lib/python2.7/dist-packages/cogent/maths/stats/cai/util.py:105: local variable 'v' is assigned to but never used
./usr/lib/python2.7/dist-packages/cogent/maths/stats/cai/util.py:106: local variable 'n' is assigned to but never used
./usr/lib/python2.7/dist-packages/cogent/maths/stats/cai/util.py:257: undefined name 'arithmetic_meani'
./usr/lib/python2.7/dist-packages/cogent/maths/stats/cai/adaptor.py:5: 'Info' imported but unused
./usr/lib/python2.7/dist-packages/cogent/maths/stats/cai/adaptor.py:8: 'GeneticCode' imported but unused
./usr/lib/python2.7/dist-packages/cogent/maths/stats/cai/adaptor.py:9: 'sort' imported but unused
./usr/lib/python2.7/dist-packages/cogent/maths/stats/cai/adaptor.py:9: 'concatenate' imported but unused
./usr/lib/python2.7/dist-packages/cogent/maths/stats/cai/adaptor.py:9: 'sqrt' imported but unused
./usr/lib/python2.7/dist-packages/cogent/maths/stats/cai/adaptor.py:9: 'zeros' imported but unused
./usr/lib/python2.7/dist-packages/cogent/maths/stats/cai/adaptor.py:11: 'argv' imported but unused
./usr/lib/python2.7/dist-packages/cogent/maths/stats/cai/adaptor.py:80: undefined name 'UnsafeCodonsFromString'
./usr/lib/python2.7/dist-packages/cogent/maths/unifrac/fast_tree.py:582: local variable 'row_result' is assigned to but never used
./usr/lib/python2.7/dist-packages/cogent/maths/unifrac/fast_unifrac.py:7: 'from cogent.maths.unifrac.fast_tree import *' used; unable to detect undefined names
./usr/lib/python2.7/dist-packages/cogent/maths/unifrac/fast_unifrac.py:11: 'from cogent.cluster.metric_scaling import *' used; unable to detect undefined names
./usr/lib/python2.7/dist-packages/cogent/maths/unifrac/fast_unifrac.py:527: local variable 'result' is assigned to but never used
./usr/lib/python2.7/dist-packages/cogent/maths/unifrac/fast_unifrac.py:958: redefinition of unused 'StringIO' from line 15
./usr/lib/python2.7/dist-packages/cogent/maths/matrix/distance.py:91: redefinition of function 'Pow' from line 85
./usr/lib/python2.7/dist-packages/cogent/app/knetfold.py:3: 'CommandLineAppResult' imported but unused
./usr/lib/python2.7/dist-packages/cogent/app/knetfold.py:5: '_find_synonym' imported but unused
./usr/lib/python2.7/dist-packages/cogent/app/knetfold.py:5: 'Parameters' imported but unused
./usr/lib/python2.7/dist-packages/cogent/app/knetfold.py:5: 'MixedParameter' imported but unused
./usr/lib/python2.7/dist-packages/cogent/app/knetfold.py:5: 'FlagParameter' imported but unused
./usr/lib/python2.7/dist-packages/cogent/app/knetfold.py:5: 'Parameter' imported but unused
./usr/lib/python2.7/dist-packages/cogent/app/ilm.py:3: 'CommandLineAppResult' imported but unused
./usr/lib/python2.7/dist-packages/cogent/app/ilm.py:3: 'ResultPath' imported but unused
./usr/lib/python2.7/dist-packages/cogent/app/ilm.py:5: 'Parameters' imported but unused
./usr/lib/python2.7/dist-packages/cogent/app/ilm.py:5: 'Parameter' imported but unused
./usr/lib/python2.7/dist-packages/cogent/app/raxml.py:12: 'choice' imported but unused
./usr/lib/python2.7/dist-packages/cogent/app/raxml.py:300: local variable 'e' is assigned to but never used
./usr/lib/python2.7/dist-packages/cogent/app/uclust.py:22: 'makedirs' imported but unused
./usr/lib/python2.7/dist-packages/cogent/app/uclust.py:22: 'remove' imported but unused
./usr/lib/python2.7/dist-packages/cogent/app/uclust.py:23: 'splitext' imported but unused
./usr/lib/python2.7/dist-packages/cogent/app/uclust.py:23: 'isfile' imported but unused
./usr/lib/python2.7/dist-packages/cogent/app/uclust.py:23: 'isdir' imported but unused
./usr/lib/python2.7/dist-packages/cogent/app/uclust.py:23: 'abspath' imported but unused
./usr/lib/python2.7/dist-packages/cogent/app/uclust.py:483: local variable 'uc_output_filepath' is assigned to but never used
./usr/lib/python2.7/dist-packages/cogent/app/uclust.py:484: local variable 'cd_hit_filepath' is assigned to but never used
./usr/lib/python2.7/dist-packages/cogent/app/uclust.py:496: local variable 'uc_filepath' is assigned to but never used
./usr/lib/python2.7/dist-packages/cogent/app/uclust.py:497: local variable 'clstr_filepath' is assigned to but never used
./usr/lib/python2.7/dist-packages/cogent/app/infernal.py:8: 'MinimalFastaParser' imported but unused
./usr/lib/python2.7/dist-packages/cogent/app/infernal.py:15: 'ViennaStructure' imported but unused
./usr/lib/python2.7/dist-packages/cogent/app/infernal.py:15: 'wuss_to_vienna' imported but unused
./usr/lib/python2.7/dist-packages/cogent/app/vienna_package.py:3: 'CommandLineAppResult' imported but unused
./usr/lib/python2.7/dist-packages/cogent/app/vienna_package.py:5: 'Parameters' imported but unused
./usr/lib/python2.7/dist-packages/cogent/app/vienna_package.py:5: 'Parameter' imported but unused
./usr/lib/python2.7/dist-packages/cogent/app/vienna_package.py:5: 'is_not_None' imported but unused
./usr/lib/python2.7/dist-packages/cogent/app/vienna_package.py:5: '_find_synonym' imported but unused
./usr/lib/python2.7/dist-packages/cogent/app/vienna_package.py:268: undefined name 'FILETYPE_TO_EXTENSION'
./usr/lib/python2.7/dist-packages/cogent/app/rnaforester.py:3: 'mkdir' imported but unused
./usr/lib/python2.7/dist-packages/cogent/app/rnaforester.py:3: 'close' imported but unused
./usr/lib/python2.7/dist-packages/cogent/app/rnaforester.py:3: 'getcwd' imported but unused
./usr/lib/python2.7/dist-packages/cogent/app/rnaforester.py:4: 'choice' imported but unused
./usr/lib/python2.7/dist-packages/cogent/app/rnaforester.py:6: 'ResultPath' imported but unused
./usr/lib/python2.7/dist-packages/cogent/app/rnaforester.py:8: 'Parameters' imported but unused
./usr/lib/python2.7/dist-packages/cogent/app/rnaforester.py:8: 'Parameter' imported but unused
./usr/lib/python2.7/dist-packages/cogent/app/rnaforester.py:8: 'ValuedParameter' imported but unused
./usr/lib/python2.7/dist-packages/cogent/app/rnaforester.py:8: 'MixedParameter' imported but unused
./usr/lib/python2.7/dist-packages/cogent/app/rnaforester.py:8: 'is_not_None' imported but unused
./usr/lib/python2.7/dist-packages/cogent/app/rnaforester.py:8: '_find_synonym' imported but unused
./usr/lib/python2.7/dist-packages/cogent/app/rnaforester.py:105: undefined name 'ApplicationError'
./usr/lib/python2.7/dist-packages/cogent/app/rnaforester.py:145: undefined name 'ApplicationError'
./usr/lib/python2.7/dist-packages/cogent/app/rnaforester.py:148: local variable 'synonyms' is assigned to but never used
./usr/lib/python2.7/dist-packages/cogent/app/rnashapes.py:13: 'CommandLineAppResult' imported but unused
./usr/lib/python2.7/dist-packages/cogent/app/rnashapes.py:13: 'ResultPath' imported but unused
./usr/lib/python2.7/dist-packages/cogent/app/rnashapes.py:15: 'is_not_None' imported but unused
./usr/lib/python2.7/dist-packages/cogent/app/rnashapes.py:15: '_find_synonym' imported but unused
./usr/lib/python2.7/dist-packages/cogent/app/rnashapes.py:15: 'Parameters' imported but unused
./usr/lib/python2.7/dist-packages/cogent/app/rnashapes.py:15: 'MixedParameter' imported but unused
./usr/lib/python2.7/dist-packages/cogent/app/rnashapes.py:15: 'Parameter' imported but unused
./usr/lib/python2.7/dist-packages/cogent/app/gctmpca.py:26: 'FilePath' imported but unused
./usr/lib/python2.7/dist-packages/cogent/app/gctmpca.py:27: 'DSO78_matrix' imported but unused
./usr/lib/python2.7/dist-packages/cogent/app/unafold.py:8: 'CommandLineAppResult' imported but unused
./usr/lib/python2.7/dist-packages/cogent/app/unafold.py:10: 'Parameters' imported but unused
./usr/lib/python2.7/dist-packages/cogent/app/unafold.py:10: 'Parameter' imported but unused
./usr/lib/python2.7/dist-packages/cogent/app/cove.py:3: 'CommandLineAppResult' imported but unused
./usr/lib/python2.7/dist-packages/cogent/app/cove.py:5: 'Parameters' imported but unused
./usr/lib/python2.7/dist-packages/cogent/app/cove.py:5: 'Parameter' imported but unused
./usr/lib/python2.7/dist-packages/cogent/app/cove.py:5: 'MixedParameter' imported but unused
./usr/lib/python2.7/dist-packages/cogent/app/cove.py:5: 'is_not_None' imported but unused
./usr/lib/python2.7/dist-packages/cogent/app/cove.py:5: '_find_synonym' imported but unused
./usr/lib/python2.7/dist-packages/cogent/app/rnaview.py:5: 'MixedParameter' imported but unused
./usr/lib/python2.7/dist-packages/cogent/app/cmfinder.py:7: 'CommandLineAppResult' imported but unused
./usr/lib/python2.7/dist-packages/cogent/app/cmfinder.py:9: 'MixedParameter' imported but unused
./usr/lib/python2.7/dist-packages/cogent/app/cmfinder.py:9: 'Parameters' imported but unused
./usr/lib/python2.7/dist-packages/cogent/app/cmfinder.py:9: 'Parameter' imported but unused
./usr/lib/python2.7/dist-packages/cogent/app/cmfinder.py:133: local variable 'motifList' is assigned to but never used
./usr/lib/python2.7/dist-packages/cogent/app/cmfinder.py:138: local variable 'inputPath' is assigned to but never used
./usr/lib/python2.7/dist-packages/cogent/app/dialign.py:17: 'guess_input_handler' imported but unused
./usr/lib/python2.7/dist-packages/cogent/app/dialign.py:17: 'get_tmp_filename' imported but unused
./usr/lib/python2.7/dist-packages/cogent/app/dialign.py:19: 'choice' imported but unused
./usr/lib/python2.7/dist-packages/cogent/app/dialign.py:20: 'DndParser' imported but unused
./usr/lib/python2.7/dist-packages/cogent/app/dialign.py:21: 'PhyloNode' imported but unused
./usr/lib/python2.7/dist-packages/cogent/app/dialign.py:22: 'MinimalFastaParser' imported but unused
./usr/lib/python2.7/dist-packages/cogent/app/comrna.py:3: 'CommandLineAppResult' imported but unused
./usr/lib/python2.7/dist-packages/cogent/app/comrna.py:3: 'ResultPath' imported but unused
./usr/lib/python2.7/dist-packages/cogent/app/comrna.py:5: 'is_not_None' imported but unused
./usr/lib/python2.7/dist-packages/cogent/app/comrna.py:5: '_find_synonym' imported but unused
./usr/lib/python2.7/dist-packages/cogent/app/comrna.py:5: 'Parameters' imported but unused
./usr/lib/python2.7/dist-packages/cogent/app/comrna.py:5: 'MixedParameter' imported but unused
./usr/lib/python2.7/dist-packages/cogent/app/comrna.py:5: 'FlagParameter' imported but unused
./usr/lib/python2.7/dist-packages/cogent/app/comrna.py:5: 'Parameter' imported but unused
./usr/lib/python2.7/dist-packages/cogent/app/stride.py:7: redefinition of unused 'StringIO' from line 5
./usr/lib/python2.7/dist-packages/cogent/app/dynalign.py:5: 'Parameters' imported but unused
./usr/lib/python2.7/dist-packages/cogent/app/dynalign.py:5: 'FlagParameter' imported but unused
./usr/lib/python2.7/dist-packages/cogent/app/dynalign.py:5: 'Parameter' imported but unused
./usr/lib/python2.7/dist-packages/cogent/app/dynalign.py:5: 'MixedParameter' imported but unused
./usr/lib/python2.7/dist-packages/cogent/app/dynalign.py:7: 'commands' imported but unused
./usr/lib/python2.7/dist-packages/cogent/app/dynalign.py:8: 'platform' imported but unused
./usr/lib/python2.7/dist-packages/cogent/app/dynalign.py:9: 'mkdir' imported but unused
./usr/lib/python2.7/dist-packages/cogent/app/dynalign.py:9: 'close' imported but unused
./usr/lib/python2.7/dist-packages/cogent/app/dynalign.py:9: 'getcwd' imported but unused
./usr/lib/python2.7/dist-packages/cogent/app/dynalign.py:168: undefined name 'ApplicationError'
./usr/lib/python2.7/dist-packages/cogent/app/dynalign.py:208: undefined name 'ApplicationError'
./usr/lib/python2.7/dist-packages/cogent/app/dynalign.py:210: local variable 'parameters' is assigned to but never used
./usr/lib/python2.7/dist-packages/cogent/app/dynalign.py:211: local variable 'synonyms' is assigned to but never used
./usr/lib/python2.7/dist-packages/cogent/app/sffinfo.py:4: 'ResultPath' imported but unused
./usr/lib/python2.7/dist-packages/cogent/app/sffinfo.py:114: undefined name 'ApplicationError'
./usr/lib/python2.7/dist-packages/cogent/app/sffinfo.py:119: local variable 'synonyms' is assigned to but never used
./usr/lib/python2.7/dist-packages/cogent/app/consan.py:4: 'ResultPath' imported but unused
./usr/lib/python2.7/dist-packages/cogent/app/consan.py:6: 'Parameters' imported but unused
./usr/lib/python2.7/dist-packages/cogent/app/consan.py:6: 'Parameter' imported but unused
./usr/lib/python2.7/dist-packages/cogent/app/consan.py:6: 'MixedParameter' imported but unused
./usr/lib/python2.7/dist-packages/cogent/app/consan.py:6: 'is_not_None' imported but unused
./usr/lib/python2.7/dist-packages/cogent/app/consan.py:6: '_find_synonym' imported but unused
./usr/lib/python2.7/dist-packages/cogent/app/consan.py:123: undefined name 'ApplicationError'
./usr/lib/python2.7/dist-packages/cogent/app/pfold.py:10: 'CommandLineAppResult' imported but unused
./usr/lib/python2.7/dist-packages/cogent/app/pfold.py:10: 'ResultPath' imported but unused
./usr/lib/python2.7/dist-packages/cogent/app/dotur.py:6: 'MixedParameter' imported but unused
./usr/lib/python2.7/dist-packages/cogent/app/dotur.py:10: 'SequenceCollection' imported but unused
./usr/lib/python2.7/dist-packages/cogent/app/dotur.py:11: 'PROTEIN' imported but unused
./usr/lib/python2.7/dist-packages/cogent/app/dotur.py:11: 'DNA' imported but unused
./usr/lib/python2.7/dist-packages/cogent/app/dotur.py:11: 'RNA' imported but unused
./usr/lib/python2.7/dist-packages/cogent/app/contrafold.py:3: 'CommandLineAppResult' imported but unused
./usr/lib/python2.7/dist-packages/cogent/app/contrafold.py:3: 'ResultPath' imported but unused
./usr/lib/python2.7/dist-packages/cogent/app/contrafold.py:5: 'is_not_None' imported but unused
./usr/lib/python2.7/dist-packages/cogent/app/contrafold.py:5: '_find_synonym' imported but unused
./usr/lib/python2.7/dist-packages/cogent/app/contrafold.py:5: 'Parameters' imported but unused
./usr/lib/python2.7/dist-packages/cogent/app/contrafold.py:5: 'MixedParameter' imported but unused
./usr/lib/python2.7/dist-packages/cogent/app/contrafold.py:5: 'ValuedParameter' imported but unused
./usr/lib/python2.7/dist-packages/cogent/app/contrafold.py:5: 'Parameter' imported but unused
./usr/lib/python2.7/dist-packages/cogent/app/clearcut.py:5: 'MixedParameter' imported but unused
./usr/lib/python2.7/dist-packages/cogent/app/clearcut.py:8: 'SequenceCollection' imported but unused
./usr/lib/python2.7/dist-packages/cogent/app/clearcut.py:9: 'PROTEIN' imported but unused
./usr/lib/python2.7/dist-packages/cogent/app/fasttree_v1.py:64: local variable 'suppress_stdout' is assigned to but never used
./usr/lib/python2.7/dist-packages/cogent/app/fasttree_v1.py:95: undefined name 'ApplicationError'
./usr/lib/python2.7/dist-packages/cogent/app/mfold.py:9: 'CommandLineAppResult' imported but unused
./usr/lib/python2.7/dist-packages/cogent/app/mfold.py:11: 'Parameters' imported but unused
./usr/lib/python2.7/dist-packages/cogent/app/mfold.py:11: 'Parameter' imported but unused
./usr/lib/python2.7/dist-packages/cogent/app/sfold.py:10: 'CommandLineAppResult' imported but unused
./usr/lib/python2.7/dist-packages/cogent/app/sfold.py:12: 'Parameters' imported but unused
./usr/lib/python2.7/dist-packages/cogent/app/sfold.py:12: 'MixedParameter' imported but unused
./usr/lib/python2.7/dist-packages/cogent/app/sfold.py:12: 'FlagParameter' imported but unused
./usr/lib/python2.7/dist-packages/cogent/app/sfold.py:12: 'Parameter' imported but unused
./usr/lib/python2.7/dist-packages/cogent/app/pknotsrg.py:3: 'CommandLineAppResult' imported but unused
./usr/lib/python2.7/dist-packages/cogent/app/pknotsrg.py:3: 'ResultPath' imported but unused
./usr/lib/python2.7/dist-packages/cogent/app/pknotsrg.py:5: 'Parameters' imported but unused
./usr/lib/python2.7/dist-packages/cogent/app/pknotsrg.py:5: 'MixedParameter' imported but unused
./usr/lib/python2.7/dist-packages/cogent/app/pknotsrg.py:5: 'Parameter' imported but unused
./usr/lib/python2.7/dist-packages/cogent/app/formatdb.py:65: local variable 'input_filepath' is assigned to but never used
./usr/lib/python2.7/dist-packages/cogent/app/fasttree.py:71: local variable 'suppress_stdout' is assigned to but never used
./usr/lib/python2.7/dist-packages/cogent/app/fasttree.py:102: undefined name 'ApplicationError'
./usr/lib/python2.7/dist-packages/cogent/app/rdp_classifier.py:20: 'Parameter' imported but unused
./usr/lib/python2.7/dist-packages/cogent/app/rdp_classifier.py:22: 'guess_input_handler' imported but unused
./usr/lib/python2.7/dist-packages/cogent/app/nupack.py:11: 'Parameters' imported but unused
./usr/lib/python2.7/dist-packages/cogent/app/nupack.py:11: 'FlagParameter' imported but unused
./usr/lib/python2.7/dist-packages/cogent/app/nupack.py:11: 'Parameter' imported but unused
./usr/lib/python2.7/dist-packages/cogent/app/nupack.py:11: 'ValuedParameter' imported but unused
./usr/lib/python2.7/dist-packages/cogent/app/nupack.py:11: 'MixedParameter' imported but unused
./usr/lib/python2.7/dist-packages/cogent/app/nupack.py:11: 'is_not_None' imported but unused
./usr/lib/python2.7/dist-packages/cogent/app/nupack.py:11: '_find_synonym' imported but unused
./usr/lib/python2.7/dist-packages/cogent/app/nupack.py:143: undefined name 'ApplicationError'
./usr/lib/python2.7/dist-packages/cogent/app/blast.py:6: 'MixedParameter' imported but unused
./usr/lib/python2.7/dist-packages/cogent/app/blast.py:7: 'get_tmp_filename' imported but unused
./usr/lib/python2.7/dist-packages/cogent/app/blast.py:10: 'QMEBlast9' imported but unused
./usr/lib/python2.7/dist-packages/cogent/app/blast.py:913: local variable 'last_num_ids' is assigned to but never used
./usr/lib/python2.7/dist-packages/cogent/app/blast.py:997: local variable 'seq_file' is assigned to but never used
./usr/lib/python2.7/dist-packages/cogent/app/util.py:2: 'commands' imported but unused
./usr/lib/python2.7/dist-packages/cogent/app/util.py:3: 'platform' imported but unused
./usr/lib/python2.7/dist-packages/cogent/app/util.py:4: 'sep' imported but unused
./usr/lib/python2.7/dist-packages/cogent/app/util.py:4: 'close' imported but unused
./usr/lib/python2.7/dist-packages/cogent/app/util.py:7: 'array' imported but unused
./usr/lib/python2.7/dist-packages/cogent/app/util.py:7: 'nonzero' imported but unused
./usr/lib/python2.7/dist-packages/cogent/app/util.py:7: 'zeros' imported but unused
./usr/lib/python2.7/dist-packages/cogent/app/util.py:7: 'max' imported but unused
./usr/lib/python2.7/dist-packages/cogent/app/util.py:8: 'Parameter' imported but unused
./usr/lib/python2.7/dist-packages/cogent/app/util.py:8: 'FlagParameter' imported but unused
./usr/lib/python2.7/dist-packages/cogent/app/util.py:8: 'ValuedParameter' imported but unused
./usr/lib/python2.7/dist-packages/cogent/app/util.py:8: 'MixedParameter' imported but unused
./usr/lib/python2.7/dist-packages/cogent/app/util.py:8: 'is_not_None' imported but unused
./usr/lib/python2.7/dist-packages/cogent/app/util.py:8: '_find_synonym' imported but unused
./usr/lib/python2.7/dist-packages/cogent/app/util.py:10: 'if_' imported but unused
./usr/lib/python2.7/dist-packages/cogent/app/util.py:366: local variable 'synonyms' is assigned to but never used
./usr/lib/python2.7/dist-packages/cogent/app/carnac.py:3: 'CommandLineAppResult' imported but unused
./usr/lib/python2.7/dist-packages/cogent/app/carnac.py:5: 'Parameters' imported but unused
./usr/lib/python2.7/dist-packages/cogent/app/carnac.py:5: 'Parameter' imported but unused
./usr/lib/python2.7/dist-packages/cogent/app/carnac.py:58: local variable 'seq_counter' is assigned to but never used
./usr/lib/python2.7/dist-packages/cogent/app/rnaalifold.py:3: 'CommandLineAppResult' imported but unused
./usr/lib/python2.7/dist-packages/cogent/app/rnaalifold.py:5: 'Parameters' imported but unused
./usr/lib/python2.7/dist-packages/cogent/app/rnaalifold.py:5: 'Parameter' imported but unused
./usr/lib/python2.7/dist-packages/cogent/app/rnaalifold.py:5: '_find_synonym' imported but unused
./usr/lib/python2.7/dist-packages/cogent/app/rnaalifold.py:10: 'rnaalifold_parser' imported but unused
./usr/lib/python2.7/dist-packages/cogent/app/rnaalifold.py:12: 'ViennaStructure' imported but unused
./usr/lib/python2.7/dist-packages/cogent/app/foldalign.py:11: 'CommandLineAppResult' imported but unused
./usr/lib/python2.7/dist-packages/cogent/app/foldalign.py:11: 'ResultPath' imported but unused
./usr/lib/python2.7/dist-packages/cogent/app/foldalign.py:13: 'is_not_None' imported but unused
./usr/lib/python2.7/dist-packages/cogent/app/foldalign.py:13: '_find_synonym' imported but unused
./usr/lib/python2.7/dist-packages/cogent/app/foldalign.py:13: 'Parameters' imported but unused
./usr/lib/python2.7/dist-packages/cogent/app/foldalign.py:13: 'MixedParameter' imported but unused
./usr/lib/python2.7/dist-packages/cogent/app/foldalign.py:13: 'Parameter' imported but unused
./usr/lib/python2.7/dist-packages/cogent/app/muscle.py:8: 'choice' imported but unused
./usr/lib/python2.7/dist-packages/cogent/app/mafft.py:7: 'get_tmp_filename' imported but unused
./usr/lib/python2.7/dist-packages/cogent/app/mafft.py:9: 'choice' imported but unused
./usr/lib/python2.7/dist-packages/cogent/app/mafft.py:11: 'PROTEIN' imported but unused
./usr/lib/python2.7/dist-packages/cogent/app/mafft.py:11: 'DNA' imported but unused
./usr/lib/python2.7/dist-packages/cogent/app/mafft.py:11: 'RNA' imported but unused
./usr/lib/python2.7/dist-packages/cogent/app/mafft.py:13: 'PhyloNode' imported but unused
./usr/lib/python2.7/dist-packages/cogent/app/mafft.py:14: 'DndParser' imported but unused
./usr/lib/python2.7/dist-packages/cogent/recalculation/calculation.py:5: 'warnings' imported but unused
./usr/lib/python2.7/dist-packages/cogent/recalculation/calculation.py:209: local variable 'detail' is assigned to but never used
./usr/lib/python2.7/dist-packages/cogent/recalculation/definition.py:67: 'warnings' imported but unused
./usr/lib/python2.7/dist-packages/cogent/recalculation/definition.py:80: 'chdtri' imported but unused
./usr/lib/python2.7/dist-packages/cogent/recalculation/definition.py:81: 'parallel' imported but unused
./usr/lib/python2.7/dist-packages/cogent/recalculation/definition.py:418: local variable 'N' is assigned to but never used
./usr/lib/python2.7/dist-packages/cogent/recalculation/scope.py:663: redefinition of function 'callback' from line 659
./usr/lib/python2.7/dist-packages/cogent/util/terminal.py:19: redefinition of unused 'curses' from line 17
./usr/lib/python2.7/dist-packages/cogent/util/table.py:538: local variable 'is_reversed' is assigned to but never used
./usr/lib/python2.7/dist-packages/cogent/util/table.py:548: local variable 'cast' is assigned to but never used
./usr/lib/python2.7/dist-packages/cogent/util/misc.py:12: 'maxint' imported but unused
./usr/lib/python2.7/dist-packages/cogent/util/misc.py:13: 'popen' imported but unused
./usr/lib/python2.7/dist-packages/cogent/util/misc.py:15: 'sum' imported but unused
./usr/lib/python2.7/dist-packages/cogent/util/misc.py:15: 'logical_not' imported but unused
./usr/lib/python2.7/dist-packages/cogent/util/misc.py:204: local variable 'e' is assigned to but never used
./usr/lib/python2.7/dist-packages/cogent/util/misc.py:1098: local variable 'ValueError' is assigned to but never used
./usr/lib/python2.7/dist-packages/cogent/util/progress_display.py:24: 'contextlib' imported but unused
./usr/lib/python2.7/dist-packages/cogent/util/progress_display.py:24: 'warnings' imported but unused
./usr/lib/python2.7/dist-packages/cogent/util/progress_display.py:25: 'atexit' imported but unused
./usr/lib/python2.7/dist-packages/cogent/util/progress_display.py:25: 'os' imported but unused
./usr/lib/python2.7/dist-packages/cogent/util/update_version.py:273: local variable 'found_version_line' is assigned to but never used
./usr/lib/python2.7/dist-packages/cogent/util/update_version.py:292: local variable 'found_version_line' is assigned to but never used
./usr/lib/python2.7/dist-packages/cogent/util/update_version.py:311: local variable 'found_version_line' is assigned to but never used
./usr/lib/python2.7/dist-packages/cogent/util/dict2d.py:234: local variable 'constructor' is assigned to but never used
./usr/lib/python2.7/dist-packages/cogent/util/dict2d.py:543: local variable 'item_lookup' is assigned to but never used
./usr/lib/python2.7/dist-packages/cogent/util/organizer.py:74: local variable 'results' is assigned to but never used
./usr/lib/python2.7/dist-packages/cogent/util/trie.py:148: local variable 'labels' is assigned to but never used
./usr/lib/python2.7/dist-packages/cogent/util/transform.py:16: 'and_' imported but unused
./usr/lib/python2.7/dist-packages/cogent/util/transform.py:16: 'or_' imported but unused
./usr/lib/python2.7/dist-packages/cogent/util/transform.py:17: 'logical_or' imported but unused
./usr/lib/python2.7/dist-packages/cogent/util/transform.py:17: 'logical_and' imported but unused
./usr/lib/python2.7/dist-packages/cogent/util/transform.py:17: 'logical_not' imported but unused
./usr/lib/python2.7/dist-packages/cogent/util/transform.py:224: redefinition of function 'result' from line 220
./usr/lib/python2.7/dist-packages/cogent/util/transform.py:499: redefinition of function 'result' from line 494
./usr/lib/python2.7/dist-packages/cogent/util/unit_test.py:36: 'TestSuite' imported but unused
./usr/lib/python2.7/dist-packages/cogent/util/unit_test.py:36: 'main' imported but unused
./usr/lib/python2.7/dist-packages/cogent/util/unit_test.py:36: 'findTestCases' imported but unused
./usr/lib/python2.7/dist-packages/cogent/util/unit_test.py:37: 'recursive_flatten' imported but unused
./usr/lib/python2.7/dist-packages/cogent/util/unit_test.py:317: local variable 'e' is assigned to but never used
./usr/lib/python2.7/dist-packages/cogent/util/parallel.py:51: redefinition of unused 'MPI' from line 48
./usr/lib/python2.7/dist-packages/cogent/util/recode_alignment.py:41: 'OptionParser' imported but unused
./usr/lib/python2.7/dist-packages/cogent/util/recode_alignment.py:43: 'Alignment' imported but unused
./usr/lib/python2.7/dist-packages/cogent/util/recode_alignment.py:45: 'PROTEIN' imported but unused
./usr/lib/python2.7/dist-packages/cogent/util/array.py:4: 'mul' imported but unused
./usr/lib/python2.7/dist-packages/cogent/util/array.py:4: 'getitem' imported but unused
./usr/lib/python2.7/dist-packages/cogent/seqsim/analysis.py:2: 'RangeNode' imported but unused
./usr/lib/python2.7/dist-packages/cogent/seqsim/analysis.py:2: 'balanced_breakpoints' imported but unused
./usr/lib/python2.7/dist-packages/cogent/seqsim/analysis.py:103: local variable 'rates' is assigned to but never used
./usr/lib/python2.7/dist-packages/cogent/seqsim/analysis.py:291: undefined name 'BalancedTree'
./usr/lib/python2.7/dist-packages/cogent/seqsim/analysis.py:294: undefined name 'xxx'
./usr/lib/python2.7/dist-packages/cogent/seqsim/analysis.py:296: undefined name 'Rates'
./usr/lib/python2.7/dist-packages/cogent/seqsim/analysis.py:297: undefined name 'scale_trace'
./usr/lib/python2.7/dist-packages/cogent/seqsim/analysis.py:302: undefined name 'random_q_matrix'
./usr/lib/python2.7/dist-packages/cogent/seqsim/analysis.py:303: undefined name 'scale_trace'
./usr/lib/python2.7/dist-packages/cogent/seqsim/analysis.py:307: undefined name 'rand_rna'
./usr/lib/python2.7/dist-packages/cogent/seqsim/analysis.py:319: undefined name 'BalancedTree'
./usr/lib/python2.7/dist-packages/cogent/seqsim/analysis.py:324: undefined name 'random_q_matrix'
./usr/lib/python2.7/dist-packages/cogent/seqsim/analysis.py:325: undefined name 'scale_trace'
./usr/lib/python2.7/dist-packages/cogent/seqsim/analysis.py:329: undefined name 'rand_rna'
./usr/lib/python2.7/dist-packages/cogent/seqsim/analysis.py:336: undefined name 'flatten_q_matrices'
./usr/lib/python2.7/dist-packages/cogent/seqsim/analysis.py:338: undefined name 'scale_trace'
./usr/lib/python2.7/dist-packages/cogent/seqsim/analysis.py:339: undefined name 'flatten_q_matrices'
./usr/lib/python2.7/dist-packages/cogent/seqsim/analysis.py:341: undefined name 'cov'
./usr/lib/python2.7/dist-packages/cogent/seqsim/analysis.py:342: undefined name 'corrcoef'
./usr/lib/python2.7/dist-packages/cogent/seqsim/analysis.py:343: undefined name 'euclidean_norm'
./usr/lib/python2.7/dist-packages/cogent/seqsim/analysis.py:344: undefined name 'euclidean_norm'
./usr/lib/python2.7/dist-packages/cogent/seqsim/analysis.py:345: undefined name 'eigenvalues'
./usr/lib/python2.7/dist-packages/cogent/seqsim/analysis.py:348: undefined name 'eigenvalues'
./usr/lib/python2.7/dist-packages/cogent/seqsim/analysis.py:351: undefined name 'ratio_two_best'
./usr/lib/python2.7/dist-packages/cogent/seqsim/analysis.py:352: undefined name 'ratio_two_best'
./usr/lib/python2.7/dist-packages/cogent/seqsim/analysis.py:353: undefined name 'ratio_best_to_sum'
./usr/lib/python2.7/dist-packages/cogent/seqsim/analysis.py:354: undefined name 'ratio_best_to_sum'
./usr/lib/python2.7/dist-packages/cogent/seqsim/analysis.py:355: undefined name 'weiss'
./usr/lib/python2.7/dist-packages/cogent/seqsim/analysis.py:357: undefined name 'dists_from_mean'
./usr/lib/python2.7/dist-packages/cogent/seqsim/analysis.py:359: undefined name 'var'
./usr/lib/python2.7/dist-packages/cogent/seqsim/analysis.py:361: undefined name 'mean'
./usr/lib/python2.7/dist-packages/cogent/seqsim/analysis.py:362: undefined name 'euclidean_distance'
./usr/lib/python2.7/dist-packages/cogent/seqsim/analysis.py:365: undefined name 'euclidean_norm'
./usr/lib/python2.7/dist-packages/cogent/seqsim/analysis.py:365: undefined name 'cov'
./usr/lib/python2.7/dist-packages/cogent/seqsim/analysis.py:378: undefined name 'all_p_from_tree'
./usr/lib/python2.7/dist-packages/cogent/seqsim/analysis.py:379: undefined name 'pair_p_from_tree'
./usr/lib/python2.7/dist-packages/cogent/seqsim/analysis.py:380: undefined name 'get_qs'
./usr/lib/python2.7/dist-packages/cogent/seqsim/analysis.py:381: undefined name 'get_qs'
./usr/lib/python2.7/dist-packages/cogent/seqsim/analysis.py:382: undefined name 'take_off_diag'
./usr/lib/python2.7/dist-packages/cogent/seqsim/analysis.py:384: undefined name 'scale_trace'
./usr/lib/python2.7/dist-packages/cogent/seqsim/analysis.py:385: undefined name 'flatten_q_matrices'
./usr/lib/python2.7/dist-packages/cogent/seqsim/analysis.py:386: undefined name 'flatten_q_matrices'
./usr/lib/python2.7/dist-packages/cogent/seqsim/analysis.py:387: undefined name 'dists_from_mean'
./usr/lib/python2.7/dist-packages/cogent/seqsim/analysis.py:389: undefined name 'var'
./usr/lib/python2.7/dist-packages/cogent/seqsim/analysis.py:390: undefined name 'dists_from_mean'
./usr/lib/python2.7/dist-packages/cogent/seqsim/analysis.py:392: undefined name 'var'
./usr/lib/python2.7/dist-packages/cogent/seqsim/analysis.py:394: undefined name 'flatten_q_matrices'
./usr/lib/python2.7/dist-packages/cogent/seqsim/analysis.py:395: undefined name 'corrcoef'
./usr/lib/python2.7/dist-packages/cogent/seqsim/analysis.py:396: undefined name 'ratio_two_best'
./usr/lib/python2.7/dist-packages/cogent/seqsim/analysis.py:396: undefined name 'eigenvalues'
./usr/lib/python2.7/dist-packages/cogent/seqsim/analysis.py:398: undefined name 'cov'
./usr/lib/python2.7/dist-packages/cogent/seqsim/analysis.py:399: undefined name 'eigenvalues'
./usr/lib/python2.7/dist-packages/cogent/seqsim/analysis.py:402: undefined name 'ratio_two_best'
./usr/lib/python2.7/dist-packages/cogent/seqsim/analysis.py:403: undefined name 'weiss'
./usr/lib/python2.7/dist-packages/cogent/seqsim/analysis.py:413: undefined name 'all_p_from_tree'
./usr/lib/python2.7/dist-packages/cogent/seqsim/analysis.py:414: undefined name 'get_qs'
./usr/lib/python2.7/dist-packages/cogent/seqsim/analysis.py:416: undefined name 'scale_trace'
./usr/lib/python2.7/dist-packages/cogent/seqsim/analysis.py:417: undefined name 'flatten_q_matrices'
./usr/lib/python2.7/dist-packages/cogent/seqsim/analysis.py:418: undefined name 'dists_from_mean'
./usr/lib/python2.7/dist-packages/cogent/seqsim/analysis.py:420: undefined name 'var'
./usr/lib/python2.7/dist-packages/cogent/seqsim/analysis.py:422: undefined name 'flatten_q_matrices'
./usr/lib/python2.7/dist-packages/cogent/seqsim/analysis.py:423: undefined name 'corrcoef'
./usr/lib/python2.7/dist-packages/cogent/seqsim/analysis.py:424: undefined name 'ratio_two_best'
./usr/lib/python2.7/dist-packages/cogent/seqsim/analysis.py:424: undefined name 'eigenvalues'
./usr/lib/python2.7/dist-packages/cogent/seqsim/analysis.py:434: undefined name 'random_mats'
./usr/lib/python2.7/dist-packages/cogent/seqsim/analysis.py:434: undefined name 'random_q_mats'
./usr/lib/python2.7/dist-packages/cogent/seqsim/analysis.py:435: undefined name 'scale_one_q'
./usr/lib/python2.7/dist-packages/cogent/seqsim/analysis.py:435: undefined name 'scale_many_q'
./usr/lib/python2.7/dist-packages/cogent/seqsim/analysis.py:437: undefined name 'svd_q'
./usr/lib/python2.7/dist-packages/cogent/seqsim/analysis.py:444: undefined name 'balanced_one_q_tree'
./usr/lib/python2.7/dist-packages/cogent/seqsim/analysis.py:445: undefined name 'all_p_from_tree'
./usr/lib/python2.7/dist-packages/cogent/seqsim/analysis.py:446: undefined name 'svd_q'
./usr/lib/python2.7/dist-packages/cogent/seqsim/analysis.py:446: undefined name 'get_qs'
./usr/lib/python2.7/dist-packages/cogent/seqsim/analysis.py:451: undefined name 'all_p_from_tree'
./usr/lib/python2.7/dist-packages/cogent/seqsim/analysis.py:452: undefined name 'svd_q'
./usr/lib/python2.7/dist-packages/cogent/seqsim/analysis.py:452: undefined name 'get_qs'
./usr/lib/python2.7/dist-packages/cogent/seqsim/analysis.py:452: undefined name 'all_p_from_tree'
./usr/lib/python2.7/dist-packages/cogent/seqsim/analysis.py:455: undefined name 'all_p_from_tree'
./usr/lib/python2.7/dist-packages/cogent/seqsim/analysis.py:457: undefined name 'svd_q'
./usr/lib/python2.7/dist-packages/cogent/seqsim/analysis.py:457: undefined name 'get_qs'
./usr/lib/python2.7/dist-packages/cogent/seqsim/analysis.py:457: undefined name 'all_p_from_tree'
./usr/lib/python2.7/dist-packages/cogent/seqsim/analysis.py:460: undefined name 'all_p_from_tree'
./usr/lib/python2.7/dist-packages/cogent/seqsim/analysis.py:461: undefined name 'get_qs'
./usr/lib/python2.7/dist-packages/cogent/seqsim/analysis.py:470: undefined name 'header'
./usr/lib/python2.7/dist-packages/cogent/seqsim/analysis.py:474: undefined name 'header'
./usr/lib/python2.7/dist-packages/cogent/seqsim/analysis.py:476: undefined name 'header'
./usr/lib/python2.7/dist-packages/cogent/seqsim/analysis.py:477: undefined name 'header'
./usr/lib/python2.7/dist-packages/cogent/seqsim/analysis.py:493: undefined name 'random'
./usr/lib/python2.7/dist-packages/cogent/seqsim/analysis.py:500: undefined name 'balanced_one_q_tree'
./usr/lib/python2.7/dist-packages/cogent/seqsim/analysis.py:513: undefined name 'balanced_one_q_tree'
./usr/lib/python2.7/dist-packages/cogent/seqsim/analysis.py:520: undefined name 'lengths'
./usr/lib/python2.7/dist-packages/cogent/seqsim/analysis.py:546: undefined name 'tree_controller'
./usr/lib/python2.7/dist-packages/cogent/seqsim/birth_death.py:404: local variable 'max_taxa' is assigned to but never used
./usr/lib/python2.7/dist-packages/cogent/seqsim/birth_death.py:405: undefined name 'num_taxa'
./usr/lib/python2.7/dist-packages/cogent/seqsim/birth_death.py:408: undefined name 'num_taxa'
./usr/lib/python2.7/dist-packages/cogent/seqsim/microarray_normalize./usr/lib/python2.7/dist-packages/cogent/draw/linear.py:1127: invalid syntax
^
.py:31: 'zeros' imported but unused
./usr/lib/python2.7/dist-packages/cogent/seqsim/microarray_normalize.py:31: 'transpose' imported but unused
./usr/lib/python2.7/dist-packages/cogent/seqsim/microarray_normalize.py:31: 'ceil' imported but unused
./usr/lib/python2.7/dist-packages/cogent/seqsim/microarray_normalize.py:97: local variable 'gmean' is assigned to but never used
./usr/lib/python2.7/dist-packages/cogent/seqsim/microarray_normalize.py:125: undefined name 'rank_row_by_variance'
./usr/lib/python2.7/dist-packages/cogent/seqsim/microarray_normalize.py:135: local variable 'constant_rank_indices' (defined in enclosing scope on line 127) referenced before assignment
./usr/lib/python2.7/dist-packages/cogent/seqsim/microarray_normalize.py:146: undefined name 'nonzero'
./usr/lib/python2.7/dist-packages/cogent/seqsim/microarray_normalize.py:188: undefined name 'NormalizationError'
./usr/lib/python2.7/dist-packages/cogent/seqsim/tree.py:6: 'array' imported but unused
./usr/lib/python2.7/dist-packages/cogent/seqsim/tree.py:494: local variable 'result' is assigned to but never used
./usr/lib/python2.7/dist-packages/cogent/seqsim/tree.py:516: local variable 'new_nodes' is assigned to but never used
./usr/lib/python2.7/dist-packages/cogent/seqsim/usage.py:25: 'mul' imported but unused
./usr/lib/python2.7/dist-packages/cogent/seqsim/usage.py:25: 'div' imported but unused
./usr/lib/python2.7/dist-packages/cogent/seqsim/usage.py:29: redefinition of unused 'log' from line 29
./usr/lib/python2.7/dist-packages/cogent/seqsim/usage.py:29: 'identity' imported but unused
./usr/lib/python2.7/dist-packages/cogent/seqsim/usage.py:822: redefinition of function 'similarity_f' from line 819
./usr/lib/python2.7/dist-packages/cogent/seqsim/usage.py:851: redefinition of function 'similarity_f' from line 847
./usr/lib/python2.7/dist-packages/cogent/seqsim/usage.py:858: redefinition of function 'similarity_f' from line 851
./usr/lib/python2.7/dist-packages/cogent/seqsim/usage.py:861: redefinition of function 'similarity_f' from line 858
./usr/lib/python2.7/dist-packages/cogent/seqsim/usage.py:934: local variable 'num_negs' is assigned to but never used
./usr/lib/python2.7/dist-packages/cogent/seqsim/usage.py:1125: undefined name 'Float64'
./usr/lib/python2.7/dist-packages/cogent/seqsim/markov.py:15: 'shuffle' imported but unused
./usr/lib/python2.7/dist-packages/cogent/seqsim/markov.py:15: 'randrange' imported but unused
./usr/lib/python2.7/dist-packages/cogent/seqsim/markov.py:19: 'copy' imported but unused
./usr/lib/python2.7/dist-packages/cogent/seqsim/markov.py:20: 'rank' imported but unused
./usr/lib/python2.7/dist-packages/cogent/seqsim/markov.py:20: 'searchsorted' imported but unused
./usr/lib/python2.7/dist-packages/cogent/seqsim/markov.py:20: 'ones' imported but unused
./usr/lib/python2.7/dist-packages/cogent/seqsim/markov.py:20: 'argsort' imported but unused
./usr/lib/python2.7/dist-packages/cogent/seqsim/markov.py:318: undefined name 'KwordError'
./usr/lib/python2.7/dist-packages/cogent/seqsim/markov.py:413: local variable 'total' is assigned to but never used
./usr/lib/python2.7/dist-packages/cogent/seqsim/sequence_generators.py:23: 'path' imported but unused
./usr/lib/python2.7/dist-packages/cogent/seqsim/sequence_generators.py:24: 'choice' imported but unused
./usr/lib/python2.7/dist-packages/cogent/draw/arrow_rates.py:4: redefinition of unused 'rc' from line 2
./usr/lib/python2.7/dist-packages/cogent/draw/arrow_rates.py:4: 'show' imported but unused
./usr/lib/python2.7/dist-packages/cogent/draw/arrow_rates.py:4: 'draw' imported but unused
./usr/lib/python2.7/dist-packages/cogent/draw/arrow_rates.py:118: local variable 'A' is assigned to but never used
./usr/lib/python2.7/dist-packages/cogent/draw/arrow_rates.py:119: local variable 'T' is assigned to but never used
./usr/lib/python2.7/dist-packages/cogent/draw/arrow_rates.py:120: local variable 'G' is assigned to but never used
./usr/lib/python2.7/dist-packages/cogent/draw/arrow_rates.py:121: local variable 'C' is assigned to but never used
./usr/lib/python2.7/dist-packages/cogent/draw/arrow_rates.py:202: local variable 'arrow_label_offset' is assigned to but never used
./usr/lib/python2.7/dist-packages/cogent/draw/multivariate_plot.py:4: 'plot' imported but unused
./usr/lib/python2.7/dist-packages/cogent/draw/multivariate_plot.py:8: 'set_trace' imported but unused
./usr/lib/python2.7/dist-packages/cogent/draw/rlg2mpl.py:8: 'Line2D' imported but unused
./usr/lib/python2.7/dist-packages/cogent/draw/rlg2mpl.py:14: 'numpy' imported but unused
./usr/lib/python2.7/dist-packages/cogent/draw/rlg2mpl.py:47: local variable 'fontname' is assigned to but never used
./usr/lib/python2.7/dist-packages/cogent/draw/rlg2mpl.py:48: local variable 'fontsize' is assigned to but never used
./usr/lib/python2.7/dist-packages/cogent/draw/rlg2mpl.py:49: local variable 'color' is assigned to but never used
./usr/lib/python2.7/dist-packages/cogent/draw/rlg2mpl.py:50: local variable 'ha' is assigned to but never used
./usr/lib/python2.7/dist-packages/cogent/draw/rlg2mpl.py:51: local variable 'va' is assigned to but never used
./usr/lib/python2.7/dist-packages/cogent/draw/codon_usage.py:43: redefinition of unused 'standard_series_colors' from line 11
./usr/lib/python2.7/dist-packages/cogent/draw/codon_usage.py:80: local variable 'colors' is assigned to but never used
./usr/lib/python2.7/dist-packages/cogent/draw/__init__.py:15: 'TrackDefn' imported but unused
./usr/lib/python2.7/dist-packages/cogent/draw/__init__.py:15: 'Diamond' imported but unused
./usr/lib/python2.7/dist-packages/cogent/draw/__init__.py:15: 'Area' imported but unused
./usr/lib/python2.7/dist-packages/cogent/draw/__init__.py:15: 'DisplayPolicy' imported but unused
./usr/lib/python2.7/dist-packages/cogent/draw/__init__.py:15: 'colors' imported but unused
./usr/lib/python2.7/dist-packages/cogent/draw/__init__.py:15: 'Arrow' imported but unused
./usr/lib/python2.7/dist-packages/cogent/draw/__init__.py:15: 'BluntArrow' imported but unused
./usr/lib/python2.7/dist-packages/cogent/draw/__init__.py:15: 'Box' imported but unused
./usr/lib/python2.7/dist-packages/cogent/draw/__init__.py:15: 'Display' imported but unused
./usr/lib/python2.7/dist-packages/cogent/draw/__init__.py:19: 'cogent' imported but unused
./usr/lib/python2.7/dist-packages/cogent/draw/legend.py:6: 'PatchCollection' imported but unused
./usr/lib/python2.7/dist-packages/cogent/draw/legend.py:7: 'Text' imported but unused
./usr/lib/python2.7/dist-packages/cogent/draw/legend.py:8: 'Affine2D' imported but unused
./usr/lib/python2.7/dist-packages/cogent/draw/legend.py:9: 'Group' imported but unused
./usr/lib/python2.7/dist-packages/cogent/draw/legend.py:35: local variable 'v' is assigned to but never used
./usr/lib/python2.7/dist-packages/cogent/draw/legend.py:47: local variable 'result' is assigned to but never used
./usr/lib/python2.7/dist-packages/cogent/draw/legend.py:84: local variable 'g' is assigned to but never used
./usr/lib/python2.7/dist-packages/cogent/draw/util.py:15: 'use' imported but unused
./usr/lib/python2.7/dist-packages/cogent/draw/util.py:33: redefinition of unused 'ImageFilter' from line 31
./usr/lib/python2.7/dist-packages/cogent/draw/util.py:33: redefinition of unused 'Image' from line 30
./usr/lib/python2.7/dist-packages/cogent/draw/util.py:34: 'shape' imported but unused
./usr/lib/python2.7/dist-packages/cogent/draw/util.py:34: 'array' imported but unused
./usr/lib/python2.7/dist-packages/cogent/draw/util.py:35: 'CodonUsage' imported but unused
./usr/lib/python2.7/dist-packages/cogent/draw/util.py:153: undefined name 'normalize'
./usr/lib/python2.7/dist-packages/cogent/draw/util.py:158: undefined name 'amax'
./usr/lib/python2.7/dist-packages/cogent/draw/util.py:158: undefined name 'amin'
./usr/lib/python2.7/dist-packages/cogent/draw/util.py:260: local variable 'label_offset' is assigned to but never used
./usr/lib/python2.7/dist-packages/cogent/draw/util.py:343: local variable 'x' is assigned to but never used
./usr/lib/python2.7/dist-packages/cogent/draw/util.py:344: local variable 'y' is assigned to but never used
./usr/lib/python2.7/dist-packages/cogent/draw/util.py:590: undef./usr/lib/python2.7/dist-packages/cogent/parse/infernal.py:50: invalid syntax
^
ined name 'reshape'
./usr/lib/python2.7/dist-packages/cogent/draw/util.py:599: undefined name 'clabel'
./usr/lib/python2.7/dist-packages/cogent/draw/util.py:758: undefined name 'xlabel'
./usr/lib/python2.7/dist-packages/cogent/parse/record.py:79: redefinition of function 'parser' from line 76
./usr/lib/python2.7/dist-packages/cogent/parse/record.py:100: redefinition of function 'parser' from line 79
./usr/lib/python2.7/dist-packages/cogent/parse/record.py:307: redefinition of function 'setter' from line 304
./usr/lib/python2.7/dist-packages/cogent/parse/record.py:445: redefinition of function 'parser' from line 442
./usr/lib/python2.7/dist-packages/cogent/parse/record.py:473: redefinition of function 'parser' from line 466
./usr/lib/python2.7/dist-packages/cogent/parse/cigar.py:20: '_LostSpan' imported but unused
./usr/lib/python2.7/dist-packages/cogent/parse/aaindex.py:48: local variable 'result' is assigned to but never used
./usr/lib/python2.7/dist-packages/cogent/parse/cutg.py:20: 'DbRef' imported but unused
./usr/lib/python2.7/dist-packages/cogent/parse/cutg.py:158: local variable 'count' is assigned to but never used
./usr/lib/python2.7/dist-packages/cogent/parse/pdb.py:7: 'AA_NAMES' imported but unused
./usr/lib/python2.7/dist-packages/cogent/parse/pdb.py:199: local variable 'current_res_id' is assigned to but never used
./usr/lib/python2.7/dist-packages/cogent/parse/blast_xml.py:204: undefined name 'MinimalPsiBlastParser9'
./usr/lib/python2.7/dist-packages/cogent/parse/blast_xml.py:206: undefined name 'MinimalBlastParser9'
./usr/lib/python2.7/dist-packages/cogent/parse/blast_xml.py:215: local variable 'iteration' is assigned to but never used
./usr/lib/python2.7/dist-packages/cogent/parse/fasta.py:6: 'DbRef' imported but unused
./usr/lib/python2.7/dist-packages/cogent/parse/fasta.py:139: local variable 'e' is assigned to but never used
./usr/lib/python2.7/dist-packages/cogent/parse/rnaforester.py:3: 'split' imported but unused
./usr/lib/python2.7/dist-packages/cogent/parse/rnaforester.py:3: 'strip' imported but unused
./usr/lib/python2.7/dist-packages/cogent/parse/rnaforester.py:4: 'Pairs' imported but unused
./usr/lib/python2.7/dist-packages/cogent/parse/rnaforester.py:80: local variable 'result' is assigned to but never used
./usr/lib/python2.7/dist-packages/cogent/parse/rnashapes.py:15: 'split' imported but unused
./usr/lib/python2.7/dist-packages/cogent/parse/rnashapes.py:15: 'strip' imported but unused
./usr/lib/python2.7/dist-packages/cogent/parse/rnashapes.py:16: 'make_trans' imported but unused
./usr/lib/python2.7/dist-packages/cogent/parse/rnashapes.py:17: 'Pairs' imported but unused
./usr/lib/python2.7/dist-packages/cogent/parse/rnashapes.py:56: local variable 'name' is assigned to but never used
./usr/lib/python2.7/dist-packages/cogent/parse/table.py:3: 'cPickle' imported but unused
./usr/lib/python2.7/dist-packages/cogent/parse/table.py:83: local variable 'cast' is assigned to but never used
./usr/lib/python2.7/dist-packages/cogent/parse/table.py:89: local variable 'v' is assigned to but never used
./usr/lib/python2.7/dist-packages/cogent/parse/rfam.py:4: 'strip' imported but unused
./usr/lib/python2.7/dist-packages/cogent/parse/rfam.py:14: 'keep_chars' imported but unused
./usr/lib/python2.7/dist-packages/cogent/parse/rfam.py:14: 'trans_all' imported but unused
./usr/lib/python2.7/dist-packages/cogent/parse/rfam.py:39: redefinition of unused 'Sequence' from line 10
./usr/lib/python2.7/dist-packages/cogent/parse/tree.py:22: 'strip' imported but unused
./usr/lib/python2.7/dist-packages/cogent/parse/flowgram_parser.py:18: 'DelimitedRecordFinder' imported but unused
./usr/lib/python2.7/dist-packages/cogent/parse/cove.py:3: 'split' imported but unused
./usr/lib/python2.7/dist-packages/cogent/parse/cove.py:3: 'strip' imported but unused
./usr/lib/python2.7/dist-packages/cogent/parse/cove.py:5: 'wuss_to_vienna' imported but unused
./usr/lib/python2.7/dist-packages/cogent/parse/mage.py:5: 'SimplexHeader' imported but unused
./usr/lib/python2.7/dist-packages/cogent/parse/cmfinder.py:3: 'make_trans' imported b./usr/lib/python2.7/dist-packages/cogent/parse/dotur.py:51: invalid syntax
^
ut unused
./usr/lib/python2.7/dist-packages/cogent/parse/cmfinder.py:4: 'Pairs' imported but unused
./usr/lib/python2.7/dist-packages/cogent/parse/comrna.py:12: 'make_trans' imported but unused
./usr/lib/python2.7/dist-packages/cogent/parse/flowgram_collection.py:19: 'Sequence' imported but unused
./usr/lib/python2.7/dist-packages/cogent/parse/flowgram_collection.py:323: local variable 'e' is assigned to but never used
./usr/lib/python2.7/dist-packages/cogent/parse/flowgram_collection.py:374: undefined name 'DataError'
./usr/lib/python2.7/dist-packages/cogent/parse/flowgram_collection.py:403: undefined name 'flows'
./usr/lib/python2.7/dist-packages/cogent/parse/flowgram_collection.py:426: undefined name 'flows'
./usr/lib/python2.7/dist-packages/cogent/parse/flowgram_collection.py:451: undefined name 'flows'
./usr/lib/python2.7/dist-packages/cogent/parse/flowgram_collection.py:537: local variable 'result' is assigned to but never used
./usr/lib/python2.7/dist-packages/cogent/parse/bpseq.py:35: 'Vienna' imported but unused
./usr/lib/python2.7/dist-packages/cogent/parse/meme.py:8: 'DelimitedSplitter' imported but unused
./usr/lib/python2.7/dist-packages/cogent/parse/meme.py:42: local variable 'protein_order' is assigned to but never used
./usr/lib/python2.7/dist-packages/cogent/parse/meme.py:96: local variable 'data_dict' is assigned to but never used
./usr/lib/python2.7/dist-packages/cogent/parse/kegg_ko.py:5: 'listdir' imported but unused
./usr/lib/python2.7/dist-packages/cogent/parse/kegg_ko.py:5: 'path' imported but unused
./usr/lib/python2.7/dist-packages/cogent/parse/kegg_ko.py:6: 'OptionParser' imported but unused
./usr/lib/python2.7/dist-packages/cogent/parse/kegg_ko.py:7: 'datetime' imported but unused
./usr/lib/python2.7/dist-packages/cogent/parse/kegg_ko.py:8: 'tarfile' imported but unused
./usr/lib/python2.7/dist-packages/cogent/parse/kegg_ko.py:355: redefinition of unused 'argv' from line 3
./usr/lib/python2.7/dist-packages/cogent/parse/ct.py:26: 'split' imported but unused
./usr/lib/python2.7/dist-packages/cogent/parse/ct.py:49: local variable 'length' is assigned to but never used
./usr/lib/python2.7/dist-packages/cogent/parse/ct.py:67: undefined name 'pairs'
./usr/lib/python2.7/dist-packages/cogent/parse/consan.py:3: 'wuss_to_vienna' imported but unused
./usr/lib/python2.7/dist-packages/cogent/parse/consan.py:24: local variable 'seqs' is assigned to but never used
./usr/lib/python2.7/dist-packages/cogent/parse/pfold.py:3: 'split' imported but unused
./usr/lib/python2.7/dist-packages/cogent/parse/pfold.py:3: 'strip' imported but unused
./usr/lib/python2.7/dist-packages/cogent/parse/pfold.py:4: 'Pairs' imported but unused
./usr/lib/python2.7/dist-packages/cogent/parse/pfold.py:4: 'ViennaStructure' imported but unused
./usr/lib/python2.7/dist-packages/cogent/parse/gcg.py:16: local variable 'alignmentdict' is assigned to but never used
./usr/lib/python2.7/dist-packages/cogent/parse/paml_matrix.py:7: 'substitution_model' imported but unused
./usr/lib/python2.7/dist-packages/cogent/parse/mothur.py:46: local variable 'num_otus' is assigned to but never used
./usr/lib/python2.7/dist-packages/cogent/parse/rdb.py:6: 'strip' imported but unused
./usr/lib/python2.7/dist-packages/cogent/parse/rdb.py:9: 'Sequence' imported but unused
./usr/lib/python2.7/dist-packages/cogent/parse/flowgram.py:280: local variable 'extra_shift' is assigned to but never used
./usr/lib/python2.7/dist-packages/cogent/parse/pknotsrg.py:9: 'split' imported but unused
./usr/lib/python2.7/dist-packages/cogent/parse/pknotsrg.py:9: 'strip' imported but unused
./usr/lib/python2.7/dist-packages/cogent/parse/pknotsrg.py:11: 'Pairs' imported but unused
./usr/lib/python2.7/dist-packages/cogent/parse/ebi.py:7: 'pformat' imported but unused
./usr/lib/python2.7/dist-packages/cogent/parse/ebi.py:8: 'is_empty' imported but unused
./usr/lib/python2.7/dist-packages/cogent/parse/ebi.py:11: 'identity' imported but unused
./usr/lib/python2.7/dist-packages/cogent/parse/ebi.py:84: redefinition of function 'add_item' from line 78
./usr/lib/python2.7/dist-packages/cogent/parse/ebi.py:97: redefinition of function 'add_item' from line 84
./usr/lib/python2.7/dist-packages/cogent/parse/ebi.py:104: redefinition of function 'add_item' from line 97
./usr/lib/python2.7/dist-packages/cogent/parse/ebi.py:206: local variable 'e' is assigned to but never used
./usr/lib/python2.7/dist-packages/cogent/parse/ebi.py:747: local variable 'e' is assigned to but never used
./usr/lib/python2.7/dist-packages/cogent/parse/ebi.py:1376: local variable 'e' is assigned to but never used
./usr/lib/python2.7/dist-packages/cogent/parse/locuslink.py:46: 'strip' imported but unused
./usr/lib/python2.7/dist-packages/cogent/parse/locuslink.py:46: 'maketrans' imported but unused
./usr/lib/python2.7/dist-packages/cogent/parse/locuslink.py:259: 'stdout' imported but unused
./usr/lib/python2.7/dist-packages/cogent/parse/nupack.py:3: 'split' imported but unused
./usr/lib/python2.7/dist-packages/cogent/parse/nupack.py:3: 'strip' imported but unused
./usr/lib/python2.7/dist-packages/cogent/parse/macsim.py:3: 'annotation' imported but unused
./usr/lib/python2.7/dist-packages/cogent/parse/blast.py:6: 'RecordError' imported but unused
./usr/lib/python2.7/dist-packages/cogent/parse/blast.py:390: local variable 'iteration' is assigned to but never used
./usr/lib/python2.7/dist-packages/cogent/parse/unigene.py:7: 'strip' imported but unused
./usr/lib/python2.7/dist-packages/cogent/parse/unigene.py:7: 'maketrans' imported but unused
./usr/lib/python2.7/dist-packages/cogent/parse/gibbs.py:147: local variable 'motif_num' is assigned to but never used
./usr/lib/python2.7/dist-packages/cogent/parse/gibbs.py:153: local variable 'cur_key' is assigned to but never used
./usr/lib/python2.7/dist-packages/cogent/parse/clustal.py:22: 'strip' imported but unused
./usr/lib/python2.7/dist-packages/cogent/parse/column.py:16: 'split' imported but unused
./usr/lib/python2.7/dist-packages/cogent/parse/rnaalifold.py:3: 'split' imported but unused
./usr/lib/python2.7/dist-packages/cogent/parse/rnaalifold.py:3: 'strip' imported but unused
./usr/lib/python2.7/dist-packages/cogent/parse/rnaalifold.py:4: 'Pairs' imported but unused
./usr/lib/python2.7/dist-packages/cogent/parse/foldalign.py:3: 'split' imported but unused
./usr/lib/python2.7/dist-packages/cogent/parse/foldalign.py:4: 'Pairs' imported but unused
./usr/lib/python2.7/dist-packages/cogent/parse/foldalign.py:5: 'adjust_base' imported but unused
./usr/lib/python2.7/dist-packages/cogent/parse/kegg_taxonomy.py:14: 'listdir' imported but unused
./usr/lib/python2.7/dist-packages/cogent/parse/kegg_taxonomy.py:14: 'path' imported but unused
./usr/lib/python2.7/dist-packages/cogent/parse/kegg_taxonomy.py:15: 'OptionParser' imported but unused
./usr/lib/python2.7/dist-packages/cogent/parse/kegg_taxonomy.py:16: 'datetime' imported but unused
./usr/lib/python2.7/dist-packages/cogent/parse/kegg_taxonomy.py:87: redefinition of unused 'argv' from line 12
./usr/lib/python2.7/dist-packages/cogent/parse/record_finder.py:16: 'FieldError' imported but unused
./usr/lib/python2.7/dist-packages/cogent/parse/sprinzl.py:5: 'maketrans' imported but unused
./usr/lib/python2.7/dist-packages/cogent/cluster/nmds.py:9: 'size' imported but unused
./usr/lib/python2.7/dist-packages/cogent/cluster/nmds.py:9: 'trace' imported but unused
./usr/lib/python2.7/dist-packages/cogent/cluster/nmds.py:9: 'transpose' imported but unused
./usr/lib/python2.7/dist-packages/cogent/cluster/nmds.py:9: 'multiply' imported but unused
./usr/lib/python2.7/dist-packages/cogent/cluster/nmds.py:259: redefinition of unused 'size' from line 9
./usr/lib/python2.7/dist-packages/cogent/cluster/nmds.py:265: redefinition of unused 'size' from line 9
./usr/lib/python2.7/dist-packages/cogent/cluster/UPGMA.py:13: 'sum' imported but unused
./usr/lib/python2.7/dist-packages/cogent/cluster/UPGMA.py:13: 'ma' imported but unused
./usr/lib/python2.7/dist-packages/cogent/cluster/UPGMA.py:155: local variable 'row_order' is assigned to but never used
./usr/lib/python2.7/dist-packages/cogent/cluster/procrustes.py:9: 'divide' imported but unused
./usr/lib/python2.7/dist-packages/cogent/cluster/procrustes.py:9: 'subtract' imported but unused
./usr/lib/python2.7/dist-packages/cogent/cluster/approximate_mds.py:90: 'floor' imported but unused
./usr/lib/python2.7/dist-packages/cogent/cluster/approximate_mds.py:92: 'argwhere' imported but unused
./usr/lib/python2.7/dist-packages/cogent/struct/pairs_util.py:16: 'searchsorted' imported but unused
./usr/lib/python2.7/dist-packages/cogent/struct/pairs_util.py:452: local variable 'pred_dict' is assigned to but never used
./usr/lib/python2.7/dist-packages/cogent/struct/dihedral.py:35: 'cos' imported but unused
./usr/lib/python2.7/dist-packages/cogent/struct/rna2d.py:443: local variable 'num_bases' is assigned to but never used
./usr/lib/python2.7/dist-packages/cogent/struct/asa.py:73: undefined name 'lattice_structures'
./usr/lib/python2.7/dist-packages/cogent/struct/asa.py:200: local variable 'models' is assigned to but never used
./usr/lib/python2.7/dist-packages/cogent/struct/annotation.py:3: 'HIERARCHY' imported but unused
./usr/lib/python2.7/dist-packages/cogent/struct/manipulation.py:6: 'HIERARCHY' imported but unused
./usr/lib/python2.7/dist-packages/cogent/motif/k_word.py:8: 'combinations' imported but unused
./usr/lib/python2.7/dist-packages/cogent/evolve/discrete_markov.py:4: 'CalcDefn' imported but unused
./usr/lib/python2.7/dist-packages/cogent/evolve/discrete_markov.py:4: 'ConstDefn' imported but unused
./usr/lib/python2.7/dist-packages/cogent/evolve/discrete_markov.py:4: 'NonParamDefn' imported but unused
./usr/lib/python2.7/dist-packages/cogent/evolve/models.py:77: local variable 'preds' is assigned to but never used
./usr/lib/python2.7/dist-packages/cogent/evolve/motif_prob_model.py:217: local variable 'positions' is assigned to but never used
./usr/lib/python2.7/dist-packages/cogent/evolve/bootstrap.py:26: 'optimisers' imported but unused
./usr/lib/python2.7/dist-packages/cogent/evolve/substitution_model.py:39: 'RateDefn' imported but unused
./usr/lib/python2.7/dist-packages/cogent/evolve/substitution_model.py:636: local variable 'const_param' is assigned to but never used
./usr/lib/python2.7/dist-packages/cogent/evolve/substitution_model.py:668: local variable 'const_param' is assigned to but never used
./usr/lib/python2.7/dist-packages/cogent/evolve/substitution_calculation.py:8: 'CallDefn' imported but unused
./usr/lib/python2.7/dist-packages/cogent/evolve/substitution_calculation.py:8: 'ConstDefn' imported but unused
./usr/lib/python2.7/dist-packages/cogent/evolve/substitution_calculation.py:8: 'PartitionDefn' imported but unused
./usr/lib/python2.7/dist-packages/cogent/evolve/substitution_calculation.py:8: 'NonParamDefn' imported but unused
./usr/lib/python2.7/dist-packages/cogent/evolve/substitution_calculation.py:8: 'GammaDefn' imported but unused
./usr/lib/python2.7/dist-packages/cogent/evolve/substitution_calculation.py:8: 'CalcDefn' imported but unused
./usr/lib/python2.7/dist-packages/cogent/evolve/substitution_calculation.py:8: 'ProductDefn' imported but unused
./usr/lib/python2.7/dist-packages/cogent/evolve/substitution_calculation.py:8: 'WeightedPartitionDefn' imported but unused
./usr/lib/python2.7/dist-packages/cogent/evolve/substitution_calculation.py:8: 'SelectForDimension' imported but unused
./usr/lib/python2.7/dist-packages/cogent/evolve/substitution_calculation.py:8: 'MonotonicDefn' imported but unused
./usr/lib/python2.7/dist-packages/cogent/evolve/substitution_calculation.py:12: 'chooseFastExponentiators' imported but unused
./usr/lib/python2.7/dist-packages/cogent/evolve/substitution_calculation.py:12: 'FastExponentiator' imported but unused
./usr/lib/python2.7/dist-packages/cogent/evolve/likelihood_calculation.py:15: '_FuncDefn' imported but unused
./usr/lib/python2.7/dist-packages/cogent/evolve/coevolution.py:56: 'splitext' imported but unused
./usr/lib/python2.7/dist-packages/cogent/evolve/coevolution.py:58: 'sqrt' imported but unused
./usr/lib/python2.7/dist-packages/cogent/evolve/coevolution.py:58: 'mean' imported but unused
./usr/lib/python2.7/dist-packages/cogent/evolve/coevolution.py:58: 'abs' import./usr/lib/python2.7/dist-packages/cogent/phylo/least_squares.py:82: invalid syntax
^
ed but unused
./usr/lib/python2.7/dist-packages/cogent/evolve/coevolution.py:58: 'transpose' imported but unused
./usr/lib/python2.7/dist-packages/cogent/evolve/coevolution.py:58: 'put' imported but unused
./usr/lib/python2.7/dist-packages/cogent/evolve/coevolution.py:58: 'float64' imported but unused
./usr/lib/python2.7/dist-packages/cogent/evolve/coevolution.py:58: 'tril' imported but unused
./usr/lib/python2.7/dist-packages/cogent/evolve/coevolution.py:58: 'reshape' imported but unused
./usr/lib/python2.7/dist-packages/cogent/evolve/coevolution.py:58: 'take' imported but unused
./usr/lib/python2.7/dist-packages/cogent/evolve/coevolution.py:58: 'exp' imported but unused
./usr/lib/python2.7/dist-packages/cogent/evolve/coevolution.py:66: 'Profile' imported but unused
./usr/lib/python2.7/dist-packages/cogent/evolve/coevolution.py:67: 'Alphabet' imported but unused
./usr/lib/python2.7/dist-packages/cogent/evolve/coevolution.py:73: 'TreeError' imported but unused
./usr/lib/python2.7/dist-packages/cogent/evolve/coevolution.py:74: 'seqs_from_fasta' imported but unused
./usr/lib/python2.7/dist-packages/cogent/evolve/coevolution.py:509: redefinition of unused 'e' from line 58
./usr/lib/python2.7/dist-packages/cogent/evolve/coevolution.py:509: local variable 'e' is assigned to but never used
./usr/lib/python2.7/dist-packages/cogent/evolve/coevolution.py:643: local variable 'num_positions' is assigned to but never used
./usr/lib/python2.7/dist-packages/cogent/evolve/coevolution.py:644: local variable 'num_seqs' is assigned to but never used
./usr/lib/python2.7/dist-packages/cogent/evolve/coevolution.py:758: local variable 'num_seqs' is assigned to but never used
./usr/lib/python2.7/dist-packages/cogent/evolve/coevolution.py:824: local variable 'num_seqs' is assigned to but never used
./usr/lib/python2.7/dist-packages/cogent/evolve/coevolution.py:1448: local variable 'e' is assigned to but never used
./usr/lib/python2.7/dist-packages/cogent/evolve/coevolution.py:2095: redefinition of function 'is_not_null_value' from line 2092
./usr/lib/python2.7/dist-packages/cogent/evolve/coevolution.py:2196: local variable 'aln' is assigned to but never used
./usr/lib/python2.7/dist-packages/cogent/evolve/coevolution.py:2209: local variable 'tree' is assigned to but never used
./usr/lib/python2.7/dist-packages/cogent/evolve/coevolution.py:2317: local variable 'extension' is assigned to but never used
./usr/lib/python2.7/dist-packages/cogent/phylo/distance.py:4: 'warning' imported but unused
./usr/lib/python2.7/dist-packages/cogent/phylo/distance.py:6: 'LoadSeqs' imported but unused
./usr/lib/python2.7/dist-packages/cogent/phylo/compatibility.py:466: 'sys' imported but unused
./usr/lib/python2.7/dist-packages/cogent/phylo/maximum_likelihood.py:4: 'exp' imported but unused
./usr/lib/python2.7/dist-packages/cogent/phylo/maximum_likelihood.py:6: 'LoadTrees' imported but unused
./usr/lib/python2.7/dist-packages/cogent/phylo/tree_collection.py:65: undefined name 'exp'
./usr/lib/python2.7/dist-packages/cogent/db/ncbi.py:8: 'urlopen' imported but unused
./usr/lib/python2.7/dist-packages/cogent/db/ncbi.py:8: 'urlretrieve' imported but unused
./usr/lib/python2.7/dist-packages/cogent/db/ncbi.py:13: 'never_ignore' imported but unused
./usr/lib/python2.7/dist-packages/cogent/db/ensembl/compara.py:7: 'get_latest_release' imported but unused
./usr/lib/python2.7/dist-packages/cogent/db/ensembl/compara.py:9: 'Coordinate' imported but unused
./usr/lib/python2.7/dist-packages/cogent/db/ensembl/region.py:10: 'location_query' imported but unused
./usr/lib/python2.7/dist-packages/cogent/db/ensembl/__init__.py:5: 'NoItemError' imported but unused
./usr/lib/python2.7/dist-packages/cogent/db/ensembl/host.py:5: 'Table' imported but unused
./usr/lib/python2.7/dist-packages/cogent/db/ensembl/host.py:8: 'asserted_one' imported but unused
./usr/lib/python2.7/dist-packages/cogent/db/ensembl/related_region.py:1: 'pprint' imported but unused
./usr/lib/python2.7/dist-packages/cogent/db/ensembl/related_region.py:8: 'NoItemError' imported but unused
./usr/lib/python2.7/dist-packages/cogent/db/ensembl/related_region.py:9: 'location_query' imported but unused
./usr/lib/python2.7/dist-packages/cogent/db/ensembl/related_region.py:10: 'Species' imported but unused
./usr/lib/python2.7/dist-packages/cogent/db/ensembl/genome.py:319: undefined name 'coord'
./usr/lib/python2.7/dist-packages/cogent/db/ensembl/genome.py:319: local variable 'coord' is assigned to but never used
./usr/lib/python2.7/dist-packages/cogent/db/ensembl/genome.py:354: local variable 'feature_coord_levels' is assigned to but never used
./usr/lib/python2.7/dist-packages/cogent/db/ensembl/util.py:1: 're' imported but unused
./usr/lib/python2.7/dist-packages/cogent/db/ensembl/util.py:2: 'create_engine' imported but unused
./usr/lib/python2.7/dist-packages/cogent/db/ensembl/util.py:2: 'Table' imported but unused
./usr/lib/python2.7/dist-packages/cogent/db/ensembl/util.py:2: 'MetaData' imported but unused
./usr/lib/python2.7/dist-packages/cogent/db/ensembl/sequence.py:4: 'Map' imported but unused
./usr/lib/python2.7/dist-packages/cogent/db/ensembl/sequence.py:6: 'Species' imported but unused
./usr/lib/python2.7/dist-packages/cogent/db/ensembl/assembly.py:3: 'Map' imported but unused
./usr/lib/python2.7/dist-packages/cogent/db/ensembl/assembly.py:6: 'DbConnection' imported but unused
./usr/lib/python2.7/dist-packages/cogent/core/entity.py:22: 'gt' imported but unused
./usr/lib/python2.7/dist-packages/cogent/core/entity.py:22: 'ne' imported but unused
./usr/lib/python2.7/dist-packages/cogent/core/entity.py:22: 'ge' imported but unused
./usr/lib/python2.7/dist-packages/cogent/core/entity.py:22: 'le' imported but unused
./usr/lib/python2.7/dist-packages/cogent/core/entity.py:22: 'lt' imported but unused
./usr/lib/python2.7/dist-packages/cogent/core/entity.py:22: 'is_' imported but unused
./usr/lib/python2.7/dist-packages/cogent/core/entity.py:22: 'or_' imported but unused
./usr/lib/python2.7/dist-packages/cogent/core/entity.py:22: 'is_not' imported but unused
./usr/lib/python2.7/dist-packages/cogent/core/entity.py:22: 'and_' imported but unused
./usr/lib/python2.7/dist-packages/cogent/core/tree.py:34: 'InverseDict' imported but unused
./usr/lib/python2.7/dist-packages/cogent/core/usage.py:14: 'mean' imported but unused
./usr/lib/python2.7/dist-packages/cogent/core/alignment.py:35: 'logical_or' imported but unused
./usr/lib/python2.7/dist-packages/cogent/core/alignment.py:35: 'zeros' imported but unused
./usr/lib/python2.7/dist-packages/cogent/core/alignment.py:350: local variable 'result' is assigned to but never used
./usr/lib/python2.7/dist-packages/cogent/core/alignment.py:520: local variable 'e' is assigned to but never used
./usr/lib/python2.7/dist-packages/cogent/core/alignment.py:654: local variable 'item_lookup' is assigned to but never used
./usr/lib/python2.7/dist-packages/cogent/core/alignment.py:721: redefinition of function 'f' from line 717
./usr/lib/python2.7/dist-packages/cogent/core/alignment.py:1246: local variable 'max_run' is assigned to but never used
./usr/lib/python2.7/dist-packages/cogent/core/alignment.py:2020: local variable 'max_label_length' is assigned to but never used
./usr/lib/python2.7/dist-packages/cogent/core/alignment.py:2176: undefined name 'CodonSequenceGap'
./usr/lib/python2.7/dist-packages/cogent/core/alignment.py:2180: undefined name 'random'
./usr/lib/python2.7/dist-packages/cogent/core/moltype.py:27: 'if_' imported but unused
./usr/lib/python2.7/dist-packages/cogent/core/moltype.py:30: 'ModelNucleicAcidSequence' imported but unused
./usr/lib/python2.7/dist-packages/cogent/core/moltype.py:46: 'uint16' imported but unused
./usr/lib/python2.7/dist-packages/cogent/core/moltype.py:46: 'arange' imported but unused
./usr/lib/python2.7/dist-packages/cogent/core/moltype.py:46: 'asarray' imported but unused
./usr/lib/python2.7/dist-packages/cogent/core/moltype.py:46: 'uint32' imported but unused
./usr/lib/python2.7/dist-packages/cogent/core/moltype.py:46: 'transpose' imported but unused
./usr/lib/python2.7/dist-packages/cogent/core/moltype.py:46: 'remainder' imported but unused
./usr/lib/python2.7/dist-package./usr/lib/python2.7/dist-packages/cogent/format/rna_struct.py:449: invalid syntax
^
s/cogent/core/moltype.py:46: 'newaxis' imported but unused
./usr/lib/python2.7/dist-packages/cogent/core/moltype.py:46: 'array' imported but unused
./usr/lib/python2.7/dist-packages/cogent/core/moltype.py:46: 'zeros' imported but unused
./usr/lib/python2.7/dist-packages/cogent/core/moltype.py:46: 'uint8' imported but unused
./usr/lib/python2.7/dist-packages/cogent/core/moltype.py:46: 'ravel' imported but unused
./usr/lib/python2.7/dist-packages/cogent/core/moltype.py:46: 'take' imported but unused
./usr/lib/python2.7/dist-packages/cogent/core/moltype.py:46: 'fromstring' imported but unused
./usr/lib/python2.7/dist-packages/cogent/core/moltype.py:46: 'sum' imported but unused
./usr/lib/python2.7/dist-packages/cogent/core/moltype.py:52: 'translate' imported but unused
./usr/lib/python2.7/dist-packages/cogent/core/moltype.py:637: local variable 'curr' is assigned to but never used
./usr/lib/python2.7/dist-packages/cogent/core/moltype.py:724: undefined name 'first_index_in_set'
./usr/lib/python2.7/dist-packages/cogent/core/moltype.py:733: undefined name 'first_index_in_set'
./usr/lib/python2.7/dist-packages/cogent/core/alphabet.py:22: 're' imported but unused
./usr/lib/python2.7/dist-packages/cogent/core/alphabet.py:23: 'string' imported but unused
./usr/lib/python2.7/dist-packages/cogent/core/alphabet.py:24: redefinition of unused 'take' from line 24
./usr/lib/python2.7/dist-packages/cogent/core/alphabet.py:24: 'remainder' imported but unused
./usr/lib/python2.7/dist-packages/cogent/core/alphabet.py:546: local variable 'result' is assigned to but never used
./usr/lib/python2.7/dist-packages/cogent/core/profile.py:11: 'concatenate' imported but unused
./usr/lib/python2.7/dist-packages/cogent/core/profile.py:11: 'log' imported but unused
./usr/lib/python2.7/dist-packages/cogent/core/profile.py:11: 'asarray' imported but unused
./usr/lib/python2.7/dist-packages/cogent/core/profile.py:11: 'reshape' imported but unused
./usr/lib/python2.7/dist-packages/cogent/core/profile.py:11: 'alltrue' imported but unused
./usr/lib/python2.7/dist-packages/cogent/core/profile.py:11: 'ravel' imported but unused
./usr/lib/python2.7/dist-packages/cogent/core/profile.py:11: 'sort' imported but unused
./usr/lib/python2.7/dist-packages/cogent/core/profile.py:11: 'uint8' imported but unused
./usr/lib/python2.7/dist-packages/cogent/core/profile.py:11: 'put' imported but unused
./usr/lib/python2.7/dist-packages/cogent/core/profile.py:11: 'isfinite' imported but unused
./usr/lib/python2.7/dist-packages/cogent/core/profile.py:89: local variable 'sums' is assigned to but never used
./usr/lib/python2.7/dist-packages/cogent/core/profile.py:92: local variable 'tfs' is assigned to but never used
./usr/lib/python2.7/dist-packages/cogent/core/profile.py:207: local variable 'max_col_idx' is assigned to but never used
./usr/lib/python2.7/dist-packages/cogent/core/profile.py:397: local variable 'sl' is assigned to but never used
./usr/lib/python2.7/dist-packages/cogent/core/sequence.py:15: 'Feature' imported but unused
./usr/lib/python2.7/dist-packages/cogent/core/sequence.py:16: 'keep_chars' imported but unused
./usr/lib/python2.7/dist-packages/cogent/core/sequence.py:16: 'per_longest' imported but unused
./usr/lib/python2.7/dist-packages/cogent/core/sequence.py:1008: undefined name 'm'
./usr/lib/python2.7/dist-packages/cogent/core/bitvector.py:254: local variable 'bits' is assigned to but never used
./usr/lib/python2.7/dist-packages/cogent/core/bitvector.py:642: local variable 'TypeError' is assigned to but never used
./usr/lib/python2.7/dist-packages/cogent/format/table.py:91: local variable 'th' is assigned to but never used
./usr/lib/python2.7/dist-packages/cogent/format/table.py:96: local variable 'td' is assigned to but never used
./usr/lib/python2.7/dist-packages/cogent/format/table.py:445: local variable 'num_row' is assigned to but never used
./usr/lib/python2.7/dist-packages/cogent/format/mage.py:19: 'fabs' imported but unused
./usr/lib/python2.7/dist-packages/cogent/format/mage.py:22: 'extract_delimited' imported but unused
./usr/lib/python2.7/dist-pac./usr/lib/python2.7/dist-packages/cogent/format/stockholm.py:93: unexpected indent
^
./usr/lib/python2.7/dist-packages/cogent/format/clustal.py:69: unexpected indent
^
./usr/lib/python2.7/dist-packages/cogent/align/partial_order_graph.py:221: invalid syntax
^
kages/cogent/format/alignment.py:33: undefined name 'FileFormatError'
./usr/lib/python2.7/dist-packages/cogent/format/alignment.py:141: undefined name 'warnings'
./usr/lib/python2.7/dist-packages/cogent/format/pdb_color.py:54: undefined name 'chain'
./usr/lib/python2.7/dist-packages/cogent/format/pdb_color.py:195: undefined name 'cmd'
./usr/lib/python2.7/dist-packages/cogent/format/pdb_color.py:203: undefined name 'cmd'
./usr/lib/python2.7/dist-packages/cogent/format/pdb_color.py:210: undefined name 'cmd'
./usr/lib/python2.7/dist-packages/cogent/format/motif.py:13: 'DNA' imported but unused
./usr/lib/python2.7/dist-packages/cogent/format/motif.py:14: 'Alignment' imported but unused
./usr/lib/python2.7/dist-packages/cogent/format/motif.py:944: local variable 'e' is assigned to but never used
./usr/lib/python2.7/dist-packages/cogent/format/motif.py:1592: local variable 'mod_id_map' is assigned to but never used
./usr/lib/python2.7/dist-packages/cogent/format/motif.py:1722: local variable 'mod_id_map' is assigned to but never used
./usr/lib/python2.7/dist-packages/cogent/align/dp_calculation.py:4: 'PositiveParamDefn' imported but unused
./usr/lib/python2.7/dist-packages/cogent/align/dp_calculation.py:8: 'numpy' imported but unused
./usr/lib/python2.7/dist-packages/cogent/align/align.py:8: 'sys' imported but unused
./usr/lib/python2.7/dist-packages/cogent/align/pairwise.py:202: undefined name 'seq'
./usr/lib/python2.7/dist-packages/cogent/align/pairwise.py:601: local variable 'rr' is assigned to but never used
./usr/lib/python2.7/dist-packages/cogent/align/indel_positions.py:14: local variable 'full_aligned_positions' is assigned to but never used
./usr/lib/python2.7/dist-packages/cogent/align/indel_positions.py:98: local variable 'l' is assigned to but never used
./usr/lib/python2.7/dist-packages/cogent/align/indel_positions.py:230: undefined name 'length'
./usr/lib/python2.7/dist-packages/cogent/align/__init__.py:3: 'make_dna_scoring_dict' imported but unused
./usr/lib/python2.7/dist-packages/cogent/align/__init__.py:3: '_align_pairwise' imported but unused
./usr/lib/python2.7/dist-packages/cogent/align/__init__.py:3: 'local_pairwise' imported but unused
./usr/lib/python2.7/dist-packages/cogent/align/__init__.py:3: 'global_pairwise' imported but unused
./usr/lib/python2.7/dist-packages/cogent/align/__init__.py:3: 'classic_align_pairwise' imported but unused
./usr/lib/python2.7/dist-packages/cogent/align/weights/methods.py:5: 'choice' imported but unused
./usr/lib/python2.7/dist-packages/cogent/align/weights/methods.py:12: 'DndParser' imported but unused
./usr/lib/python2.7/dist-packages/cogent/align/weights/methods.py:14: 'RNA_ORDER' imported but unused
./usr/lib/python2.7/dist-packages/cogent/align/weights/methods.py:432: redefinition of unused 'Alignment' from line 11
./usr/lib/python2.7/dist-packages/cogent/align/weights/util.py:7: 'asarray' imported but unused
./usr/lib/python2.7/dist-packages/cogent/align/weights/util.py:7: 'sqrt' imported but unused
./usr/lib/python2.7/dist-packages/cogent/align/weights/util.py:7: 'take' imported but unused
./usr/lib/python2.7/dist-packages/cogent/align/weights/util.py:13: 'Alignment' imported but unused
This report was generated on Fri, 10 Jun 2011 06:43:02 +0000, based on results by pyflakes 0.4.0-1