CloneDigger Report

This file was obtained by applying Clone Digger tool to the source code of the Bio Python project.
The fragments of code, which are cited below, are not necessary clones. 
Even more so the presense of this code in the project does not lead to defects in it.

The code below falls under the following license:

                 Biopython License Agreement

Permission to use, copy, modify, and distribute this software and its
documentation with or without modifications and for any purpose and
without fee is hereby granted, provided that any copyright notices
appear in all copies and that both those copyright notices and this
permission notice appear in supporting documentation, and that the
names of the contributors or copyright holders not be used in
advertising or publicity pertaining to distribution of the software
without specific prior permission.

THE CONTRIBUTORS AND COPYRIGHT HOLDERS OF THIS SOFTWARE DISCLAIM ALL
WARRANTIES WITH REGARD TO THIS SOFTWARE, INCLUDING ALL IMPLIED
WARRANTIES OF MERCHANTABILITY AND FITNESS, IN NO EVENT SHALL THE
CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY SPECIAL, INDIRECT
OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES WHATSOEVER RESULTING FROM LOSS
OF USE, DATA OR PROFITS, WHETHER IN AN ACTION OF CONTRACT, NEGLIGENCE
OR OTHER TORTIOUS ACTION, ARISING OUT OF OR IN CONNECTION WITH THE USE
OR PERFORMANCE OF THIS SOFTWARE.

Source files:
/home/peter/clone_digger/biopython-1.44/Bio/utils.py,
/home/peter/clone_digger/biopython-1.44/Bio/Std.py,
/home/peter/clone_digger/biopython-1.44/Bio/triefind.py,
/home/peter/clone_digger/biopython-1.44/Bio/listfns.py,
/home/peter/clone_digger/biopython-1.44/Bio/biblio.py,
/home/peter/clone_digger/biopython-1.44/Bio/EZRetrieve.py,
/home/peter/clone_digger/biopython-1.44/Bio/Decode.py,
/home/peter/clone_digger/biopython-1.44/Bio/NetCatch.py,
/home/peter/clone_digger/biopython-1.44/Bio/HotRand.py,
/home/peter/clone_digger/biopython-1.44/Bio/distance.py,
/home/peter/clone_digger/biopython-1.44/Bio/MaxEntropy.py,
/home/peter/clone_digger/biopython-1.44/Bio/PropertyManager.py,
/home/peter/clone_digger/biopython-1.44/Bio/SeqRecord.py,
/home/peter/clone_digger/biopython-1.44/Bio/kNN.py,
/home/peter/clone_digger/biopython-1.44/Bio/ParserSupport.py,
/home/peter/clone_digger/biopython-1.44/Bio/FormatIO.py,
/home/peter/clone_digger/biopython-1.44/Bio/Seq.py,
/home/peter/clone_digger/biopython-1.44/Bio/LogisticRegression.py,
/home/peter/clone_digger/biopython-1.44/Bio/MarkovModel.py,
/home/peter/clone_digger/biopython-1.44/Bio/File.py,
/home/peter/clone_digger/biopython-1.44/Bio/stringfns.py,
/home/peter/clone_digger/biopython-1.44/Bio/Search.py,
/home/peter/clone_digger/biopython-1.44/Bio/StdHandler.py,
/home/peter/clone_digger/biopython-1.44/Bio/NaiveBayes.py,
/home/peter/clone_digger/biopython-1.44/Bio/DBXRef.py,
/home/peter/clone_digger/biopython-1.44/Bio/Index.py,
/home/peter/clone_digger/biopython-1.44/Bio/Writer.py,
/home/peter/clone_digger/biopython-1.44/Bio/lcc.py,
/home/peter/clone_digger/biopython-1.44/Bio/DocSQL.py,
/home/peter/clone_digger/biopython-1.44/Bio/MarkupEditor.py,
/home/peter/clone_digger/biopython-1.44/Bio/Translate.py,
/home/peter/clone_digger/biopython-1.44/Bio/crc.py,
/home/peter/clone_digger/biopython-1.44/Bio/mathfns.py,
/home/peter/clone_digger/biopython-1.44/Bio/PubMed.py,
/home/peter/clone_digger/biopython-1.44/Bio/SeqFeature.py,
/home/peter/clone_digger/biopython-1.44/Bio/pairwise2.py,
/home/peter/clone_digger/biopython-1.44/Bio/__init__.py,
/home/peter/clone_digger/biopython-1.44/Bio/SGMLExtractor.py,
/home/peter/clone_digger/biopython-1.44/Bio/FilteredReader.py,
/home/peter/clone_digger/biopython-1.44/Bio/Transcribe.py,
/home/peter/clone_digger/biopython-1.44/Bio/Align/FormatConvert.py,
/home/peter/clone_digger/biopython-1.44/Bio/Align/Generic.py,
/home/peter/clone_digger/biopython-1.44/Bio/Align/AlignInfo.py,
/home/peter/clone_digger/biopython-1.44/Bio/Align/__init__.py,
/home/peter/clone_digger/biopython-1.44/Bio/Clustalw/clustal_format.py,
/home/peter/clone_digger/biopython-1.44/Bio/Clustalw/__init__.py,
/home/peter/clone_digger/biopython-1.44/Bio/PopGen/__init__.py,
/home/peter/clone_digger/biopython-1.44/Bio/PopGen/FDist/Async.py,
/home/peter/clone_digger/biopython-1.44/Bio/PopGen/FDist/Utils.py,
/home/peter/clone_digger/biopython-1.44/Bio/PopGen/FDist/Controller.py,
/home/peter/clone_digger/biopython-1.44/Bio/PopGen/FDist/__init__.py,
/home/peter/clone_digger/biopython-1.44/Bio/PopGen/Async/Local.py,
/home/peter/clone_digger/biopython-1.44/Bio/PopGen/Async/__init__.py,
/home/peter/clone_digger/biopython-1.44/Bio/PopGen/GenePop/Utils.py,
/home/peter/clone_digger/biopython-1.44/Bio/PopGen/GenePop/__init__.py,
/home/peter/clone_digger/biopython-1.44/Bio/expressions/fasta.py,
/home/peter/clone_digger/biopython-1.44/Bio/expressions/genbank.py,
/home/peter/clone_digger/biopython-1.44/Bio/expressions/hmmpfam.py,
/home/peter/clone_digger/biopython-1.44/Bio/expressions/transfac.py,
/home/peter/clone_digger/biopython-1.44/Bio/expressions/blocks.py,
/home/peter/clone_digger/biopython-1.44/Bio/expressions/__init__.py,
/home/peter/clone_digger/biopython-1.44/Bio/expressions/blast/wublast.py,
/home/peter/clone_digger/biopython-1.44/Bio/expressions/blast/ncbiblast.py,
/home/peter/clone_digger/biopython-1.44/Bio/expressions/blast/__init__.py,
/home/peter/clone_digger/biopython-1.44/Bio/expressions/swissprot/speclist.py,
/home/peter/clone_digger/biopython-1.44/Bio/expressions/swissprot/sprot38.py,
/home/peter/clone_digger/biopython-1.44/Bio/expressions/swissprot/sprot40.py,
/home/peter/clone_digger/biopython-1.44/Bio/expressions/swissprot/ipi.py,
/home/peter/clone_digger/biopython-1.44/Bio/expressions/swissprot/__init__.py,
/home/peter/clone_digger/biopython-1.44/Bio/expressions/embl/embl65.py,
/home/peter/clone_digger/biopython-1.44/Bio/expressions/embl/__init__.py,
/home/peter/clone_digger/biopython-1.44/Bio/IntelliGenetics/intelligenetics_format.py,
/home/peter/clone_digger/biopython-1.44/Bio/IntelliGenetics/Record.py,
/home/peter/clone_digger/biopython-1.44/Bio/IntelliGenetics/__init__.py,
/home/peter/clone_digger/biopython-1.44/Bio/Graphics/BasicChromosome.py,
/home/peter/clone_digger/biopython-1.44/Bio/Graphics/Distribution.py,
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/home/peter/clone_digger/biopython-1.44/Bio/Graphics/DisplayRepresentation.py,
/home/peter/clone_digger/biopython-1.44/Bio/Graphics/__init__.py,
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/home/peter/clone_digger/biopython-1.44/Bio/UniGene/__init__.py,
/home/peter/clone_digger/biopython-1.44/Bio/Application/__init__.py,
/home/peter/clone_digger/biopython-1.44/Bio/SCOP/FileIndex.py,
/home/peter/clone_digger/biopython-1.44/Bio/SCOP/Raf.py,
/home/peter/clone_digger/biopython-1.44/Bio/SCOP/Dom.py,
/home/peter/clone_digger/biopython-1.44/Bio/SCOP/Residues.py,
/home/peter/clone_digger/biopython-1.44/Bio/SCOP/Cla.py,
/home/peter/clone_digger/biopython-1.44/Bio/SCOP/Des.py,
/home/peter/clone_digger/biopython-1.44/Bio/SCOP/Hie.py,
/home/peter/clone_digger/biopython-1.44/Bio/SCOP/__init__.py,
/home/peter/clone_digger/biopython-1.44/Bio/Geo/Record.py,
/home/peter/clone_digger/biopython-1.44/Bio/Geo/__init__.py,
/home/peter/clone_digger/biopython-1.44/Bio/PDB/StructureBuilder.py,
/home/peter/clone_digger/biopython-1.44/Bio/PDB/Dice.py,
/home/peter/clone_digger/biopython-1.44/Bio/PDB/AbstractPropertyMap.py,
/home/peter/clone_digger/biopython-1.44/Bio/PDB/NACCESS.py,
/home/peter/clone_digger/biopython-1.44/Bio/PDB/Entity.py,
/home/peter/clone_digger/biopython-1.44/Bio/PDB/parse_pdb_header.py,
/home/peter/clone_digger/biopython-1.44/Bio/PDB/PDBList.py,
/home/peter/clone_digger/biopython-1.44/Bio/PDB/PDBExceptions.py,
/home/peter/clone_digger/biopython-1.44/Bio/PDB/Polypeptide.py,
/home/peter/clone_digger/biopython-1.44/Bio/PDB/Residue.py,
/home/peter/clone_digger/biopython-1.44/Bio/PDB/PSEA.py,
/home/peter/clone_digger/biopython-1.44/Bio/PDB/HSExposure.py,
/home/peter/clone_digger/biopython-1.44/Bio/PDB/FragmentMapper.py,
/home/peter/clone_digger/biopython-1.44/Bio/PDB/NeighborSearch.py,
/home/peter/clone_digger/biopython-1.44/Bio/PDB/PDBIO.py,
/home/peter/clone_digger/biopython-1.44/Bio/PDB/Structure.py,
/home/peter/clone_digger/biopython-1.44/Bio/PDB/PDBParser.py,
/home/peter/clone_digger/biopython-1.44/Bio/PDB/Vector.py,
/home/peter/clone_digger/biopython-1.44/Bio/PDB/DSSP.py,
/home/peter/clone_digger/biopython-1.44/Bio/PDB/Selection.py,
/home/peter/clone_digger/biopython-1.44/Bio/PDB/Superimposer.py,
/home/peter/clone_digger/biopython-1.44/Bio/PDB/ResidueDepth.py,
/home/peter/clone_digger/biopython-1.44/Bio/PDB/MMCIF2Dict.py,
/home/peter/clone_digger/biopython-1.44/Bio/PDB/Atom.py,
/home/peter/clone_digger/biopython-1.44/Bio/PDB/Chain.py,
/home/peter/clone_digger/biopython-1.44/Bio/PDB/MMCIFParser.py,
/home/peter/clone_digger/biopython-1.44/Bio/PDB/__init__.py,
/home/peter/clone_digger/biopython-1.44/Bio/PDB/Model.py,
/home/peter/clone_digger/biopython-1.44/Bio/PDB/StructureAlignment.py,
/home/peter/clone_digger/biopython-1.44/Bio/PDB/mmCIF/__init__.py,
/home/peter/clone_digger/biopython-1.44/Bio/SubsMat/MatrixInfo.py,
/home/peter/clone_digger/biopython-1.44/Bio/SubsMat/FreqTable.py,
/home/peter/clone_digger/biopython-1.44/Bio/SubsMat/__init__.py,
/home/peter/clone_digger/biopython-1.44/Bio/SeqIO/ClustalIO.py,
/home/peter/clone_digger/biopython-1.44/Bio/SeqIO/Interfaces.py,
/home/peter/clone_digger/biopython-1.44/Bio/SeqIO/StockholmIO.py,
/home/peter/clone_digger/biopython-1.44/Bio/SeqIO/FASTA.py,
/home/peter/clone_digger/biopython-1.44/Bio/SeqIO/FastaIO.py,
/home/peter/clone_digger/biopython-1.44/Bio/SeqIO/PhylipIO.py,
/home/peter/clone_digger/biopython-1.44/Bio/SeqIO/InsdcIO.py,
/home/peter/clone_digger/biopython-1.44/Bio/SeqIO/SwissIO.py,
/home/peter/clone_digger/biopython-1.44/Bio/SeqIO/generic.py,
/home/peter/clone_digger/biopython-1.44/Bio/SeqIO/NexusIO.py,
/home/peter/clone_digger/biopython-1.44/Bio/SeqIO/__init__.py,
/home/peter/clone_digger/biopython-1.44/Bio/Prosite/Pattern.py,
/home/peter/clone_digger/biopython-1.44/Bio/Prosite/Prodoc.py,
/home/peter/clone_digger/biopython-1.44/Bio/Prosite/__init__.py,
/home/peter/clone_digger/biopython-1.44/Bio/KEGG/__init__.py,
/home/peter/clone_digger/biopython-1.44/Bio/KEGG/Compound/__init__.py,
/home/peter/clone_digger/biopython-1.44/Bio/KEGG/Enzyme/__init__.py,
/home/peter/clone_digger/biopython-1.44/Bio/KEGG/Map/__init__.py,
/home/peter/clone_digger/biopython-1.44/Bio/NeuralNetwork/Training.py,
/home/peter/clone_digger/biopython-1.44/Bio/NeuralNetwork/StopTraining.py,
/home/peter/clone_digger/biopython-1.44/Bio/NeuralNetwork/__init__.py,
/home/peter/clone_digger/biopython-1.44/Bio/NeuralNetwork/Gene/Pattern.py,
/home/peter/clone_digger/biopython-1.44/Bio/NeuralNetwork/Gene/Motif.py,
/home/peter/clone_digger/biopython-1.44/Bio/NeuralNetwork/Gene/Signature.py,
/home/peter/clone_digger/biopython-1.44/Bio/NeuralNetwork/Gene/Schema.py,
/home/peter/clone_digger/biopython-1.44/Bio/NeuralNetwork/Gene/__init__.py,
/home/peter/clone_digger/biopython-1.44/Bio/NeuralNetwork/BackPropagation/Layer.py,
/home/peter/clone_digger/biopython-1.44/Bio/NeuralNetwork/BackPropagation/__init__.py,
/home/peter/clone_digger/biopython-1.44/Bio/NeuralNetwork/BackPropagation/Network.py,
/home/peter/clone_digger/biopython-1.44/Bio/InterPro/__init__.py,
/home/peter/clone_digger/biopython-1.44/Bio/CAPS/__init__.py,
/home/peter/clone_digger/biopython-1.44/Bio/Gobase/__init__.py,
/home/peter/clone_digger/biopython-1.44/Bio/EUtils/Config.py,
/home/peter/clone_digger/biopython-1.44/Bio/EUtils/Datatypes.py,
/home/peter/clone_digger/biopython-1.44/Bio/EUtils/ThinClient.py,
/home/peter/clone_digger/biopython-1.44/Bio/EUtils/Mixins.py,
/home/peter/clone_digger/biopython-1.44/Bio/EUtils/ReseekFile.py,
/home/peter/clone_digger/biopython-1.44/Bio/EUtils/parse.py,
/home/peter/clone_digger/biopython-1.44/Bio/EUtils/HistoryClient.py,
/home/peter/clone_digger/biopython-1.44/Bio/EUtils/sourcegen.py,
/home/peter/clone_digger/biopython-1.44/Bio/EUtils/dtd2py.py,
/home/peter/clone_digger/biopython-1.44/Bio/EUtils/DBIdsClient.py,
/home/peter/clone_digger/biopython-1.44/Bio/EUtils/MultiDict.py,
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/home/peter/clone_digger/biopython-1.44/Bio/EUtils/DTDs/ePost_020511.py,
/home/peter/clone_digger/biopython-1.44/Bio/EUtils/DTDs/eSummary_020511.py,
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/home/peter/clone_digger/biopython-1.44/Bio/EUtils/DTDs/eInfo_020511.py,
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/home/peter/clone_digger/biopython-1.44/Bio/SVDSuperimposer/SVDSuperimposer.py,
/home/peter/clone_digger/biopython-1.44/Bio/SVDSuperimposer/__init__.py,
/home/peter/clone_digger/biopython-1.44/Bio/NMR/NOEtools.py,
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/home/peter/clone_digger/biopython-1.44/Bio/Restriction/PrintFormat.py,
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/home/peter/clone_digger/biopython-1.44/Bio/Restriction/Restriction.py,
/home/peter/clone_digger/biopython-1.44/Bio/Restriction/RanaConfig.py,
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/home/peter/clone_digger/biopython-1.44/Bio/Restriction/_Update/Update.py,
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/home/peter/clone_digger/biopython-1.44/Bio/GA/Selection/RouletteWheel.py,
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/home/peter/clone_digger/biopython-1.44/Bio/GA/Selection/__init__.py,
/home/peter/clone_digger/biopython-1.44/Bio/GA/Mutation/General.py,
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/home/peter/clone_digger/biopython-1.44/Bio/GA/Mutation/__init__.py,
/home/peter/clone_digger/biopython-1.44/Bio/Blast/NCBIStandalone.py,
/home/peter/clone_digger/biopython-1.44/Bio/Blast/NCBIXML.py,
/home/peter/clone_digger/biopython-1.44/Bio/Blast/Record.py,
/home/peter/clone_digger/biopython-1.44/Bio/Blast/NCBIWWW.py,
/home/peter/clone_digger/biopython-1.44/Bio/Blast/ParseBlastTable.py,
/home/peter/clone_digger/biopython-1.44/Bio/Blast/Applications.py,
/home/peter/clone_digger/biopython-1.44/Bio/Blast/__init__.py,
/home/peter/clone_digger/biopython-1.44/Bio/Crystal/__init__.py,
/home/peter/clone_digger/biopython-1.44/Bio/Sequencing/Phd.py,
/home/peter/clone_digger/biopython-1.44/Bio/Sequencing/Ace.py,
/home/peter/clone_digger/biopython-1.44/Bio/Sequencing/__init__.py,
/home/peter/clone_digger/biopython-1.44/Bio/SwissProt/SProt.py,
/home/peter/clone_digger/biopython-1.44/Bio/SwissProt/__init__.py,
/home/peter/clone_digger/biopython-1.44/Bio/SwissProt/KeyWList.py,
/home/peter/clone_digger/biopython-1.44/Bio/Enzyme/__init__.py,
/home/peter/clone_digger/biopython-1.44/Bio/builders/__init__.py,
/home/peter/clone_digger/biopython-1.44/Bio/builders/Search/search.py,
/home/peter/clone_digger/biopython-1.44/Bio/builders/Search/__init__.py,
/home/peter/clone_digger/biopython-1.44/Bio/builders/SeqRecord/sequence.py,
/home/peter/clone_digger/biopython-1.44/Bio/builders/SeqRecord/__init__.py,
/home/peter/clone_digger/biopython-1.44/Bio/Statistics/lowess.py,
/home/peter/clone_digger/biopython-1.44/Bio/Statistics/__init__.py,
/home/peter/clone_digger/biopython-1.44/Bio/KDTree/__init__.py,
/home/peter/clone_digger/biopython-1.44/Bio/KDTree/KDTree.py,
/home/peter/clone_digger/biopython-1.44/Bio/KDTree/CKDTree.py,
/home/peter/clone_digger/biopython-1.44/Bio/Compass/__init__.py,
/home/peter/clone_digger/biopython-1.44/Bio/MetaTool/metatool_format.py,
/home/peter/clone_digger/biopython-1.44/Bio/MetaTool/Record.py,
/home/peter/clone_digger/biopython-1.44/Bio/MetaTool/Input.py,
/home/peter/clone_digger/biopython-1.44/Bio/MetaTool/__init__.py,
/home/peter/clone_digger/biopython-1.44/Bio/LocusLink/locus_format.py,
/home/peter/clone_digger/biopython-1.44/Bio/LocusLink/web_parse.py,
/home/peter/clone_digger/biopython-1.44/Bio/LocusLink/__init__.py,
/home/peter/clone_digger/biopython-1.44/Bio/Ais/__init__.py,
/home/peter/clone_digger/biopython-1.44/Bio/dbdefs/fasta.py,
/home/peter/clone_digger/biopython-1.44/Bio/dbdefs/genbank.py,
/home/peter/clone_digger/biopython-1.44/Bio/dbdefs/interpro.py,
/home/peter/clone_digger/biopython-1.44/Bio/dbdefs/prosite.py,
/home/peter/clone_digger/biopython-1.44/Bio/dbdefs/_support.py,
/home/peter/clone_digger/biopython-1.44/Bio/dbdefs/swissprot.py,
/home/peter/clone_digger/biopython-1.44/Bio/dbdefs/prodoc.py,
/home/peter/clone_digger/biopython-1.44/Bio/dbdefs/embl.py,
/home/peter/clone_digger/biopython-1.44/Bio/dbdefs/pdb.py,
/home/peter/clone_digger/biopython-1.44/Bio/dbdefs/__init__.py,
/home/peter/clone_digger/biopython-1.44/Bio/dbdefs/medline.py,
/home/peter/clone_digger/biopython-1.44/Bio/HMM/DynamicProgramming.py,
/home/peter/clone_digger/biopython-1.44/Bio/HMM/Utilities.py,
/home/peter/clone_digger/biopython-1.44/Bio/HMM/Trainer.py,
/home/peter/clone_digger/biopython-1.44/Bio/HMM/MarkovModel.py,
/home/peter/clone_digger/biopython-1.44/Bio/HMM/__init__.py,
/home/peter/clone_digger/biopython-1.44/Bio/AlignAce/AlignAceStandalone.py,
/home/peter/clone_digger/biopython-1.44/Bio/AlignAce/Motif.py,
/home/peter/clone_digger/biopython-1.44/Bio/AlignAce/Parser.py,
/home/peter/clone_digger/biopython-1.44/Bio/AlignAce/CompareAceStandalone.py,
/home/peter/clone_digger/biopython-1.44/Bio/AlignAce/Scanner.py,
/home/peter/clone_digger/biopython-1.44/Bio/AlignAce/Applications.py,
/home/peter/clone_digger/biopython-1.44/Bio/AlignAce/__init__.py,
/home/peter/clone_digger/biopython-1.44/Bio/ECell/ecell_format.py,
/home/peter/clone_digger/biopython-1.44/Bio/ECell/Record.py,
/home/peter/clone_digger/biopython-1.44/Bio/ECell/__init__.py,
/home/peter/clone_digger/biopython-1.44/Bio/writers/__init__.py,
/home/peter/clone_digger/biopython-1.44/Bio/writers/SeqRecord/empty.py,
/home/peter/clone_digger/biopython-1.44/Bio/writers/SeqRecord/fasta.py,
/home/peter/clone_digger/biopython-1.44/Bio/writers/SeqRecord/embl.py,
/home/peter/clone_digger/biopython-1.44/Bio/writers/SeqRecord/__init__.py,
/home/peter/clone_digger/biopython-1.44/Bio/Fasta/FastaAlign.py,
/home/peter/clone_digger/biopython-1.44/Bio/Fasta/__init__.py,
/home/peter/clone_digger/biopython-1.44/Bio/Rebase/__init__.py,
/home/peter/clone_digger/biopython-1.44/Bio/Mindy/Location.py,
/home/peter/clone_digger/biopython-1.44/Bio/Mindy/SimpleSeqRecord.py,
/home/peter/clone_digger/biopython-1.44/Bio/Mindy/BerkeleyDB.py,
/home/peter/clone_digger/biopython-1.44/Bio/Mindy/BaseDB.py,
/home/peter/clone_digger/biopython-1.44/Bio/Mindy/compression.py,
/home/peter/clone_digger/biopython-1.44/Bio/Mindy/XPath.py,
/home/peter/clone_digger/biopython-1.44/Bio/Mindy/FlatDB.py,
/home/peter/clone_digger/biopython-1.44/Bio/Mindy/__init__.py,
/home/peter/clone_digger/biopython-1.44/Bio/SeqUtils/ProtParam.py,
/home/peter/clone_digger/biopython-1.44/Bio/SeqUtils/CodonUsageIndices.py,
/home/peter/clone_digger/biopython-1.44/Bio/SeqUtils/CheckSum.py,
/home/peter/clone_digger/biopython-1.44/Bio/SeqUtils/ProtParamData.py,
/home/peter/clone_digger/biopython-1.44/Bio/SeqUtils/lcc.py,
/home/peter/clone_digger/biopython-1.44/Bio/SeqUtils/IsoelectricPoint.py,
/home/peter/clone_digger/biopython-1.44/Bio/SeqUtils/MeltingTemp.py,
/home/peter/clone_digger/biopython-1.44/Bio/SeqUtils/__init__.py,
/home/peter/clone_digger/biopython-1.44/Bio/SeqUtils/CodonUsage.py,
/home/peter/clone_digger/biopython-1.44/Bio/Saf/Record.py,
/home/peter/clone_digger/biopython-1.44/Bio/Saf/saf_format.py,
/home/peter/clone_digger/biopython-1.44/Bio/Saf/__init__.py,
/home/peter/clone_digger/biopython-1.44/Bio/MultiProc/Scheduler.py,
/home/peter/clone_digger/biopython-1.44/Bio/MultiProc/copen.py,
/home/peter/clone_digger/biopython-1.44/Bio/MultiProc/Task.py,
/home/peter/clone_digger/biopython-1.44/Bio/MultiProc/__init__.py,
/home/peter/clone_digger/biopython-1.44/Bio/GenBank/utils.py,
/home/peter/clone_digger/biopython-1.44/Bio/GenBank/Record.py,
/home/peter/clone_digger/biopython-1.44/Bio/GenBank/Scanner.py,
/home/peter/clone_digger/biopython-1.44/Bio/GenBank/__init__.py,
/home/peter/clone_digger/biopython-1.44/Bio/GenBank/LocationParser.py,
/home/peter/clone_digger/biopython-1.44/Bio/Alphabet/IUPAC.py,
/home/peter/clone_digger/biopython-1.44/Bio/Alphabet/__init__.py,
/home/peter/clone_digger/biopython-1.44/Bio/Alphabet/Reduced.py,
/home/peter/clone_digger/biopython-1.44/Bio/Wise/dnal.py,
/home/peter/clone_digger/biopython-1.44/Bio/Wise/psw.py,
/home/peter/clone_digger/biopython-1.44/Bio/Wise/__init__.py,
/home/peter/clone_digger/biopython-1.44/Bio/Pathway/__init__.py,
/home/peter/clone_digger/biopython-1.44/Bio/Pathway/Rep/HashSet.py,
/home/peter/clone_digger/biopython-1.44/Bio/Pathway/Rep/Graph.py,
/home/peter/clone_digger/biopython-1.44/Bio/Pathway/Rep/MultiGraph.py,
/home/peter/clone_digger/biopython-1.44/Bio/Pathway/Rep/__init__.py,
/home/peter/clone_digger/biopython-1.44/Bio/Medline/nlmmedline_031101_format.py,
/home/peter/clone_digger/biopython-1.44/Bio/Medline/NLMMedlineXML.py,
/home/peter/clone_digger/biopython-1.44/Bio/Medline/nlmmedline_001211_format.py,
/home/peter/clone_digger/biopython-1.44/Bio/Medline/nlmmedline_011101_format.py,
/home/peter/clone_digger/biopython-1.44/Bio/Medline/nlmmedline_010319_format.py,
/home/peter/clone_digger/biopython-1.44/Bio/Medline/__init__.py,
/home/peter/clone_digger/biopython-1.44/Bio/Affy/CelFile.py,
/home/peter/clone_digger/biopython-1.44/Bio/Affy/__init__.py,
/home/peter/clone_digger/biopython-1.44/Bio/MEME/Motif.py,
/home/peter/clone_digger/biopython-1.44/Bio/MEME/Parser.py,
/home/peter/clone_digger/biopython-1.44/Bio/MEME/__init__.py,
/home/peter/clone_digger/biopython-1.44/Bio/Emboss/primer3_format.py,
/home/peter/clone_digger/biopython-1.44/Bio/Emboss/Primer.py,
/home/peter/clone_digger/biopython-1.44/Bio/Emboss/Applications.py,
/home/peter/clone_digger/biopython-1.44/Bio/Emboss/primersearch_format.py,
/home/peter/clone_digger/biopython-1.44/Bio/Emboss/__init__.py,
/home/peter/clone_digger/biopython-1.44/Bio/GFF/binning.py,
/home/peter/clone_digger/biopython-1.44/Bio/GFF/GenericTools.py,
/home/peter/clone_digger/biopython-1.44/Bio/GFF/__init__.py,
/home/peter/clone_digger/biopython-1.44/Bio/GFF/easy.py,
/home/peter/clone_digger/biopython-1.44/Bio/Ndb/__init__.py,
/home/peter/clone_digger/biopython-1.44/Bio/FSSP/fssp_rec.py,
/home/peter/clone_digger/biopython-1.44/Bio/FSSP/FSSPTools.py,
/home/peter/clone_digger/biopython-1.44/Bio/FSSP/__init__.py

Clones detected: 1695

Parameters
clustering_threshold = 10
distance_threshold = 5
length_threshold = 30
hashing_depth = 1
clusterize_using_hash = False

Time elapsed
Construction of AST : 46.16 seconds
Building statement hash : 0.48 seconds
Building patterns : 2097.18 seconds
Marking similar statements : 3935.12 seconds
Finding similar sequences of statements : 23.38 seconds
Refining candidates : 1478.60 seconds
Total time: 7580.93

Clone # 1
Anti-unification distance between two trees = 4
Total size of two trees = 472
Total length of sequences = 130
Source file "/home/peter/clone_digger/biopython-1.44/Bio/Medline/nlmmedline_011101_format.py"
The first line is 133 Source file "/home/peter/clone_digger/biopython-1.44/Bio/Medline/nlmmedline_010319_format.py"
The first line is 128
group_elem("MeshHeadingList", Rep1(MeshHeading)) group_elem("MeshHeadingList", Rep1(MeshHeading))

simple_elem("MedlinePgn") simple_elem("MedlinePgn")

simple_elem("EndPage") simple_elem("EndPage")

simple_elem("StartPage") simple_elem("StartPage")

group_elem("Pagination",
Alt(StartPage + Opt(EndPage) + Opt(MedlinePgn), MedlinePgn)) group_elem("Pagination",
Alt(StartPage + Opt(EndPage) + Opt(MedlinePgn), MedlinePgn))

simple_elem("Affiliation") simple_elem("Affiliation")

group_elem("Author", author_name + Opt(Affiliation)) group_elem("Author", author_name + Opt(Affiliation))

group_elem("AuthorList", Rep1(Author), "CompleteYN") group_elem("AuthorList", Rep1(Author), "CompleteYN")

simple_elem("Language") simple_elem("Language")

simple_elem("PublicationType") simple_elem("PublicationType")

group_elem("PublicationTypeList", Rep1(PublicationType)) group_elem("PublicationTypeList", Rep1(PublicationType))

simple_elem("Title") # These were moved up, so that the definitions simple_elem("Title") # These were moved up, so that the definitions

simple_elem("Volume") # will be before Book. simple_elem("Volume") # will be before Book.

simple_elem("VernacularTitle") simple_elem("VernacularTitle")

simple_elem("CollectionTitle") simple_elem("CollectionTitle")

simple_elem("ArticleTitle") simple_elem("ArticleTitle")

simple_elem("Publisher") simple_elem("Publisher")

group_elem("PubDate", pub_date) group_elem("PubDate", pub_date)

group_elem("Book", PubDate + Publisher + Title +
Opt(AuthorList) + Opt(CollectionTitle) + Opt(Volume)) group_elem("Book", PubDate + Publisher + Title +
Opt(AuthorList) + Opt(CollectionTitle) + Opt(Volume))

simple_elem("Country") simple_elem("Country")

simple_elem("MedlineTA") simple_elem("MedlineTA")

simple_elem("MedlineCode") simple_elem("MedlineCode")

group_elem("MedlineJournalInfo",
Opt(Country) + MedlineTA + Opt(MedlineCode) + Opt(NlmUniqueID)) group_elem("MedlineJournalInfo",
Opt(Country) + MedlineTA + Opt(MedlineCode) + Opt(NlmUniqueID))

simple_elem("DateOfElectronicPublication") simple_elem("DateOfElectronicPublication")

simple_elem("ISOAbbreviation") simple_elem("ISOAbbreviation")

simple_elem("Coden") simple_elem("Coden")

simple_elem("Issue") simple_elem("Issue")

group_elem("JournalIssue", Opt(Volume) + Opt(Issue) + PubDate) group_elem("JournalIssue", Opt(Volume) + Opt(Issue) + PubDate)

simple_elem("ISSN") simple_elem("ISSN")

group_elem("Journal",
Opt(ISSN) + \
JournalIssue + \
Opt(Coden) + \
Opt(Title) + \
Opt(ISOAbbreviation) group_elem("Journal",
Opt(ISSN) + \
JournalIssue + \
Opt(Coden) + \
Opt(Title) + \
Opt(ISOAbbreviation)

simple_elem("GrantID") simple_elem("GrantID")

simple_elem("Acronym") simple_elem("Acronym")

simple_elem("Agency") simple_elem("Agency")

group_elem("Grant", Opt(GrantID) + Opt(Acronym) + Opt(Agency)) group_elem("Grant", Opt(GrantID) + Opt(Acronym) + Opt(Agency))

group_elem("GrantList", Rep1(Grant), "CompleteYN") group_elem("GrantList", Rep1(Grant), "CompleteYN")

simple_elem("AccessionNumber") simple_elem("AccessionNumber")

group_elem("AccessionNumberList", Rep1(AccessionNumber)) group_elem("AccessionNumberList", Rep1(AccessionNumber))

simple_elem("DataBankName") simple_elem("DataBankName")

group_elem("DataBank", DataBankName + Opt(AccessionNumberList)) group_elem("DataBank", DataBankName + Opt(AccessionNumberList))

group_elem("DataBankList", Rep1(DataBank), "CompleteYN") group_elem("DataBankList", Rep1(DataBank), "CompleteYN")

group_elem("Article",
Alt(Journal, Book) + \
ArticleTitle + \
Pagination + \
Opt(Abstract) + \
Opt(Affiliation) + \
Opt(AuthorList) + \
Rep1(Language) + \
Opt(DataBankList) + \
Opt(GrantList) + \
PublicationTypeList + \
Opt(VernacularTitle) + \
Opt(DateOfElectronicPublication) group_elem("Article",
Alt(Journal, Book) + \
ArticleTitle + \
Pagination + \
Opt(Abstract) + \
Opt(Affiliation) + \
Opt(AuthorList) + \
Rep1(Language) + \
Opt(DataBankList) + \
Opt(GrantList) + \
PublicationTypeList + \
Opt(VernacularTitle) + \
Opt(DateOfElectronicPublication)

group_elem("NCBIArticle", PMID + Article + Opt(MedlineJournalInfo)) group_elem("NCBIArticle", PMID + Article + Opt(MedlineJournalInfo))

simple_elem("MedlineID") simple_elem("MedlineID")

simple_elem("Note") simple_elem("Note")

simple_elem("RefSource") simple_elem("RefSource")

Ref_template = RefSource + Opt(Alt(PMID, MedlineID)) + Opt(Note) Ref_template = RefSource + Opt(MedlineID) + Opt(Note)

group_elem("OriginalReportIn", Ref_template) group_elem("OriginalReportIn", Ref_template)

group_elem("SummaryForPatientsIn", Ref_template) group_elem("SummaryForPatientsIn", Ref_template)

group_elem("CommentOn", Ref_template) group_elem("CommentOn", Ref_template)

group_elem("CommentIn", Ref_template) group_elem("CommentIn", Ref_template)

group_elem("ErratumIn", Ref_template) group_elem("ErratumIn", Ref_template)

group_elem("RepublishedFrom", Ref_template) group_elem("RepublishedFrom", Ref_template)

group_elem("RepublishedIn", Ref_template) group_elem("RepublishedIn", Ref_template)

group_elem("RetractionOf", Ref_template) group_elem("RetractionOf", Ref_template)

group_elem("RetractionIn", Ref_template) group_elem("RetractionIn", Ref_template)

group_elem("UpdateIn", Ref_template) group_elem("UpdateIn", Ref_template)

group_elem("UpdateOf", Ref_template) group_elem("UpdateOf", Ref_template)

group_elem("CommentsCorrections",
Rep(CommentOn) + Rep(CommentIn) + \
Rep(ErratumIn) + \
Rep(RepublishedFrom) + Rep(RepublishedIn) + \
Rep(RetractionOf) + Rep(RetractionIn) + \
Rep(UpdateIn) + Rep(UpdateOf) + \
Rep(SummaryForPatientsIn) + Rep(OriginalReportIn) group_elem("CommentsCorrections",
Rep(CommentOn) + Rep(CommentIn) + \
Rep(ErratumIn) + \
Rep(RepublishedFrom) + Rep(RepublishedIn) + \
Rep(RetractionOf) + Rep(RetractionIn) + \
Rep(UpdateIn) + Rep(UpdateOf) + \
Rep(SummaryForPatientsIn) + Rep(OriginalReportIn)

simple_elem("NumberOfReferences") simple_elem("NumberOfReferences")

group_elem("PersonalNameSubject", personal_name) group_elem("PersonalNameSubject", personal_name)

group_elem("PersonalNameSubjectList", Rep1(PersonalNameSubject)) group_elem("PersonalNameSubjectList", Rep1(PersonalNameSubject))

simple_elem("GeneSymbol") simple_elem("GeneSymbol")

group_elem("GeneSymbolList", Rep1(GeneSymbol)) group_elem("GeneSymbolList", Rep1(GeneSymbol))

simple_elem("NameOfSubstance") simple_elem("NameOfSubstance")

simple_elem("CASRegistryNumber") simple_elem("CASRegistryNumber")

Clone # 13
Anti-unification distance between two trees = 4
Total size of two trees = 158
Total length of sequences = 4
Source file "/home/peter/clone_digger/biopython-1.44/Bio/Gobase/__init__.py"
The first line is 133 Source file "/home/peter/clone_digger/biopython-1.44/Bio/Rebase/__init__.py"
The first line is 78
class Iterator:
def __init__(self, handle, parser=None):
if type(handle) is not FileType and type(handle) is not InstanceType:
raise ValueError, "I expected a file handle or file-like object"
self._uhandle = SGMLHandle( File.UndoHandle( handle ) )
self._parser = parser
def next(self):
lines = []
first_tag = 'Recognition Sequence'
while 1:
line = self._uhandle.readline()
if not line:
break
if line[:len( first_tag )] == 'first_tag':
self._uhandle.saveline(line)
break
if not line:
return None
if self._parser is not None:
return self._parser.parse(File.StringHandle(data))
return data
def __iter__(self):
return iter(self.next, None) class Iterator:
def __init__(self, handle, parser=None):
if type(handle) is not FileType and type(handle) is not InstanceType:
raise ValueError, "I expected a file handle or file-like object"
self._uhandle = SGMLHandle( File.UndoHandle( handle ) )
self._parser = parser
def next(self):
lines = []
first_tag = 'Recognition Sequence'
while 1:
line = self._uhandle.readline()
if not line:
break
if line[:len( first_tag )] == 'first_tag':
self._uhandle.saveline(line)
break
if not line:
return None
if self._parser is not None:
return self._parser.parse(File.StringHandle(data))
return data
def __iter__(self):
return iter(self.next, None)

class Dictionary:
__filename_key = '__filename'
def __init__(self, indexname, parser=None):
self._index = Index.Index(indexname)
self._handle = open(self._index[Dictionary.__filename_key])
self._parser = parser
def __len__(self):
return len(self._index)
def __getitem__(self, key):
start, len = self._index[key]
self._handle.seek(start)
data = self._handle.read(len)
if self._parser is not None:
return self._parser.parse(File.StringHandle(data))
return data
def __getattr__(self, name):
return getattr(self._index, name) class Dictionary:
__filename_key = '__filename'
def __init__(self, indexname, parser=None):
self._index = Index.Index(indexname)
self._handle = open(self._index[Dictionary.__filename_key])
self._parser = parser
def __len__(self):
return len(self._index)
def __getitem__(self, key):
start, len = self._index[key]
self._handle.seek(start)
data = self._handle.read(len)
if self._parser is not None:
return self._parser.parse(File.StringHandle(data))
return data
def __getattr__(self, name):
return getattr(self._index, name)

Clone # 20
Anti-unification distance between two trees = 3
Total size of two trees = 142
Total length of sequences = 22
Source file "/home/peter/clone_digger/biopython-1.44/Bio/SwissProt/SProt.py"
The first line is 224 Source file "/home/peter/clone_digger/biopython-1.44/Bio/PubMed.py"
The first line is 39
def __init__(self, delay=5.0, parser=None):
self.parser = parser
self.limiter = RequestLimiter(delay) def __init__(self, delay=5.0, parser=None):
self.parser = parser
self.limiter = RequestLimiter(delay)

def __len__(self):
raise NotImplementedError, "SwissProt contains lots of entries" def __len__(self):
raise NotImplementedError, "PubMed contains lots of entries"

def clear(self):
raise NotImplementedError, "This is a read-only dictionary" def clear(self):
raise NotImplementedError, "This is a read-only dictionary"

def __setitem__(self, key, item):
raise NotImplementedError, "This is a read-only dictionary" def __setitem__(self, key, item):
raise NotImplementedError, "This is a read-only dictionary"

def update(self):
raise NotImplementedError, "This is a read-only dictionary" def update(self):
raise NotImplementedError, "This is a read-only dictionary"

def copy(self):
raise NotImplementedError, "You don't need to do this..." def copy(self):
raise NotImplementedError, "You don't need to do this..."

def keys(self):
raise NotImplementedError, "You don't really want to do this..." def keys(self):
raise NotImplementedError, "You don't really want to do this..."

def items(self):
raise NotImplementedError, "You don't really want to do this..." def items(self):
raise NotImplementedError, "You don't really want to do this..."

def values(self):
raise NotImplementedError, "You don't really want to do this..." def values(self):
raise NotImplementedError, "You don't really want to do this..."

def has_key(self, id):
try:
self[id]
except KeyError:
return 0
return 1 def has_key(self, id):
try:
self[id]
except KeyError:
return 0
return 1

def get(self, id, failobj=None):
try:
return self[id]
except KeyError:
return failobj
raise "How did I get here?" def get(self, id, failobj=None):
try:
return self[id]
except KeyError:
return failobj
raise "How did I get here?"

Clone # 24
Anti-unification distance between two trees = 0
Total size of two trees = 120
Total length of sequences = 12
Source file "/home/peter/clone_digger/biopython-1.44/Bio/MEME/Parser.py"
The first line is 318 Source file "/home/peter/clone_digger/biopython-1.44/Bio/MEME/Parser.py"
The first line is 267
ls = line.split() ls = line.split()

self.data._add_diagram_for_sequence(ls[1], self._current_seq) self.data._add_diagram_for_sequence(ls[1], self._current_seq)

ds = ls[1].split('_') ds = ls[1].split('_')

i = 0 i = 0

start = 0 start = 0

for i in range(0,len(ds)):
if ds[i].find('[') != -1 or ds[i].find('<') != -1:
inst = Motif.Instance()
inst._seqname (self._current_seq)
inst._start (start)
r = re.compile('\d+')
mn = r.findall(ds[i])[0]
if ds[i].find('-') != -1:
inst.strand = '-'
inst.strand = '+'
motif = self.data.get_motif_by_name(mn)
motif.add_instance(inst)
start += motif.length
start += int(ds[i]) for i in range(0,len(ds)):
if ds[i].find('[') != -1 or ds[i].find('<') != -1:
inst = Motif.Instance()
inst._seqname (self._current_seq)
inst._start (start)
r = re.compile('\d+')
mn = r.findall(ds[i])[0]
if ds[i].find('-') != -1:
inst.strand = '-'
inst.strand = '+'
motif = self.data.get_motif_by_name(mn)
motif.add_instance(inst)
start += motif.length
start += int(ds[i])

Clone # 25
Anti-unification distance between two trees = 3
Total size of two trees = 120
Total length of sequences = 20
Source file "/home/peter/clone_digger/biopython-1.44/Bio/Restriction/Restriction.py"
The first line is 1164 Source file "/home/peter/clone_digger/biopython-1.44/Bio/Restriction/Restriction.py"
The first line is 927
def catalyse(self, dna, linear=True) :
r = self.search(dna, linear)
d = self.dna
if not r : return d[1:],
fragments = []
length = len(r)-1
if d.is_linear() :
fragments.append(d[1:r[0]])
if length :
fragments += [d[r[x]:r[x+1]] for x in xrange(length)]
fragments.append(d[r[-1]:])
fragments.append(d[r[-1]:]+d[1:r[0]])
if not length:
return tuple(fragments)
fragments += [d[r[x]:r[x+1]] for x in xrange(length)]
return tuple(fragments) def catalyse(self, dna, linear=True) :
r = self.search(dna, linear)
d = self.dna
if not r : return d[1:],
fragments = []
length = len(r)-1
if d.is_linear() :
fragments.append(d[1:r[0]])
if length :
fragments += [d[r[x]:r[x+1]] for x in xrange(length)]
fragments.append(d[r[-1]:])
fragments.append(d[r[-1]:]+d[1:r[0]])
if not length:
return tuple(fragments)
fragments += [d[r[x]:r[x+1]] for x in xrange(length)]
return tuple(fragments)

catalyze = catalyse = classmethod(catalyse) catalyze = catalyse = classmethod(catalyse)

def is_blunt(self) :
return False def is_blunt(self) :
return True

is_blunt = classmethod(is_blunt) is_blunt = classmethod(is_blunt)

def is_5overhang(self) :
return False def is_5overhang(self) :
return False

is_5overhang = classmethod(is_5overhang) is_5overhang = classmethod(is_5overhang)

def is_3overhang(self) :
return True def is_3overhang(self) :
return False

is_3overhang = classmethod(is_3overhang) is_3overhang = classmethod(is_3overhang)

def overhang(self) :
return "3'  overhang" def overhang(self) :
return 'blunt'

overhang = classmethod(overhang) overhang = classmethod(overhang)

Clone # 26
Anti-unification distance between two trees = 2
Total size of two trees = 118
Total length of sequences = 20
Source file "/home/peter/clone_digger/biopython-1.44/Bio/GenBank/__init__.py"
The first line is 1302 Source file "/home/peter/clone_digger/biopython-1.44/Bio/Prosite/__init__.py"
The first line is 284
def __len__(self):
raise NotImplementedError, "GenBank contains lots of entries" def __len__(self):
raise NotImplementedError, "Prosite contains lots of entries"

def clear(self):
raise NotImplementedError, "This is a read-only dictionary" def clear(self):
raise NotImplementedError, "This is a read-only dictionary"

def __setitem__(self, key, item):
raise NotImplementedError, "This is a read-only dictionary" def __setitem__(self, key, item):
raise NotImplementedError, "This is a read-only dictionary"

def update(self):
raise NotImplementedError, "This is a read-only dictionary" def update(self):
raise NotImplementedError, "This is a read-only dictionary"

def copy(self):
raise NotImplementedError, "You don't need to do this..." def copy(self):
raise NotImplementedError, "You don't need to do this..."

def keys(self):
raise NotImplementedError, "You don't really want to do this..." def keys(self):
raise NotImplementedError, "You don't really want to do this..."

def items(self):
raise NotImplementedError, "You don't really want to do this..." def items(self):
raise NotImplementedError, "You don't really want to do this..."

def values(self):
raise NotImplementedError, "You don't really want to do this..." def values(self):
raise NotImplementedError, "You don't really want to do this..."

def has_key(self, id):
try:
self[id]
except KeyError:
return 0
return 1 def has_key(self, id):
try:
self[id]
except KeyError:
return 0
return 1

def get(self, id, failobj=None):
try:
return self[id]
except KeyError:
return failobj
raise "How did I get here?" def get(self, id, failobj=None):
try:
return self[id]
except KeyError:
return failobj
raise "How did I get here?"

Clone # 35
Anti-unification distance between two trees = 1
Total size of two trees = 110
Total length of sequences = 4
Source file "/home/peter/clone_digger/biopython-1.44/Bio/UniGene/__init__.py"
The first line is 333 Source file "/home/peter/clone_digger/biopython-1.44/Bio/Enzyme/__init__.py"
The first line is 167
class RecordParser(AbstractParser):
def __init__(self):
self._scanner = _Scanner()
self._consumer = _RecordConsumer()
def parse(self, handle):
if isinstance(handle, File.UndoHandle):
uhandle = handle
uhandle = File.UndoHandle(handle)
self._scanner.feed(uhandle, self._consumer)
return self._consumer.unigene_record class RecordParser(AbstractParser):
def __init__(self):
self._scanner = _Scanner()
self._consumer = _RecordConsumer()
def parse(self, handle):
if isinstance(handle, File.UndoHandle):
uhandle = handle
uhandle = File.UndoHandle(handle)
self._scanner.feed(uhandle, self._consumer)
return self._consumer.enzyme_record

class Iterator:
def __init__(self, handle, parser=None):
self._uhandle = File.UndoHandle(handle)
def next(self):
self._parser = RecordParser()
lines = []
while 1:
line = self._uhandle.readline()
if not line: break
if line[:2] == '//':
break
lines.append(line)
if not lines:
return None
lines.append('//')
data = string.join(lines,'')
if self._parser is not None:
return self._parser.parse(File.StringHandle(data))
return data
def __iter__(self):
return iter(self.next, None) class Iterator:
def __init__(self, handle, parser=None):
self._uhandle = File.UndoHandle(handle)
def next(self):
self._parser = RecordParser()
lines = []
while 1:
line = self._uhandle.readline()
if not line: break
if line[:2] == '//':
break
lines.append(line)
if not lines:
return None
lines.append('//')
data = string.join(lines,'')
if self._parser is not None:
return self._parser.parse(File.StringHandle(data))
return data
def __iter__(self):
return iter(self.next, None)

Clone # 36
Anti-unification distance between two trees = 3
Total size of two trees = 110
Total length of sequences = 16
Source file "/home/peter/clone_digger/biopython-1.44/Bio/Restriction/Restriction.py"
The first line is 1290 Source file "/home/peter/clone_digger/biopython-1.44/Bio/Restriction/Restriction.py"
The first line is 1425
def _drop(self) :
length = len(self.dna)
drop = itertools.dropwhile
take = itertools.takewhile
if self.dna.is_linear() :
self.results = [x for x in drop(lambda x:x<1, self.results)]
self.results = [x for x in take(lambda x:x for index, location in enumerate(self.results) :
if location < 1 :
self.results[index] += length
break
for index, location in enumerate(self.results[::-1]) :
if location > length :
self.results[-(index+1)] -= length
break
return def _drop(self) :
length = len(self.dna)
drop = itertools.dropwhile
take = itertools.takewhile
if self.dna.is_linear() :
self.results = [x for x in drop(lambda x : x < 1, self.results)]
self.results = [x for x in take(lambda x : x for index, location in enumerate(self.results) :
if location < 1 :
self.results[index] += length
break
for index, location in enumerate(self.results[::-1]) :
if location > length :
self.results[-(index+1)] -= length
break
return

_drop = classmethod(_drop) _drop = classmethod(_drop)

def is_defined(self) :
return True def is_defined(self) :
return False

is_defined = classmethod(is_defined) is_defined = classmethod(is_defined)

def is_ambiguous(self) :
return False def is_ambiguous(self) :
return True

is_ambiguous = classmethod(is_ambiguous) is_ambiguous = classmethod(is_ambiguous)

def is_unknown(self) :
return False def is_unknown(self) :
return False

is_unknown = classmethod(is_unknown) is_unknown = classmethod(is_unknown)

Clone # 38
Anti-unification distance between two trees = 2
Total size of two trees = 105
Total length of sequences = 10
Source file "/home/peter/clone_digger/biopython-1.44/Bio/Rebase/__init__.py"
The first line is 129 Source file "/home/peter/clone_digger/biopython-1.44/Bio/SwissProt/SProt.py"
The first line is 184
__filename_key = '__filename' __filename_key = '__filename'

def __init__(self, indexname, parser=None):
self._index = Index.Index(indexname)
self._handle = open(self._index[Dictionary.__filename_key])
self._parser = parser def __init__(self, indexname, parser=None):
self._index = Index.Index(indexname)
self._handle = open(self._index[self.__filename_key])
self._parser = parser

def __len__(self):
return len(self._index) def __len__(self):
return len(self._index)

def __getitem__(self, key):
start, len = self._index[key]
self._handle.seek(start)
data = self._handle.read(len)
if self._parser is not None:
return self._parser.parse(File.StringHandle(data))
return data def __getitem__(self, key):
start, len = self._index[key]
self._handle.seek(start)
data = self._handle.read(len)
if self._parser is not None:
return self._parser.parse(File.StringHandle(data))
return data

def __getattr__(self, name):
return getattr(self._index, name) def __getattr__(self, name):
return getattr(self._index, name)

Clone # 42
Anti-unification distance between two trees = 4
Total size of two trees = 104
Total length of sequences = 16
Source file "/home/peter/clone_digger/biopython-1.44/Bio/Nexus/Nexus.py"
The first line is 964 Source file "/home/peter/clone_digger/biopython-1.44/Bio/Nexus/Nexus.py"
The first line is 939
charpartition={} taxpartition={}

quotelevel=False quotelevel=False

opts=CharBuffer(options) opts=CharBuffer(options)

name=self._name_n_vector(opts) name=self._name_n_vector(opts)

if not name:
raise NexusError, 'Formatting error in charpartition: %s ' % options if not name:
raise NexusError, 'Formatting error in taxpartition: %s ' % options

sub='' sub=''

while True:
w=opts.next()
if w is None or (w==',' and not quotelevel):
subname,subindices=self._get_indices(sub,set_type=CHARSET,separator=':')
charpartition[subname]=_make_unique(subindices)
sub=''
if w is None:
break
if w=="'":
quotelevel=not quotelevel
sub+=w while True:
w=opts.next()
if w is None or (w==',' and not quotelevel):
subname,subindices=self._get_indices(sub,set_type=TAXSET,separator=':')
taxpartition[subname]=_make_unique(subindices)
sub=''
if w is None:
break
if w=="'":
quotelevel=not quotelevel
sub+=w

self.charpartitions[name]=charpartition self.taxpartitions[name]=taxpartition

Clone # 45
Anti-unification distance between two trees = 4
Total size of two trees = 102
Total length of sequences = 28
Source file "/home/peter/clone_digger/biopython-1.44/Bio/Medline/nlmmedline_010319_format.py"
The first line is 243 Source file "/home/peter/clone_digger/biopython-1.44/Bio/Medline/nlmmedline_011101_format.py"
The first line is 249
group_elem("Chemical", CASRegistryNumber + NameOfSubstance) group_elem("Chemical", Alt(CASRegistryNumber, RegistryNumber) + \
NameOfSubstance)

group_elem("ChemicalList", Rep1(Chemical)) group_elem("ChemicalList", Rep1(Chemical))

simple_elem("CitationSubset") simple_elem("CitationSubset")

simple_elem("GeneralNote", "Owner") simple_elem("GeneralNote", "Owner")

group_elem("Investigator", personal_name + Opt(Affiliation)) group_elem("Investigator", personal_name + Opt(Affiliation))

group_elem("InvestigatorList", Rep1(Investigator)) group_elem("InvestigatorList", Rep1(Investigator))

simple_elem("OtherID", "Source") simple_elem("OtherID", "Source")

simple_elem("SpaceFlightMission") simple_elem("SpaceFlightMission")

simple_elem("Keyword", "MajorTopicYN") simple_elem("Keyword", "MajorTopicYN")

group_elem("KeywordList", Rep1(Keyword), "Owner") group_elem("KeywordList", Rep1(Keyword), "Owner")

group_elem("OtherAbstract",
AbstractText + Opt(CopyrightInformation),
"Type") group_elem("OtherAbstract",
AbstractText + Opt(CopyrightInformation),
"Type")

group_elem("DateRevised", normal_date) group_elem("DateRevised", normal_date)

group_elem("DateCompleted", normal_date) group_elem("DateCompleted", normal_date)

group_elem("DateCreated", normal_date) group_elem("DateCreated", normal_date)

Clone # 54
Anti-unification distance between two trees = 2
Total size of two trees = 99
Total length of sequences = 14
Source file "/home/peter/clone_digger/biopython-1.44/Bio/GenBank/__init__.py"
The first line is 555 Source file "/home/peter/clone_digger/biopython-1.44/Bio/GenBank/__init__.py"
The first line is 1084
def authors(self, content):
self._current_ref.authors = content def authors(self, content):
self._cur_reference.authors = content

def consrtm(self, content):
self._current_ref.consrtm = content def consrtm(self, content):
self._cur_reference.consrtm = content

def title(self, content):
self._current_ref.title = content def title(self, content):
self._cur_reference.title = content

def journal(self, content):
self._current_ref.journal = content def journal(self, content):
self._cur_reference.journal = content

def medline_id(self, content):
self._current_ref.medline_id = content def medline_id(self, content):
self._cur_reference.medline_id = content

def pubmed_id(self, content):
self._current_ref.pubmed_id = content def pubmed_id(self, content):
self._cur_reference.pubmed_id = content

def remark(self, content):
self._current_ref.comment = content def remark(self, content):
self._cur_reference.remark = content

Clone # 55
Anti-unification distance between two trees = 4
Total size of two trees = 97
Total length of sequences = 18
Source file "/home/peter/clone_digger/biopython-1.44/Bio/MEME/Parser.py"
The first line is 325 Source file "/home/peter/clone_digger/biopython-1.44/Bio/MEME/Parser.py"
The first line is 299
inst = Motif.Instance() inst = Motif.Instance()

inst._seqname (self._current_seq) inst._seqname (ls[0])

inst._start (start) inst._start (start)

r = re.compile('\d+') r = re.compile('\d+')

mn = r.findall(ds[i])[0] mn = r.findall(ds[i])[0]

if ds[i].find('-') != -1:
inst.strand = '-'
inst.strand = '+' if ds[i].find('-') != -1:
inst.strand = '-'
inst.strand = '+'

motif = self.data.get_motif_by_name(mn) motif = self.data.get_motif_by_name(mn)

motif.add_instance(inst) motif.add_instance(inst)

start += motif.length start += motif.length

Clone # 62
Anti-unification distance between two trees = 4
Total size of two trees = 87
Total length of sequences = 8
Source file "/home/peter/clone_digger/biopython-1.44/Bio/Blast/NCBIStandalone.py"
The first line is 1482 Source file "/home/peter/clone_digger/biopython-1.44/Bio/Blast/NCBIStandalone.py"
The first line is 1426
def end_alignment(self):
_AlignmentConsumer.end_alignment(self)
if self._alignment.hsps:
self._round.alignments.append(self._alignment)
if self._multiple_alignment:
self._round.multiple_alignment = self._multiple_alignment def end_alignment(self):
_AlignmentConsumer.end_alignment(self)
if self._alignment.hsps:
self.data.alignments.append(self._alignment)
if self._multiple_alignment.alignment:
self.data.multiple_alignment = self._multiple_alignment

def end_hsp(self):
_HSPConsumer.end_hsp(self)
try:
self._alignment.hsps.append(self._hsp)
except AttributeError:
raise SyntaxError, "Found an HSP before an alignment" def end_hsp(self):
_HSPConsumer.end_hsp(self)
try:
self._alignment.hsps.append(self._hsp)
except AttributeError:
raise SyntaxError, "Found an HSP before an alignment"

def end_database_report(self):
_DatabaseReportConsumer.end_database_report(self)
self.data.__dict__.update(self._dr.__dict__) def end_database_report(self):
_DatabaseReportConsumer.end_database_report(self)
self.data.__dict__.update(self._dr.__dict__)

def end_parameters(self):
_ParametersConsumer.end_parameters(self)
self.data.__dict__.update(self._params.__dict__) def end_parameters(self):
_ParametersConsumer.end_parameters(self)
self.data.__dict__.update(self._params.__dict__)

(*) Warning: the highlighting of differences is based on diff and doesn't reflect the tree-based clone detection algorithm.

Clone Digger is aimed to find software clones in Python and Java programs. It is provided under the GPL license and can be downloaded from the site http://clonedigger.sourceforge.net

Source file "/home/peter/clone_digger/biopython-1.44/Bio/Medline/nlmmedline_011101_format.py" The first line is 133		Source file "/home/peter/clone_digger/biopython-1.44/Bio/Medline/nlmmedline_010319_format.py" The first line is 128
group_elem("MeshHeadingList", Rep1(MeshHeading))		group_elem("MeshHeadingList", Rep1(MeshHeading))
simple_elem("MedlinePgn")		simple_elem("MedlinePgn")
simple_elem("EndPage")		simple_elem("EndPage")
simple_elem("StartPage")		simple_elem("StartPage")
group_elem("Pagination", Alt(StartPage + Opt(EndPage) + Opt(MedlinePgn), MedlinePgn))		group_elem("Pagination", Alt(StartPage + Opt(EndPage) + Opt(MedlinePgn), MedlinePgn))
simple_elem("Affiliation")		simple_elem("Affiliation")
group_elem("Author", author_name + Opt(Affiliation))		group_elem("Author", author_name + Opt(Affiliation))
group_elem("AuthorList", Rep1(Author), "CompleteYN")		group_elem("AuthorList", Rep1(Author), "CompleteYN")
simple_elem("Language")		simple_elem("Language")
simple_elem("PublicationType")		simple_elem("PublicationType")
group_elem("PublicationTypeList", Rep1(PublicationType))		group_elem("PublicationTypeList", Rep1(PublicationType))
simple_elem("Title") # These were moved up, so that the definitions		simple_elem("Title") # These were moved up, so that the definitions
simple_elem("Volume") # will be before Book.		simple_elem("Volume") # will be before Book.
simple_elem("VernacularTitle")		simple_elem("VernacularTitle")
simple_elem("CollectionTitle")		simple_elem("CollectionTitle")
simple_elem("ArticleTitle")		simple_elem("ArticleTitle")
simple_elem("Publisher")		simple_elem("Publisher")
group_elem("PubDate", pub_date)		group_elem("PubDate", pub_date)
group_elem("Book", PubDate + Publisher + Title + Opt(AuthorList) + Opt(CollectionTitle) + Opt(Volume))		group_elem("Book", PubDate + Publisher + Title + Opt(AuthorList) + Opt(CollectionTitle) + Opt(Volume))
simple_elem("Country")		simple_elem("Country")
simple_elem("MedlineTA")		simple_elem("MedlineTA")
simple_elem("MedlineCode")		simple_elem("MedlineCode")
group_elem("MedlineJournalInfo", Opt(Country) + MedlineTA + Opt(MedlineCode) + Opt(NlmUniqueID))		group_elem("MedlineJournalInfo", Opt(Country) + MedlineTA + Opt(MedlineCode) + Opt(NlmUniqueID))
simple_elem("DateOfElectronicPublication")		simple_elem("DateOfElectronicPublication")
simple_elem("ISOAbbreviation")		simple_elem("ISOAbbreviation")
simple_elem("Coden")		simple_elem("Coden")
simple_elem("Issue")		simple_elem("Issue")
group_elem("JournalIssue", Opt(Volume) + Opt(Issue) + PubDate)		group_elem("JournalIssue", Opt(Volume) + Opt(Issue) + PubDate)
simple_elem("ISSN")		simple_elem("ISSN")
group_elem("Journal", Opt(ISSN) + \ JournalIssue + \ Opt(Coden) + \ Opt(Title) + \ Opt(ISOAbbreviation)		group_elem("Journal", Opt(ISSN) + \ JournalIssue + \ Opt(Coden) + \ Opt(Title) + \ Opt(ISOAbbreviation)
simple_elem("GrantID")		simple_elem("GrantID")
simple_elem("Acronym")		simple_elem("Acronym")
simple_elem("Agency")		simple_elem("Agency")
group_elem("Grant", Opt(GrantID) + Opt(Acronym) + Opt(Agency))		group_elem("Grant", Opt(GrantID) + Opt(Acronym) + Opt(Agency))
group_elem("GrantList", Rep1(Grant), "CompleteYN")		group_elem("GrantList", Rep1(Grant), "CompleteYN")
simple_elem("AccessionNumber")		simple_elem("AccessionNumber")
group_elem("AccessionNumberList", Rep1(AccessionNumber))		group_elem("AccessionNumberList", Rep1(AccessionNumber))
simple_elem("DataBankName")		simple_elem("DataBankName")
group_elem("DataBank", DataBankName + Opt(AccessionNumberList))		group_elem("DataBank", DataBankName + Opt(AccessionNumberList))
group_elem("DataBankList", Rep1(DataBank), "CompleteYN")		group_elem("DataBankList", Rep1(DataBank), "CompleteYN")
group_elem("Article", Alt(Journal, Book) + \ ArticleTitle + \ Pagination + \ Opt(Abstract) + \ Opt(Affiliation) + \ Opt(AuthorList) + \ Rep1(Language) + \ Opt(DataBankList) + \ Opt(GrantList) + \ PublicationTypeList + \ Opt(VernacularTitle) + \ Opt(DateOfElectronicPublication)		group_elem("Article", Alt(Journal, Book) + \ ArticleTitle + \ Pagination + \ Opt(Abstract) + \ Opt(Affiliation) + \ Opt(AuthorList) + \ Rep1(Language) + \ Opt(DataBankList) + \ Opt(GrantList) + \ PublicationTypeList + \ Opt(VernacularTitle) + \ Opt(DateOfElectronicPublication)
group_elem("NCBIArticle", PMID + Article + Opt(MedlineJournalInfo))		group_elem("NCBIArticle", PMID + Article + Opt(MedlineJournalInfo))
simple_elem("MedlineID")		simple_elem("MedlineID")
simple_elem("Note")		simple_elem("Note")
simple_elem("RefSource")		simple_elem("RefSource")
Ref_template = RefSource + Opt(Alt(PMID, MedlineID)) + Opt(Note)		Ref_template = RefSource + Opt(MedlineID) + Opt(Note)
group_elem("OriginalReportIn", Ref_template)		group_elem("OriginalReportIn", Ref_template)
group_elem("SummaryForPatientsIn", Ref_template)		group_elem("SummaryForPatientsIn", Ref_template)
group_elem("CommentOn", Ref_template)		group_elem("CommentOn", Ref_template)
group_elem("CommentIn", Ref_template)		group_elem("CommentIn", Ref_template)
group_elem("ErratumIn", Ref_template)		group_elem("ErratumIn", Ref_template)
group_elem("RepublishedFrom", Ref_template)		group_elem("RepublishedFrom", Ref_template)
group_elem("RepublishedIn", Ref_template)		group_elem("RepublishedIn", Ref_template)
group_elem("RetractionOf", Ref_template)		group_elem("RetractionOf", Ref_template)
group_elem("RetractionIn", Ref_template)		group_elem("RetractionIn", Ref_template)
group_elem("UpdateIn", Ref_template)		group_elem("UpdateIn", Ref_template)
group_elem("UpdateOf", Ref_template)		group_elem("UpdateOf", Ref_template)
group_elem("CommentsCorrections", Rep(CommentOn) + Rep(CommentIn) + \ Rep(ErratumIn) + \ Rep(RepublishedFrom) + Rep(RepublishedIn) + \ Rep(RetractionOf) + Rep(RetractionIn) + \ Rep(UpdateIn) + Rep(UpdateOf) + \ Rep(SummaryForPatientsIn) + Rep(OriginalReportIn)		group_elem("CommentsCorrections", Rep(CommentOn) + Rep(CommentIn) + \ Rep(ErratumIn) + \ Rep(RepublishedFrom) + Rep(RepublishedIn) + \ Rep(RetractionOf) + Rep(RetractionIn) + \ Rep(UpdateIn) + Rep(UpdateOf) + \ Rep(SummaryForPatientsIn) + Rep(OriginalReportIn)
simple_elem("NumberOfReferences")		simple_elem("NumberOfReferences")
group_elem("PersonalNameSubject", personal_name)		group_elem("PersonalNameSubject", personal_name)
group_elem("PersonalNameSubjectList", Rep1(PersonalNameSubject))		group_elem("PersonalNameSubjectList", Rep1(PersonalNameSubject))
simple_elem("GeneSymbol")		simple_elem("GeneSymbol")
group_elem("GeneSymbolList", Rep1(GeneSymbol))		group_elem("GeneSymbolList", Rep1(GeneSymbol))
simple_elem("NameOfSubstance")		simple_elem("NameOfSubstance")
simple_elem("CASRegistryNumber")		simple_elem("CASRegistryNumber")

Source file "/home/peter/clone_digger/biopython-1.44/Bio/Gobase/__init__.py" The first line is 133		Source file "/home/peter/clone_digger/biopython-1.44/Bio/Rebase/__init__.py" The first line is 78
class Iterator: def __init__(self, handle, parser=None): if type(handle) is not FileType and type(handle) is not InstanceType: raise ValueError, "I expected a file handle or file-like object" self._uhandle = SGMLHandle( File.UndoHandle( handle ) ) self._parser = parser def next(self): lines = [] first_tag = 'Recognition Sequence' while 1: line = self._uhandle.readline() if not line: break if line[:len( first_tag )] == 'first_tag': self._uhandle.saveline(line) break if not line: return None if self._parser is not None: return self._parser.parse(File.StringHandle(data)) return data def __iter__(self): return iter(self.next, None)		class Iterator: def __init__(self, handle, parser=None): if type(handle) is not FileType and type(handle) is not InstanceType: raise ValueError, "I expected a file handle or file-like object" self._uhandle = SGMLHandle( File.UndoHandle( handle ) ) self._parser = parser def next(self): lines = [] first_tag = 'Recognition Sequence' while 1: line = self._uhandle.readline() if not line: break if line[:len( first_tag )] == 'first_tag': self._uhandle.saveline(line) break if not line: return None if self._parser is not None: return self._parser.parse(File.StringHandle(data)) return data def __iter__(self): return iter(self.next, None)
class Dictionary: __filename_key = '__filename' def __init__(self, indexname, parser=None): self._index = Index.Index(indexname) self._handle = open(self._index[Dictionary.__filename_key]) self._parser = parser def __len__(self): return len(self._index) def __getitem__(self, key): start, len = self._index[key] self._handle.seek(start) data = self._handle.read(len) if self._parser is not None: return self._parser.parse(File.StringHandle(data)) return data def __getattr__(self, name): return getattr(self._index, name)		class Dictionary: __filename_key = '__filename' def __init__(self, indexname, parser=None): self._index = Index.Index(indexname) self._handle = open(self._index[Dictionary.__filename_key]) self._parser = parser def __len__(self): return len(self._index) def __getitem__(self, key): start, len = self._index[key] self._handle.seek(start) data = self._handle.read(len) if self._parser is not None: return self._parser.parse(File.StringHandle(data)) return data def __getattr__(self, name): return getattr(self._index, name)

Source file "/home/peter/clone_digger/biopython-1.44/Bio/SwissProt/SProt.py" The first line is 224		Source file "/home/peter/clone_digger/biopython-1.44/Bio/PubMed.py" The first line is 39
def __init__(self, delay=5.0, parser=None): self.parser = parser self.limiter = RequestLimiter(delay)		def __init__(self, delay=5.0, parser=None): self.parser = parser self.limiter = RequestLimiter(delay)
def __len__(self): raise NotImplementedError, "SwissProt contains lots of entries"		def __len__(self): raise NotImplementedError, "PubMed contains lots of entries"
def clear(self): raise NotImplementedError, "This is a read-only dictionary"		def clear(self): raise NotImplementedError, "This is a read-only dictionary"
def __setitem__(self, key, item): raise NotImplementedError, "This is a read-only dictionary"		def __setitem__(self, key, item): raise NotImplementedError, "This is a read-only dictionary"
def update(self): raise NotImplementedError, "This is a read-only dictionary"		def update(self): raise NotImplementedError, "This is a read-only dictionary"
def copy(self): raise NotImplementedError, "You don't need to do this..."		def copy(self): raise NotImplementedError, "You don't need to do this..."
def keys(self): raise NotImplementedError, "You don't really want to do this..."		def keys(self): raise NotImplementedError, "You don't really want to do this..."
def items(self): raise NotImplementedError, "You don't really want to do this..."		def items(self): raise NotImplementedError, "You don't really want to do this..."
def values(self): raise NotImplementedError, "You don't really want to do this..."		def values(self): raise NotImplementedError, "You don't really want to do this..."
def has_key(self, id): try: self[id] except KeyError: return 0 return 1		def has_key(self, id): try: self[id] except KeyError: return 0 return 1
def get(self, id, failobj=None): try: return self[id] except KeyError: return failobj raise "How did I get here?"		def get(self, id, failobj=None): try: return self[id] except KeyError: return failobj raise "How did I get here?"

Source file "/home/peter/clone_digger/biopython-1.44/Bio/MEME/Parser.py" The first line is 318		Source file "/home/peter/clone_digger/biopython-1.44/Bio/MEME/Parser.py" The first line is 267
ls = line.split()		ls = line.split()
self.data._add_diagram_for_sequence(ls[1], self._current_seq)		self.data._add_diagram_for_sequence(ls[1], self._current_seq)
ds = ls[1].split('_')		ds = ls[1].split('_')
i = 0		i = 0
start = 0		start = 0
for i in range(0,len(ds)): if ds[i].find('[') != -1 or ds[i].find('<') != -1: inst = Motif.Instance() inst._seqname (self._current_seq) inst._start (start) r = re.compile('\d+') mn = r.findall(ds[i])[0] if ds[i].find('-') != -1: inst.strand = '-' inst.strand = '+' motif = self.data.get_motif_by_name(mn) motif.add_instance(inst) start += motif.length start += int(ds[i])		for i in range(0,len(ds)): if ds[i].find('[') != -1 or ds[i].find('<') != -1: inst = Motif.Instance() inst._seqname (self._current_seq) inst._start (start) r = re.compile('\d+') mn = r.findall(ds[i])[0] if ds[i].find('-') != -1: inst.strand = '-' inst.strand = '+' motif = self.data.get_motif_by_name(mn) motif.add_instance(inst) start += motif.length start += int(ds[i])

Source file "/home/peter/clone_digger/biopython-1.44/Bio/Restriction/Restriction.py" The first line is 1164		Source file "/home/peter/clone_digger/biopython-1.44/Bio/Restriction/Restriction.py" The first line is 927
def catalyse(self, dna, linear=True) : r = self.search(dna, linear) d = self.dna if not r : return d[1:], fragments = [] length = len(r)-1 if d.is_linear() : fragments.append(d[1:r[0]]) if length : fragments += [d[r[x]:r[x+1]] for x in xrange(length)] fragments.append(d[r[-1]:]) fragments.append(d[r[-1]:]+d[1:r[0]]) if not length: return tuple(fragments) fragments += [d[r[x]:r[x+1]] for x in xrange(length)] return tuple(fragments)		def catalyse(self, dna, linear=True) : r = self.search(dna, linear) d = self.dna if not r : return d[1:], fragments = [] length = len(r)-1 if d.is_linear() : fragments.append(d[1:r[0]]) if length : fragments += [d[r[x]:r[x+1]] for x in xrange(length)] fragments.append(d[r[-1]:]) fragments.append(d[r[-1]:]+d[1:r[0]]) if not length: return tuple(fragments) fragments += [d[r[x]:r[x+1]] for x in xrange(length)] return tuple(fragments)
catalyze = catalyse = classmethod(catalyse)		catalyze = catalyse = classmethod(catalyse)
def is_blunt(self) : return False		def is_blunt(self) : return True
is_blunt = classmethod(is_blunt)		is_blunt = classmethod(is_blunt)
def is_5overhang(self) : return False		def is_5overhang(self) : return False
is_5overhang = classmethod(is_5overhang)		is_5overhang = classmethod(is_5overhang)
def is_3overhang(self) : return True		def is_3overhang(self) : return False
is_3overhang = classmethod(is_3overhang)		is_3overhang = classmethod(is_3overhang)
def overhang(self) : return "3'  overhang"		def overhang(self) : return 'blunt'
overhang = classmethod(overhang)		overhang = classmethod(overhang)

Source file "/home/peter/clone_digger/biopython-1.44/Bio/UniGene/__init__.py" The first line is 333		Source file "/home/peter/clone_digger/biopython-1.44/Bio/Enzyme/__init__.py" The first line is 167
class RecordParser(AbstractParser): def __init__(self): self._scanner = _Scanner() self._consumer = _RecordConsumer() def parse(self, handle): if isinstance(handle, File.UndoHandle): uhandle = handle uhandle = File.UndoHandle(handle) self._scanner.feed(uhandle, self._consumer) return self._consumer.unigene_record		class RecordParser(AbstractParser): def __init__(self): self._scanner = _Scanner() self._consumer = _RecordConsumer() def parse(self, handle): if isinstance(handle, File.UndoHandle): uhandle = handle uhandle = File.UndoHandle(handle) self._scanner.feed(uhandle, self._consumer) return self._consumer.enzyme_record
class Iterator: def __init__(self, handle, parser=None): self._uhandle = File.UndoHandle(handle) def next(self): self._parser = RecordParser() lines = [] while 1: line = self._uhandle.readline() if not line: break if line[:2] == '//': break lines.append(line) if not lines: return None lines.append('//') data = string.join(lines,'') if self._parser is not None: return self._parser.parse(File.StringHandle(data)) return data def __iter__(self): return iter(self.next, None)		class Iterator: def __init__(self, handle, parser=None): self._uhandle = File.UndoHandle(handle) def next(self): self._parser = RecordParser() lines = [] while 1: line = self._uhandle.readline() if not line: break if line[:2] == '//': break lines.append(line) if not lines: return None lines.append('//') data = string.join(lines,'') if self._parser is not None: return self._parser.parse(File.StringHandle(data)) return data def __iter__(self): return iter(self.next, None)

Source file "/home/peter/clone_digger/biopython-1.44/Bio/Restriction/Restriction.py" The first line is 1290		Source file "/home/peter/clone_digger/biopython-1.44/Bio/Restriction/Restriction.py" The first line is 1425
def _drop(self) : length = len(self.dna) drop = itertools.dropwhile take = itertools.takewhile if self.dna.is_linear() : self.results = [x for x in drop(lambda x:x<1, self.results)] self.results = [x for x in take(lambda x:x for index, location in enumerate(self.results) : if location < 1 : self.results[index] += length break for index, location in enumerate(self.results[::-1]) : if location > length : self.results[-(index+1)] -= length break return		def _drop(self) : length = len(self.dna) drop = itertools.dropwhile take = itertools.takewhile if self.dna.is_linear() : self.results = [x for x in drop(lambda x : x < 1, self.results)] self.results = [x for x in take(lambda x : x for index, location in enumerate(self.results) : if location < 1 : self.results[index] += length break for index, location in enumerate(self.results[::-1]) : if location > length : self.results[-(index+1)] -= length break return
_drop = classmethod(_drop)		_drop = classmethod(_drop)
def is_defined(self) : return True		def is_defined(self) : return False
is_defined = classmethod(is_defined)		is_defined = classmethod(is_defined)
def is_ambiguous(self) : return False		def is_ambiguous(self) : return True
is_ambiguous = classmethod(is_ambiguous)		is_ambiguous = classmethod(is_ambiguous)
def is_unknown(self) : return False		def is_unknown(self) : return False
is_unknown = classmethod(is_unknown)		is_unknown = classmethod(is_unknown)

Source file "/home/peter/clone_digger/biopython-1.44/Bio/Rebase/__init__.py" The first line is 129		Source file "/home/peter/clone_digger/biopython-1.44/Bio/SwissProt/SProt.py" The first line is 184
__filename_key = '__filename'		__filename_key = '__filename'
def __init__(self, indexname, parser=None): self._index = Index.Index(indexname) self._handle = open(self._index[Dictionary.__filename_key]) self._parser = parser		def __init__(self, indexname, parser=None): self._index = Index.Index(indexname) self._handle = open(self._index[self.__filename_key]) self._parser = parser
def __len__(self): return len(self._index)		def __len__(self): return len(self._index)
def __getitem__(self, key): start, len = self._index[key] self._handle.seek(start) data = self._handle.read(len) if self._parser is not None: return self._parser.parse(File.StringHandle(data)) return data		def __getitem__(self, key): start, len = self._index[key] self._handle.seek(start) data = self._handle.read(len) if self._parser is not None: return self._parser.parse(File.StringHandle(data)) return data
def __getattr__(self, name): return getattr(self._index, name)		def __getattr__(self, name): return getattr(self._index, name)

Source file "/home/peter/clone_digger/biopython-1.44/Bio/Nexus/Nexus.py" The first line is 964		Source file "/home/peter/clone_digger/biopython-1.44/Bio/Nexus/Nexus.py" The first line is 939
charpartition={}		taxpartition={}
quotelevel=False		quotelevel=False
opts=CharBuffer(options)		opts=CharBuffer(options)
name=self._name_n_vector(opts)		name=self._name_n_vector(opts)
if not name: raise NexusError, 'Formatting error in charpartition: %s ' % options		if not name: raise NexusError, 'Formatting error in taxpartition: %s ' % options
sub=''		sub=''
while True: w=opts.next() if w is None or (w==',' and not quotelevel): subname,subindices=self._get_indices(sub,set_type=CHARSET,separator=':') charpartition[subname]=_make_unique(subindices) sub='' if w is None: break if w=="'": quotelevel=not quotelevel sub+=w		while True: w=opts.next() if w is None or (w==',' and not quotelevel): subname,subindices=self._get_indices(sub,set_type=TAXSET,separator=':') taxpartition[subname]=_make_unique(subindices) sub='' if w is None: break if w=="'": quotelevel=not quotelevel sub+=w
self.charpartitions[name]=charpartition		self.taxpartitions[name]=taxpartition

Source file "/home/peter/clone_digger/biopython-1.44/Bio/Medline/nlmmedline_010319_format.py" The first line is 243		Source file "/home/peter/clone_digger/biopython-1.44/Bio/Medline/nlmmedline_011101_format.py" The first line is 249
group_elem("Chemical", CASRegistryNumber + NameOfSubstance)		group_elem("Chemical", Alt(CASRegistryNumber, RegistryNumber) + \ NameOfSubstance)
group_elem("ChemicalList", Rep1(Chemical))		group_elem("ChemicalList", Rep1(Chemical))
simple_elem("CitationSubset")		simple_elem("CitationSubset")
simple_elem("GeneralNote", "Owner")		simple_elem("GeneralNote", "Owner")
group_elem("Investigator", personal_name + Opt(Affiliation))		group_elem("Investigator", personal_name + Opt(Affiliation))
group_elem("InvestigatorList", Rep1(Investigator))		group_elem("InvestigatorList", Rep1(Investigator))
simple_elem("OtherID", "Source")		simple_elem("OtherID", "Source")
simple_elem("SpaceFlightMission")		simple_elem("SpaceFlightMission")
simple_elem("Keyword", "MajorTopicYN")		simple_elem("Keyword", "MajorTopicYN")
group_elem("KeywordList", Rep1(Keyword), "Owner")		group_elem("KeywordList", Rep1(Keyword), "Owner")
group_elem("OtherAbstract", AbstractText + Opt(CopyrightInformation), "Type")		group_elem("OtherAbstract", AbstractText + Opt(CopyrightInformation), "Type")
group_elem("DateRevised", normal_date)		group_elem("DateRevised", normal_date)
group_elem("DateCompleted", normal_date)		group_elem("DateCompleted", normal_date)
group_elem("DateCreated", normal_date)		group_elem("DateCreated", normal_date)

Source file "/home/peter/clone_digger/biopython-1.44/Bio/GenBank/__init__.py" The first line is 555		Source file "/home/peter/clone_digger/biopython-1.44/Bio/GenBank/__init__.py" The first line is 1084
def authors(self, content): self._current_ref.authors = content		def authors(self, content): self._cur_reference.authors = content
def consrtm(self, content): self._current_ref.consrtm = content		def consrtm(self, content): self._cur_reference.consrtm = content
def title(self, content): self._current_ref.title = content		def title(self, content): self._cur_reference.title = content
def journal(self, content): self._current_ref.journal = content		def journal(self, content): self._cur_reference.journal = content
def medline_id(self, content): self._current_ref.medline_id = content		def medline_id(self, content): self._cur_reference.medline_id = content
def pubmed_id(self, content): self._current_ref.pubmed_id = content		def pubmed_id(self, content): self._cur_reference.pubmed_id = content
def remark(self, content): self._current_ref.comment = content		def remark(self, content): self._cur_reference.remark = content

Source file "/home/peter/clone_digger/biopython-1.44/Bio/MEME/Parser.py" The first line is 325		Source file "/home/peter/clone_digger/biopython-1.44/Bio/MEME/Parser.py" The first line is 299
inst = Motif.Instance()		inst = Motif.Instance()
inst._seqname (self._current_seq)		inst._seqname (ls[0])
inst._start (start)		inst._start (start)
r = re.compile('\d+')		r = re.compile('\d+')
mn = r.findall(ds[i])[0]		mn = r.findall(ds[i])[0]
if ds[i].find('-') != -1: inst.strand = '-' inst.strand = '+'		if ds[i].find('-') != -1: inst.strand = '-' inst.strand = '+'
motif = self.data.get_motif_by_name(mn)		motif = self.data.get_motif_by_name(mn)
motif.add_instance(inst)		motif.add_instance(inst)
start += motif.length		start += motif.length

Source file "/home/peter/clone_digger/biopython-1.44/Bio/Blast/NCBIStandalone.py" The first line is 1482		Source file "/home/peter/clone_digger/biopython-1.44/Bio/Blast/NCBIStandalone.py" The first line is 1426
def end_alignment(self): _AlignmentConsumer.end_alignment(self) if self._alignment.hsps: self._round.alignments.append(self._alignment) if self._multiple_alignment: self._round.multiple_alignment = self._multiple_alignment		def end_alignment(self): _AlignmentConsumer.end_alignment(self) if self._alignment.hsps: self.data.alignments.append(self._alignment) if self._multiple_alignment.alignment: self.data.multiple_alignment = self._multiple_alignment
def end_hsp(self): _HSPConsumer.end_hsp(self) try: self._alignment.hsps.append(self._hsp) except AttributeError: raise SyntaxError, "Found an HSP before an alignment"		def end_hsp(self): _HSPConsumer.end_hsp(self) try: self._alignment.hsps.append(self._hsp) except AttributeError: raise SyntaxError, "Found an HSP before an alignment"
def end_database_report(self): _DatabaseReportConsumer.end_database_report(self) self.data.__dict__.update(self._dr.__dict__)		def end_database_report(self): _DatabaseReportConsumer.end_database_report(self) self.data.__dict__.update(self._dr.__dict__)
def end_parameters(self): _ParametersConsumer.end_parameters(self) self.data.__dict__.update(self._params.__dict__)		def end_parameters(self): _ParametersConsumer.end_parameters(self) self.data.__dict__.update(self._params.__dict__)