Automated Code Analysis

pyflakes analysis of python-biopython_1.57-1_i386.deb

./usr/share/pyshared/Bio/DocSQL.py:144: local variable 'message' is assigned to but never used
./usr/share/pyshared/Bio/pairwise2.py:157: local variable 'x' is assigned to but never used
./usr/share/pyshared/Bio/ParserSupport.py:30: 'traceback' imported but unused
./usr/share/pyshared/Bio/ParserSupport.py:31: 'from types import *' used; unable to detect undefined names
./usr/share/pyshared/Bio/HotRand.py:69: undefined name 'hex_convert'
./usr/share/pyshared/Bio/_py3k.py:28: undefined name 'bytes'
./usr/share/pyshared/Bio/_py3k.py:48: redefinition of function '_as_unicode' from line 15
./usr/share/pyshared/Bio/_py3k.py:55: redefinition of function '_as_bytes' from line 23
./usr/share/pyshared/Bio/_py3k.py:61: redefinition of function '_is_int_or_long' from line 35
./usr/share/pyshared/Bio/Compass/__init__.py:224: 'from Bio.ParserSupport import *' used; unable to detect undefined names
./usr/share/pyshared/Bio/Wise/dnal.py:18: 'os' imported but unused
./usr/share/pyshared/Bio/Motif/_Motif.py:10: 'random' imported but unused
./usr/share/pyshared/Bio/Motif/_Motif.py:477: local variable 's' is assigned to but never used
./usr/share/pyshared/Bio/Motif/_Motif.py:526: local variable 's' is assigned to but never used
./usr/share/pyshared/Bio/Motif/__init__.py:15: 'ScoreDistribution' imported but unused
./usr/share/pyshared/Bio/Motif/Thresholds.py:8: 'random' imported but unused
./usr/share/pyshared/Bio/Motif/Thresholds.py:8: 'math' imported but unused
./usr/share/pyshared/Bio/Motif/Parsers/MAST.py:128: undefined name 'sequence'
./usr/share/pyshared/Bio/Motif/Parsers/MEME.py:10: 'sqrt' imported but unused
./usr/share/pyshared/Bio/Motif/Parsers/MEME.py:365: 'from Bio.ParserSupport import *' used; unable to detect undefined names
./usr/share/pyshared/Bio/Motif/Parsers/AlignAce.py:58: 'from Bio.ParserSupport import *' used; unable to detect undefined names
./usr/share/pyshared/Bio/Motif/Applications/__init__.py:7: 'AlignAceCommandline' imported but unused
./usr/share/pyshared/Bio/Motif/Applications/__init__.py:8: 'CompareAceCommandline' imported but unused
./usr/share/pyshared/Bio/Nexus/Nexus.py:19: 'NodeData' imported but unused
./usr/share/pyshared/Bio/Nexus/Nexus.py:115: local variable 'skip' is assigned to but never used
./usr/share/pyshared/Bio/Nexus/Nexus.py:920: local variable 'dummy' is assigned to but never used
./usr/share/pyshared/Bio/Nexus/Nexus.py:928: local variable 'open' is assigned to but never used
./usr/share/pyshared/Bio/Nexus/Nexus.py:935: local variable 'closing' is assigned to but never used
./usr/share/pyshared/Bio/Nexus/Nexus.py:1062: local variable 'close' is assigned to but never used
./usr/share/pyshared/Bio/Nexus/Nexus.py:1091: local variable 'hyphen' is assigned to but never used
./usr/share/pyshared/Bio/Nexus/Nexus.py:1095: local variable 'backslash' is assigned to but never used
./usr/share/pyshared/Bio/Nexus/Nexus.py:1734: redefinition of function '_get_command_lines' from line 1729
./usr/share/pyshared/Bio/Nexus/Trees.py:15: 'copy' imported but unused
./usr/share/pyshared/Bio/Nexus/Trees.py:791: local variable 'max_support' is assigned to but never used
./usr/share/pyshared/Bio/Affy/CelFile.py:77: 'from numpy import *' used; unable to detect undefined names
./usr/share/pyshared/Bio/Graphics/BasicChromosome.py:29: 'os' imported but unused
./usr/share/pyshared/Bio/Graphics/BasicChromosome.py:32: 'canvas' imported but unused
./usr/share/pyshared/Bio/Graphics/BasicChromosome.py:38: 'renderPS' imported but unused
./usr/share/pyshared/Bio/Graphics/BasicChromosome.py:38: 'renderPDF' imported but unused
./usr/share/pyshared/Bio/Graphics/__init__.py:12: redefinition of unused 'r' from line 11
./usr/share/pyshared/Bio/Graphics/__init__.py:45: redefinition of unused 'renderPM' from line 40
./usr/share/pyshared/Bio/Graphics/Comparative.py:8: 'canvas' imported but unused
./usr/share/pyshared/Bio/Graphics/Comparative.py:14: 'Group' imported but unused
./usr/share/pyshared/Bio/Graphics/Comparative.py:15: 'renderPS' imported but unused
./usr/share/pyshared/Bio/Graphics/Comparative.py:15: 'renderPDF' imported but unused
./usr/share/pyshared/Bio/Graphics/Comparative.py:16: 'from reportlab.graphics.charts.markers import *' used; unable to detect undefined names
./usr/share/pyshared/Bio/Graphics/Distribution.py:14: 'canvas' imported but unused
./usr/share/pyshared/Bio/Graphics/Distribution.py:23: 'renderPS' imported but unused
./usr/share/pyshared/Bio/Graphics/Distribution.py:23: 'renderPDF' imported but unused
./usr/share/pyshared/Bio/Graphics/GenomeDiagram/_Track.py:381: 'SeqFeature' imported but unused
./usr/share/pyshared/Bio/Graphics/GenomeDiagram/_Track.py:382: redefinition of unused 'FeatureSet' from line 34
./usr/share/pyshared/Bio/Graphics/GenomeDiagram/_Track.py:383: redefinition of unused 'GraphSet' from line 35
./usr/share/pyshared/Bio/Graphics/GenomeDiagram/_FeatureSet.py:37: '_fontdata' imported but unused
./usr/share/pyshared/Bio/Graphics/GenomeDiagram/_FeatureSet.py:38: 'colors' imported but unused
./usr/share/pyshared/Bio/Graphics/GenomeDiagram/_FeatureSet.py:151: local variable 'changed' is assigned to but never used
./usr/share/pyshared/Bio/Graphics/GenomeDiagram/_FeatureSet.py:284: 'SeqFeature' imported but unused
./usr/share/pyshared/Bio/Graphics/GenomeDiagram/_Feature.py:32: 'string' imported but unused
./usr/share/pyshared/Bio/Graphics/GenomeDiagram/_Diagram.py:32: 'renderSVG' imported but unused
./usr/share/pyshared/Bio/Graphics/GenomeDiagram/_Diagram.py:32: 'renderPS' imported but unused
./usr/share/pyshared/Bio/Graphics/GenomeDiagram/_Diagram.py:32: 'renderPDF' imported but unused
./usr/share/pyshared/Bio/Graphics/GenomeDiagram/_Diagram.py:37: redefinition of unused 'renderPM' from line 34
./usr/share/pyshared/Bio/Graphics/GenomeDiagram/_Diagram.py:38: 'pagesizes' imported but unused
./usr/share/pyshared/Bio/Graphics/GenomeDiagram/_Diagram.py:46: 'sys' imported but unused
./usr/share/pyshared/Bio/Graphics/GenomeDiagram/__init__.py:15: 'Diagram' imported but unused
./usr/share/pyshared/Bio/Graphics/GenomeDiagram/__init__.py:16: 'Track' imported but unused
./usr/share/pyshared/Bio/Graphics/GenomeDiagram/__init__.py:17: 'FeatureSet' imported but unused
./usr/share/pyshared/Bio/Graphics/GenomeDiagram/__init__.py:18: 'GraphSet' imported but unused
./usr/share/pyshared/Bio/Graphics/GenomeDiagram/_CircularDrawer.py:30: 'from reportlab.graphics.shapes import *' used; unable to detect undefined names
./usr/share/pyshared/Bio/Graphics/GenomeDiagram/_CircularDrawer.py:32: '_fontdata' imported but unused
./usr/share/pyshared/Bio/Graphics/GenomeDiagram/_CircularDrawer.py:40: 'asin' imported but unused
./usr/share/pyshared/Bio/Graphics/GenomeDiagram/_CircularDrawer.py:40: 'ceil' imported but unused
./usr/share/pyshared/Bio/Graphics/GenomeDiagram/_CircularDrawer.py:575: local variable 'data' is assigned to but never used
./usr/share/pyshared/Bio/Graphics/GenomeDiagram/_CircularDrawer.py:632: local variable 'midval' is assigned to but never used
./usr/share/pyshared/Bio/Graphics/GenomeDiagram/_CircularDrawer.py:634: local variable 'trackheight' is assigned to but never used
./usr/share/pyshared/Bio/Graphics/GenomeDiagram/_LinearDrawer.py:30: 'from reportlab.graphics.shapes import *' used; unable to detect undefined names
./usr/share/pyshared/Bio/Graphics/GenomeDiagram/_LinearDrawer.py:602: local variable 'tctr' is assigned to but never used
./usr/share/pyshared/Bio/Graphics/GenomeDiagram/_LinearDrawer.py:904: local variable 'tempval' is assigned to but never used
./usr/share/pyshared/Bio/Graphics/GenomeDiagram/_LinearDrawer.py:937: local variable 'midval' is assigned to but never used
./usr/share/pyshared/Bio/Graphics/GenomeDiagram/_LinearDrawer.py:939: local variable 'trackheight' is assigned to but never used
./usr/share/pyshared/Bio/Graphics/GenomeDiagram/_LinearDrawer.py:1018: local variable 'data' is assigned to but never used
./usr/share/pyshared/Bio/Graphics/GenomeDiagram/_AbstractDrawer.py:45: 'from reportlab.graphics.shapes import *' used; unable to detect undefined names
./usr/share/pyshared/Bio/Application/__init__.py:23: 'StringIO' imported but unused
./usr/share/pyshared/Bio/Application/__init__.py:32: redefinition of unused '_ProcessCalledError' from line 29
./usr/share/pyshared/Bio/Application/__init__.py:34: 'File' imported but unused
./usr/share/pyshared/Bio/PopGen/Async/Local.py:12: 'FileRetriever' imported but unused
./usr/share/pyshared/Bio/PopGen/SimCoal/Async.py:11: 'debug' imported but unused
./usr/share/pyshared/Bio/PopGen/SimCoal/Async.py:12: 'exit' imported but unused
./usr/share/pyshared/Bio/PopGen/SimCoal/Async.py:14: 'tarfile' imported but unused
./usr/share/pyshared/Bio/PopGen/SimCoal/Async.py:15: 'tempfile' imported but unused
./usr/share/pyshared/Bio/PopGen/SimCoal/Async.py:17: 'SimCoalController' imported but unused
./usr/share/pyshared/Bio/PopGen/SimCoal/Cache.py:9: 'debug' imported but unused
./usr/share/pyshared/Bio/PopGen/SimCoal/Cache.py:10: 'exit' imported but unused
./usr/share/pyshared/Bio/PopGen/SimCoal/Cache.py:13: 'tempfile' imported but unused
./usr/share/pyshared/Bio/PopGen/SimCoal/Template.py:6: 'sqrt' imported but unused
./usr/share/pyshared/Bio/PopGen/SimCoal/Template.py:7: 'exit' imported but unused
./usr/share/pyshared/Bio/PopGen/SimCoal/Template.py:7: 'argv' imported but unused
./usr/share/pyshared/Bio/PopGen/SimCoal/Template.py:8: 'mkdir' imported but unused
./usr/share/pyshared/Bio/PopGen/SimCoal/Controller.py:13: 'tempfile' imported but unused
./usr/share/pyshared/Bio/PopGen/SimCoal/Controller.py:14: 'copyfile' imported but unused
./usr/share/pyshared/Bio/PopGen/SimCoal/Controller.py:15: 'debug' imported but unused
./usr/share/pyshared/Bio/PopGen/FDist/__init__.py:97: 'from Bio.ParserSupport import *' used; unable to detect undefined names
./usr/share/pyshared/Bio/PopGen/FDist/Controller.py:17: 'tempfile' imported but unused
./usr/share/pyshared/Bio/PopGen/FDist/Controller.py:19: 'copyfile' imported but unused
./usr/share/pyshared/Bio/PopGen/FDist/Controller.py:20: 'random' imported but unused
./usr/share/pyshared/Bio/PopGen/FDist/Controller.py:54: local variable 'exec_counts' is assigned to but never used
./usr/share/pyshared/Bio/PopGen/FDist/Controller.py:91: local variable 'curr_dir' is assigned to but never used
./usr/share/pyshared/Bio/PopGen/FDist/Controller.py:233: local variable 'old_fst' is assigned to but never used
./usr/share/pyshared/Bio/PopGen/FDist/Controller.py:268: local variable 'curr_dir' is assigned to but never used
./usr/share/pyshared/Bio/PopGen/FDist/Utils.py:7: 'os' imported but unused
./usr/share/pyshared/Bio/PopGen/FDist/Utils.py:8: 'GenePop' imported but unused
./usr/share/pyshared/Bio/PopGen/GenePop/LargeFileParser.py:20: 'deepcopy' imported but unused
./usr/share/pyshared/Bio/PopGen/GenePop/FileParser.py:24: 'deepcopy' imported but unused
./usr/share/pyshared/Bio/PopGen/GenePop/FileParser.py:176: local variable 'marker_len' is assigned to but never used
./usr/share/pyshared/Bio/PopGen/GenePop/Controller.py:16: 'subprocess' imported but unused
./usr/share/pyshared/Bio/PopGen/GenePop/Controller.py:17: 'sys' imported but unused
./usr/share/pyshared/Bio/PopGen/GenePop/Controller.py:18: 'tempfile' imported but unused
./usr/share/pyshared/Bio/PopGen/GenePop/Controller.py:20: '_Option' imported but unused
./usr/share/pyshared/Bio/PopGen/GenePop/Utils.py:7: 'GenePop' imported but unused
./usr/share/pyshared/Bio/PopGen/GenePop/Utils.py:8: 'deepcopy' imported but unused
./usr/share/pyshared/Bio/FSSP/__init__.py:15: 'Generic' imported but unused
./usr/share/pyshared/Bio/FSSP/__init__.py:16: 'Alphabet' imported but unused
./usr/share/pyshared/Bio/FSSP/FSSPTools.py:5: 'time' imported but unused
./usr/share/pyshared/Bio/Align/Applications/_TCoffee.py:8: '_Argument' imported but unused
./usr/share/pyshared/Bio/Align/Applications/_Probcons.py:8: 'types' imported but unused
./usr/share/pyshared/Bio/Align/Applications/__init__.py:6: 'MuscleCommandline' imported but unused
./usr/share/pyshared/Bio/Align/Applications/__init__.py:7: 'ClustalwCommandline' imported but unused
./usr/share/pyshared/Bio/Align/Applications/__init__.py:8: 'PrankCommandline' imported but unused
./usr/share/pyshared/Bio/Align/Applications/__init__.py:9: 'MafftCommandline' imported but unused
./usr/share/pyshared/Bio/Align/Applications/__init__.py:10: 'DialignCommandline' imported but unused
./usr/share/pyshared/Bio/Align/Applications/__init__.py:11: 'ProbconsCommandline' imported but unused
./usr/share/pyshared/Bio/Align/Applications/__init__.py:12: 'TCoffeeCommandline' imported but unused
./usr/share/pyshared/Bio/Align/Applications/_Prank.py:110: undefined name 'bytes'
./usr/share/pyshared/Bio/SVDSuperimposer/__init__.py:8: 'from SVDSuperimposer import *' used; unable to detect undefined names
./usr/share/pyshared/Bio/ExPASy/ScanProsite.py:2: 'expatreader' imported but unused
./usr/share/pyshared/Bio/ExPASy/ScanProsite.py:2: 'make_parser' imported but unused
./usr/share/pyshared/Bio/ExPASy/ScanProsite.py:4: 'SAXParseException' imported but unused
./usr/share/pyshared/Bio/UniGene/UniGene.py:21: 'operator' imported but unused
./usr/share/pyshared/Bio/UniGene/UniGene.py:22: 'urllib' imported but unused
./usr/share/pyshared/Bio/UniGene/__init__.py:328: 'from Bio.ParserSupport import *' used; unable to detect undefined names
./usr/share/pyshared/Bio/UniGene/__init__.py:558: redefinition of function 'GENE_ID' from line 554
./usr/share/pyshared/Bio/HMM/DynamicProgramming.py:130: local variable 'first_letter' is assigned to but never used
./usr/share/pyshared/Bio/HMM/Utilities.py:39: local variable 'extension' is assigned to but never used
./usr/share/pyshared/Bio/HMM/MarkovModel.py:194: local variable 'pseudcount' is assigned to but never used
./usr/share/pyshared/Bio/KDTree/__init__.py:10: 'KDTree' imported but unused
./usr/share/pyshared/Bio/KDTree/KDTree.py:17: 'dtype' imported but unused
./usr/share/pyshared/Bio/KDTree/KDTree.py:221: redefinition of unused 'random' from line 18
./usr/share/pyshared/Bio/AlignIO/NexusIO.py:17: 'Seq' imported but unused
./usr/share/pyshared/Bio/AlignIO/FastaIO.py:202: local variable 'align_consensus' is assigned to but never used
./usr/share/pyshared/Bio/AlignIO/PhylipIO.py:25: 'single_letter_alphabet' imported but unused
./usr/share/pyshared/Bio/AlignIO/PhylipIO.py:131: local variable 'number_of_seqs' is assigned to but never used
./usr/share/pyshared/Bio/AlignIO/PhylipIO.py:132: local variable 'length_of_seqs' is assigned to but never used
./usr/share/pyshared/Bio/AlignIO/PhylipIO.py:156: local variable 'length_of_seqs' is assigned to but never used
./usr/share/pyshared/Bio/AlignIO/__init__.py:137: 'StringIO' imported but unused
./usr/share/pyshared/Bio/AlignIO/__init__.py:138: 'Seq' imported but unused
./usr/share/pyshared/Bio/AlignIO/__init__.py:139: 'SeqRecord' imported but unused
./usr/share/pyshared/Bio/AlignIO/Interfaces.py:12: 'Gapped' imported but unused
./usr/share/pyshared/Bio/Entrez/Parser.py:499: undefined name 'RuntimeException'
./usr/share/pyshared/Bio/Entrez/__init__.py:66: 'os' imported but unused
./usr/share/pyshared/Bio/GA/Crossover/General.py:10: 'Organism' imported but unused
./usr/share/pyshared/Bio/GA/Crossover/GeneralPoint.py:85: local variable 'xlocs' is assigned to but never used
./usr/share/pyshared/Bio/GA/Selection/Diversity.py:11: 'MutableSeq' imported but unused
./usr/share/pyshared/Bio/GA/Selection/Diversity.py:15: 'TournamentSelection' imported but unused
./usr/share/pyshared/Bio/GA/Mutation/General.py:7: 'Organism' imported but unused
./usr/share/pyshared/Bio/GenBank/Scanner.py:29: 'os' imported but unused
./usr/share/pyshared/Bio/GenBank/Scanner.py:33: 'generic_alphabet' imported but unused
./usr/share/pyshared/Bio/GenBank/Scanner.py:656: local variable 'EMBL_SPACER' is assigned to but never used
./usr/share/pyshared/Bio/GenBank/Scanner.py:932: local variable 'GENBANK_SPACER' is assigned to but never used
./usr/share/pyshared/Bio/GenBank/__init__.py:45: 'cStringIO' imported but unused
./usr/share/pyshared/Bio/GenBank/__init__.py:51: 'Entrez' imported but unused
./usr/share/pyshared/Bio/Phylo/BaseTree.py:18: 'warnings' imported but unused
./usr/share/pyshared/Bio/Phylo/BaseTree.py:19: 'Bio' imported but unused
./usr/share/pyshared/Bio/Phylo/PhyloXML.py:22: 'Bio' imported but unused
./usr/share/pyshared/Bio/Phylo/PhyloXMLIO.py:31: redefinition of unused 'ElementTree' from line 28
./usr/share/pyshared/Bio/Phylo/PhyloXMLIO.py:35: redefinition of unused 'ElementTree' from line 31
./usr/share/pyshared/Bio/Phylo/PhyloXMLIO.py:39: redefinition of unused 'ElementTree' from line 35
./usr/share/pyshared/Bio/Phylo/PhyloXMLIO.py:42: redefinition of unused 'ElementTree' from line 39
./usr/share/pyshared/Bio/Phylo/PhyloXMLIO.py:45: redefinition of unused 'ElementTree' from line 42
./usr/share/pyshared/Bio/Phylo/NewickIO.py:219: redefinition of function 'make_info_string' from line 214
./usr/share/pyshared/Bio/Phylo/NewickIO.py:228: redefinition of function 'make_info_string' from line 219
./usr/share/pyshared/Bio/Phylo/NewickIO.py:233: redefinition of function 'make_info_string' from line 228
./usr/share/pyshared/Bio/Phylo/__init__.py:12: 'write' imported but unused
./usr/share/pyshared/Bio/Phylo/__init__.py:12: 'convert' imported but unused
./usr/share/pyshared/Bio/Phylo/__init__.py:12: 'read' imported but unused
./usr/share/pyshared/Bio/Phylo/__init__.py:12: 'parse' imported but unused
./usr/share/pyshared/Bio/Phylo/__init__.py:13: 'to_networkx' imported but unused
./usr/share/pyshared/Bio/Phylo/__init__.py:13: 'draw_graphviz' imported but unused
./usr/share/pyshared/Bio/Phylo/__init__.py:13: 'draw_ascii' imported but unused
./usr/share/pyshared/Bio/Phylo/Newick.py:12: 'warnings' imported but unused
./usr/share/pyshared/Bio/Pathway/__init__.py:34: 'from Bio.Pathway.Rep.HashSet import *' used; unable to detect undefined names
./usr/share/pyshared/Bio/Pathway/__init__.py:35: 'from Bio.Pathway.Rep.MultiGraph import *' used; unable to detect undefined names
./usr/share/pyshared/Bio/Pathway/Rep/Graph.py:7: 'from Bio.Pathway.Rep.HashSet import *' used; unable to detect undefined names
./usr/share/pyshared/Bio/Pathway/Rep/MultiGraph.py:7: 'from Bio.Pathway.Rep.HashSet import *' used; unable to detect undefined names
./usr/share/pyshared/Bio/Medline/__init__.py:130: undefined name 'key'
./usr/share/pyshared/Bio/Sequencing/Applications/__init__.py:3: 'NovoalignCommandline' imported but unused
./usr/share/pyshared/Bio/PDB/StructureAlignment.py:29: local variable 's1' is assigned to but never used
./usr/share/pyshared/Bio/PDB/StructureAlignment.py:30: local variable 's2' is assigned to but never used
./usr/share/pyshared/Bio/PDB/MMCIF2Dict.py:40: local variable 'SEMICOLONS' is assigned to but never used
./usr/share/pyshared/Bio/PDB/MMCIF2Dict.py:41: local variable 'DOUBLEQUOTED' is assigned to but never used
./usr/share/pyshared/Bio/PDB/MMCIF2Dict.py:42: local variable 'QUOTED' is assigned to but never used
./usr/share/pyshared/Bio/PDB/MMCIF2Dict.py:43: local variable 'SIMPLE' is assigned to but never used
./usr/share/pyshared/Bio/PDB/MMCIF2Dict.py:50: local variable 'current_name' is assigned to but never used
./usr/share/pyshared/Bio/PDB/NACCESS.py:53: local variable 'stdout' is assigned to but never used
./usr/share/pyshared/Bio/PDB/NACCESS.py:55: local variable 'stderr' is assigned to but never used
./usr/share/pyshared/Bio/PDB/NACCESS.py:99: local variable 'atom_serial' is assigned to but never used
./usr/share/pyshared/Bio/PDB/NACCESS.py:102: local variable 'altloc' is assigned to but never used
./usr/share/pyshared/Bio/PDB/NACCESS.py:103: local variable 'resname' is assigned to but never used
./usr/share/pyshared/Bio/PDB/NACCESS.py:110: local variable 'vdw' is assigned to but never used
./usr/share/pyshared/Bio/PDB/NACCESS.py:122: local variable 'res_list' is assigned to but never used
./usr/share/pyshared/Bio/PDB/NACCESS.py:151: local variable 'atom_list' is assigned to but never used
./usr/share/pyshared/Bio/PDB/NACCESS.py:175: redefinition of unused 'sys' from line 8
./usr/share/pyshared/Bio/PDB/__init__.py:15: 'PDBParser' imported but unused
./usr/share/pyshared/Bio/PDB/__init__.py:19: 'MMCIFParser' imported but unused
./usr/share/pyshared/Bio/PDB/__init__.py:25: 'PDBList' imported but unused
./usr/share/pyshared/Bio/PDB/__init__.py:28: 'parse_pdb_header' imported but unused
./usr/share/pyshared/Bio/PDB/__init__.py:31: 'standard_aa_names' imported but unused
./usr/share/pyshared/Bio/PDB/__init__.py:31: 'PPBuilder' imported but unused
./usr/share/pyshared/Bio/PDB/__init__.py:31: 'CaPPBuilder' imported but unused
./usr/share/pyshared/Bio/PDB/__init__.py:31: 'is_aa' imported but unused
./usr/share/pyshared/Bio/PDB/__init__.py:33: 'to_one_letter_code' imported but unused
./usr/share/pyshared/Bio/PDB/__init__.py:36: 'PDBIO' imported but unused
./usr/share/pyshared/Bio/PDB/__init__.py:36: 'Select' imported but unused
./usr/share/pyshared/Bio/PDB/__init__.py:40: 'Selection' imported but unused
./usr/share/pyshared/Bio/PDB/__init__.py:43: 'Superimposer' imported but unused
./usr/share/pyshared/Bio/PDB/__init__.py:46: 'rotaxis2m' imported but unused
./usr/share/pyshared/Bio/PDB/__init__.py:46: 'm2rotaxis' imported but unused
./usr/share/pyshared/Bio/PDB/__init__.py:46: 'rotmat' imported but unused
./usr/share/pyshared/Bio/PDB/__init__.py:46: 'vector_to_axis' imported but unused
./usr/share/pyshared/Bio/PDB/__init__.py:46: 'calc_dihedral' imported but unused
./usr/share/pyshared/Bio/PDB/__init__.py:46: 'refmat' imported but unused
./usr/share/pyshared/Bio/PDB/__init__.py:46: 'Vector' imported but unused
./usr/share/pyshared/Bio/PDB/__init__.py:46: 'calc_angle' imported but unused
./usr/share/pyshared/Bio/PDB/__init__.py:46: 'rotaxis' imported but unused
./usr/share/pyshared/Bio/PDB/__init__.py:50: 'StructureAlignment' imported but unused
./usr/share/pyshared/Bio/PDB/__init__.py:54: 'make_dssp_dict' imported but unused
./usr/share/pyshared/Bio/PDB/__init__.py:54: 'DSSP' imported but unused
./usr/share/pyshared/Bio/PDB/__init__.py:58: 'ResidueDepth' imported but unused
./usr/share/pyshared/Bio/PDB/__init__.py:58: 'get_surface' imported but unused
./usr/share/pyshared/Bio/PDB/__init__.py:61: 'HSExposureCA' imported but unused
./usr/share/pyshared/Bio/PDB/__init__.py:61: 'ExposureCN' imported but unused
./usr/share/pyshared/Bio/PDB/__init__.py:61: 'HSExposureCB' imported but unused
./usr/share/pyshared/Bio/PDB/__init__.py:64: 'FragmentMapper' imported but unused
./usr/share/pyshared/Bio/PDB/__init__.py:67: 'extract' imported but unused
./usr/share/pyshared/Bio/PDB/__init__.py:72: 'NeighborSearch' imported but unused
./usr/share/pyshared/Bio/PDB/Polypeptide.py:57: 'Residue' imported but unused
./usr/share/pyshared/Bio/PDB/Polypeptide.py:57: 'DisorderedResidue' imported but unused
./usr/share/pyshared/Bio/PDB/Entity.py:8: 'PDBException' imported but unused
./usr/share/pyshared/Bio/PDB/parse_pdb_header.py:147: local variable 'src_molid' is assigned to but never used
./usr/share/pyshared/Bio/InterPro/__init__.py:124: local variable 'val' is assigned to but never used
./usr/share/pyshared/Bio/Geo/Record.py:57: undefined name 'val'
./usr/share/pyshared/Bio/Geo/Record.py:58: undefined name 'val'
./usr/share/pyshared/Bio/Cluster/__init__.py:3: 'from Bio.Cluster.cluster import *' used; unable to detect undefined names
./usr/share/pyshared/Bio/Blast/NCBIXML.py:690: 'os' imported but unused
./usr/share/pyshared/Bio/Blast/NCBIStandalone.py:59: 'from Bio.ParserSupport import *' used; unable to detect undefined names
./usr/share/pyshared/Bio/Blast/NCBIStandalone.py:61: '_escape_filename' imported but unused
./usr/share/pyshared/Bio/Blast/NCBIStandalone.py:2166: local variable 'msg' is assigned to but never used
./usr/share/pyshared/Bio/Blast/NCBIWWW.py:18: 'sys' imported but unused
./usr/share/pyshared/Bio/Blast/NCBIWWW.py:22: redefinition of unused 'StringIO' from line 20
./usr/share/pyshared/Bio/NMR/NOEtools.py:43: local variable 'aveDetectedPPM' is assigned to but never used
./usr/share/pyshared/Bio/NMR/xpktools.py:39: local variable 'e' is assigned to but never used
./usr/share/pyshared/Bio/NMR/xpktools.py:119: local variable 'e' is assigned to but never used
./usr/share/pyshared/Bio/NMR/xpktools.py:128: local variable 'e' is assigned to but never used
./usr/share/pyshared/Bio/SubsMat/MatrixInfo.py:87: redefinition of function '_temp' from line 28
./usr/share/pyshared/Bio/SubsMat/__init__.py:116: 'warnings' imported but unused
./usr/share/pyshared/Bio/SubsMat/__init__.py:119: 'Bio' imported but unused
./usr/share/pyshared/Bio/SCOP/Cla.py:22: 'from Residues import *' used; unable to detect undefined names
./usr/share/pyshared/Bio/SCOP/__init__.py:50: 'from types import *' used; unable to detect undefined names
./usr/share/pyshared/Bio/SCOP/__init__.py:56: 'from Residues import *' used; unable to detect undefined names
./usr/share/pyshared/Bio/Crystal/__init__.py:96: local variable 'i' is assigned to but never used
./usr/share/pyshared/Bio/Restriction/PrintFormat.py:12: 'itertools' imported but unused
./usr/share/pyshared/Bio/Restriction/__init__.py:61: 'from Bio.Restriction.Restriction import *' used; unable to detect undefined names
./usr/share/pyshared/Bio/Restriction/Restriction.py:85: 'IUPAC' imported but unused
./usr/share/pyshared/Bio/Restriction/Restriction.py:90: 'from Bio.Restriction.RanaConfig import *' used; unable to detect undefined names
./usr/share/pyshared/Bio/Restriction/Restriction.py:244: local variable 'err' is assigned to but never used
./usr/share/pyshared/Bio/Restriction/Restriction_Dictionary.py:43: redefinition of function '_temp' from line 21
./usr/share/pyshared/Bio/Restriction/Restriction_Dictionary.py:65: redefinition of function '_temp' from line 43
./usr/share/pyshared/Bio/Restriction/Restriction_Dictionary.py:87: redefinition of function '_temp' from line 65
./usr/share/pyshared/Bio/Restriction/Restriction_Dictionary.py:109: redefinition of function '_temp' from line 87
./usr/share/pyshared/Bio/Restriction/Restriction_Dictionary.py:131: redefinition of function '_temp' from line 109
./usr/share/pyshared/Bio/Restriction/Restriction_Dictionary.py:153: redefinition of function '_temp' from line 131
./usr/share/pyshared/Bio/Restriction/Restriction_Dictionary.py:175: redefinition of function '_temp' from line 153
./usr/share/pyshared/Bio/Restriction/Restriction_Dictionary.py:197: redefinition of function '_temp' from line 175
./usr/share/pyshared/Bio/Restriction/Restriction_Dictionary.py:219: redefinition of function '_temp' from line 197
./usr/share/pyshared/Bio/Restriction/Restriction_Dictionary.py:241: redefinition of function '_temp' from line 219
./usr/share/pyshared/Bio/Restriction/Restriction_Dictionary.py:263: redefinition of function '_temp' from line 241
./usr/share/pyshared/Bio/Restriction/Restriction_Dictionary.py:285: redefinition of function '_temp' from line 263
./usr/share/pyshared/Bio/Restriction/Restriction_Dictionary.py:307: redefinition of function '_temp' from line 285
./usr/share/pyshared/Bio/Restriction/Restriction_Dictionary.py:329: redefinition of function '_temp' from line 307
./usr/share/pyshared/Bio/Restriction/Restriction_Dictionary.py:351: redefinition of function '_temp' from line 329
./usr/share/pyshared/Bio/Restriction/Restriction_Dictionary.py:373: redefinition of function '_temp' from line 351
./usr/share/pyshared/Bio/Restriction/Restriction_Dictionary.py:395: redefinition of function '_temp' from line 373
./usr/share/pyshared/Bio/Restriction/Restriction_Dictionary.py:417: redefinition of function '_temp' from line 395
./usr/share/pyshared/Bio/Restriction/Restriction_Dictionary.py:439: redefinition of function '_temp' from line 417
./usr/share/pyshared/Bio/Restriction/Restriction_Dictionary.py:461: redefinition of function '_temp' from line 439
./usr/share/pyshared/Bio/Restriction/Restriction_Dictionary.py:483: redefinition of function '_temp' from line 461
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./usr/share/pyshared/Bio/Restriction/Restriction_Dictionary.py:571: redefinition of function '_temp' from line 549
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./usr/share/pyshared/Bio/Restriction/Restriction_Dictionary.py:637: redefinition of function '_temp' from line 615
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./usr/share/pyshared/Bio/Restriction/Restriction_Dictionary.py:681: redefinition of function '_temp' from line 659
./usr/share/pyshared/Bio/Restriction/Restriction_Dictionary.py:703: redefinition of function '_temp' from line 681
./usr/share/pyshared/Bio/Restriction/Restriction_Dictionary.py:725: redefinition of function '_temp' from line 703
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./usr/share/pyshared/Bio/Restriction/Restriction_Dictionary.py:813: redefinition of function '_temp' from line 791
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./usr/share/pyshared/Bio/Restriction/Restriction_Dictionary.py:857: redefinition of function '_temp' from line 835
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./usr/share/pyshared/Bio/Restriction/Restriction_Dictionary.py:945: redefinition of function '_temp' from line 923
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./usr/share/pyshared/Bio/Restriction/Restriction_Dictionary.py:1033: redefinition of function '_temp' from line 1011
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./usr/share/pyshared/Bio/Restriction/Restriction_Dictionary.py:1209: redefinition of function '_temp' from line 1187
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./usr/share/pyshared/Bio/Restriction/RanaConfig.py:10: 'os' imported but unused
./usr/share/pyshared/Bio/Restriction/_Update/Update.py:16: 'sre' imported but unused
./usr/share/pyshared/Bio/Restriction/_Update/Update.py:18: 'gzip' imported but unused
./usr/share/pyshared/Bio/Restriction/_Update/Update.py:21: 'from Bio.Restriction.RanaConfig import *' used; unable to detect undefined names
./usr/share/pyshared/Bio/Restriction/_Update/RestrictionCompiler.py:40: 'sre' imported but unused
./usr/share/pyshared/Bio/Restriction/_Update/RestrictionCompiler.py:45: 'site' imported but unused
./usr/share/pyshared/Bio/Restriction/_Update/RestrictionCompiler.py:49: 'IUPAC' imported but unused
./usr/share/pyshared/Bio/Restriction/_Update/RestrictionCompiler.py:58: 'from Bio.Restriction.Restriction import *' used; unable to detect undefined names
./usr/share/pyshared/Bio/Restriction/_Update/RestrictionCompiler.py:305: local variable 'All' is assigned to but never used
./usr/share/pyshared/Bio/Restriction/_Update/RestrictionCompiler.py:448: local variable 'supplier' is assigned to but never used
./usr/share/pyshared/Bio/Restriction/_Update/RestrictionCompiler.py:692: redefinition of unused 'site' from line 45
./usr/share/pyshared/Bio/Restriction/_Update/RestrictionCompiler.py:929: local variable 'oldblock' is assigned to but never used
./usr/share/pyshared/Bio/SeqIO/InsdcIO.py:361: local variable 'i' is assigned to but never used
./usr/share/pyshared/Bio/SeqIO/QualityIO.py:513: redefinition of unused 'warnings' from line 372
./usr/share/pyshared/Bio/SeqIO/_index.py:30: redefinition of unused '_dict_base' from line 28
./usr/share/pyshared/Bio/SeqIO/_index.py:42: redefinition of unused '_sqlite' from line 36
./usr/share/pyshared/Bio/SeqIO/_index.py:45: '_as_string' imported but unused
./usr/share/pyshared/Bio/SeqIO/_index.py:161: redefinition of function 'items' from line 128
./usr/share/pyshared/Bio/SeqIO/_index.py:166: redefinition of function 'values' from line 116
./usr/share/pyshared/Bio/SeqIO/_index.py:171: redefinition of function 'keys' from line 140
./usr/share/pyshared/Bio/SeqIO/_index.py:501: redefinition of function '_parse' from line 496
./usr/share/pyshared/Bio/SeqIO/_index.py:812: local variable 'done' is assigned to but never used
./usr/share/pyshared/Bio/SeqIO/_index.py:902: local variable 'marker_re' is assigned to but never used
./usr/share/pyshared/Bio/SeqIO/_index.py:1011: local variable 'identifier' is assigned to but never used
./usr/share/pyshared/Bio/SeqIO/_index.py:1027: local variable 'pos' is assigned to but never used
./usr/share/pyshared/Bio/SeqIO/__init__.py:305: 'Seq' imported but unused
./usr/share/pyshared/Bio/SeqIO/__init__.py:308: 'Alignment' imported but unused
./usr/share/pyshared/Bio/SeqIO/_convert.py:224: local variable 'trunc_char' is assigned to but never used
./usr/share/pyshared/Bio/SeqIO/SffIO.py:726: local variable 'read_flow_size' is assigned to but never used
./usr/share/pyshared/Bio/SeqIO/SffIO.py:1065: redefinition of unused 'BytesIO' from line 1063
./usr/share/pyshared/Bio/SeqIO/UniprotIO.py:27: redefinition of unused 'StringIO' from line 25
./usr/share/pyshared/Bio/SeqIO/UniprotIO.py:28: 'warnings' imported but unused
./usr/share/pyshared/Bio/SeqIO/UniprotIO.py:34: redefinition of unused 'ElementTree' from line 32
./usr/share/pyshared/Bio/SeqIO/UniprotIO.py:37: redefinition of unused 'ElementTree' from line 34
./usr/share/pyshared/Bio/SeqIO/UniprotIO.py:41: redefinition of unused 'ElementTree' from line 37
./usr/share/pyshared/Bio/SeqIO/UniprotIO.py:44: redefinition of unused 'ElementTree' from line 41
./usr/share/pyshared/Bio/SeqIO/UniprotIO.py:47: redefinition of unused 'ElementTree' from line 44
./usr/share/pyshared/Bio/SeqIO/UniprotIO.py:49: redefinition of unused 'ElementTree' from line 47
./usr/share/pyshared/Bio/SeqIO/UniprotIO.py:412: local variable 'err' is assigned to but never used
./usr/share/pyshared/Bio/Statistics/lowess.py:31: redefinition of unused 'median' from line 26
./usr/share/pyshared/Bio/SeqUtils/__init__.py:121: 'log' imported but unused
./usr/share/pyshared/Bio/SeqUtils/__init__.py:204: local variable 'l' is assigned to but never used
./usr/share/pyshared/Bio/SeqUtils/__init__.py:372: local variable 'entries' is assigned to but never used
./usr/share/pyshared/Bio/SeqUtils/CheckSum.py:117: 'os' imported but unused

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