From eee7cff8c52fe82c56d639f8d8f431632e9343b9 Mon Sep 17 00:00:00 2001 From: espie Date: Tue, 3 Aug 2004 11:18:02 +0000 Subject: [PATCH] new-style MODULES, PLIST. --- biology/py-biopython/Makefile | 7 +- biology/py-biopython/pkg/PLIST | 246 ++++++++++++++++----------------- 2 files changed, 126 insertions(+), 127 deletions(-) diff --git a/biology/py-biopython/Makefile b/biology/py-biopython/Makefile index e034707feb0..bc58f5383c6 100644 --- a/biology/py-biopython/Makefile +++ b/biology/py-biopython/Makefile @@ -1,7 +1,6 @@ -# $OpenBSD: Makefile,v 1.1.1.1 2004/05/07 08:57:15 xsa Exp $ - -NOT_FOR_ARCHS= ${NO_SHARED_ARCHS} +# $OpenBSD: Makefile,v 1.2 2004/08/03 11:18:02 espie Exp $ +SHARED_ONLY= Yes COMMENT= "Python tools for computational molecular biology" DISTNAME= biopython-1.24 @@ -20,7 +19,7 @@ PERMIT_DISTFILES_FTP= Yes MASTER_SITES= ${HOMEPAGE}files/ -MODULES= python +MODULES= lang/python BUILD_DEPENDS= ${RUN_DEPENDS} RUN_DEPENDS= ::devel/py-mxDateTime \ diff --git a/biology/py-biopython/pkg/PLIST b/biology/py-biopython/pkg/PLIST index 6dc916b5736..da7ad9f9c3d 100644 --- a/biology/py-biopython/pkg/PLIST +++ b/biology/py-biopython/pkg/PLIST @@ -1,8 +1,11 @@ -@comment $OpenBSD: PLIST,v 1.1.1.1 2004/05/07 08:57:20 xsa Exp $ +@comment $OpenBSD: PLIST,v 1.2 2004/08/03 11:18:02 espie Exp $ +lib/python${MODPY_VERSION}/site-packages/Bio/ +lib/python${MODPY_VERSION}/site-packages/Bio/Ais/ lib/python${MODPY_VERSION}/site-packages/Bio/Ais/__init__.py lib/python${MODPY_VERSION}/site-packages/Bio/Ais/__init__.pyc lib/python${MODPY_VERSION}/site-packages/Bio/Ais/example_ais2.py lib/python${MODPY_VERSION}/site-packages/Bio/Ais/example_ais2.pyc +lib/python${MODPY_VERSION}/site-packages/Bio/Align/ lib/python${MODPY_VERSION}/site-packages/Bio/Align/AlignInfo.py lib/python${MODPY_VERSION}/site-packages/Bio/Align/AlignInfo.pyc lib/python${MODPY_VERSION}/site-packages/Bio/Align/FormatConvert.py @@ -11,6 +14,7 @@ lib/python${MODPY_VERSION}/site-packages/Bio/Align/Generic.py lib/python${MODPY_VERSION}/site-packages/Bio/Align/Generic.pyc lib/python${MODPY_VERSION}/site-packages/Bio/Align/__init__.py lib/python${MODPY_VERSION}/site-packages/Bio/Align/__init__.pyc +lib/python${MODPY_VERSION}/site-packages/Bio/AlignAce/ lib/python${MODPY_VERSION}/site-packages/Bio/AlignAce/AlignAceStandalone.py lib/python${MODPY_VERSION}/site-packages/Bio/AlignAce/AlignAceStandalone.pyc lib/python${MODPY_VERSION}/site-packages/Bio/AlignAce/Applications.py @@ -23,12 +27,15 @@ lib/python${MODPY_VERSION}/site-packages/Bio/AlignAce/Scanner.py lib/python${MODPY_VERSION}/site-packages/Bio/AlignAce/Scanner.pyc lib/python${MODPY_VERSION}/site-packages/Bio/AlignAce/__init__.py lib/python${MODPY_VERSION}/site-packages/Bio/AlignAce/__init__.pyc +lib/python${MODPY_VERSION}/site-packages/Bio/Alphabet/ lib/python${MODPY_VERSION}/site-packages/Bio/Alphabet/IUPAC.py lib/python${MODPY_VERSION}/site-packages/Bio/Alphabet/IUPAC.pyc lib/python${MODPY_VERSION}/site-packages/Bio/Alphabet/__init__.py lib/python${MODPY_VERSION}/site-packages/Bio/Alphabet/__init__.pyc +lib/python${MODPY_VERSION}/site-packages/Bio/Application/ lib/python${MODPY_VERSION}/site-packages/Bio/Application/__init__.py lib/python${MODPY_VERSION}/site-packages/Bio/Application/__init__.pyc +lib/python${MODPY_VERSION}/site-packages/Bio/Blast/ lib/python${MODPY_VERSION}/site-packages/Bio/Blast/Applications.py lib/python${MODPY_VERSION}/site-packages/Bio/Blast/Applications.pyc lib/python${MODPY_VERSION}/site-packages/Bio/Blast/NCBIStandalone.py @@ -41,25 +48,30 @@ lib/python${MODPY_VERSION}/site-packages/Bio/Blast/Record.py lib/python${MODPY_VERSION}/site-packages/Bio/Blast/Record.pyc lib/python${MODPY_VERSION}/site-packages/Bio/Blast/__init__.py lib/python${MODPY_VERSION}/site-packages/Bio/Blast/__init__.pyc +lib/python${MODPY_VERSION}/site-packages/Bio/CDD/ lib/python${MODPY_VERSION}/site-packages/Bio/CDD/Record.py lib/python${MODPY_VERSION}/site-packages/Bio/CDD/Record.pyc lib/python${MODPY_VERSION}/site-packages/Bio/CDD/__init__.py lib/python${MODPY_VERSION}/site-packages/Bio/CDD/__init__.pyc lib/python${MODPY_VERSION}/site-packages/Bio/CDD/cdd_format.py lib/python${MODPY_VERSION}/site-packages/Bio/CDD/cdd_format.pyc +lib/python${MODPY_VERSION}/site-packages/Bio/Clustalw/ lib/python${MODPY_VERSION}/site-packages/Bio/Clustalw/__init__.py lib/python${MODPY_VERSION}/site-packages/Bio/Clustalw/__init__.pyc lib/python${MODPY_VERSION}/site-packages/Bio/Clustalw/clustal_format.py lib/python${MODPY_VERSION}/site-packages/Bio/Clustalw/clustal_format.pyc +lib/python${MODPY_VERSION}/site-packages/Bio/Cluster/ lib/python${MODPY_VERSION}/site-packages/Bio/Cluster/__init__.py lib/python${MODPY_VERSION}/site-packages/Bio/Cluster/__init__.pyc lib/python${MODPY_VERSION}/site-packages/Bio/Cluster/cluster.so lib/python${MODPY_VERSION}/site-packages/Bio/Cluster/data.py lib/python${MODPY_VERSION}/site-packages/Bio/Cluster/data.pyc +lib/python${MODPY_VERSION}/site-packages/Bio/Crystal/ lib/python${MODPY_VERSION}/site-packages/Bio/Crystal/__init__.py lib/python${MODPY_VERSION}/site-packages/Bio/Crystal/__init__.pyc lib/python${MODPY_VERSION}/site-packages/Bio/DBXRef.py lib/python${MODPY_VERSION}/site-packages/Bio/DBXRef.pyc +lib/python${MODPY_VERSION}/site-packages/Bio/Data/ lib/python${MODPY_VERSION}/site-packages/Bio/Data/CodonTable.py lib/python${MODPY_VERSION}/site-packages/Bio/Data/CodonTable.pyc lib/python${MODPY_VERSION}/site-packages/Bio/Data/IUPACData.py @@ -70,16 +82,19 @@ lib/python${MODPY_VERSION}/site-packages/Bio/Decode.py lib/python${MODPY_VERSION}/site-packages/Bio/Decode.pyc lib/python${MODPY_VERSION}/site-packages/Bio/DocSQL.py lib/python${MODPY_VERSION}/site-packages/Bio/DocSQL.pyc +lib/python${MODPY_VERSION}/site-packages/Bio/ECell/ lib/python${MODPY_VERSION}/site-packages/Bio/ECell/Record.py lib/python${MODPY_VERSION}/site-packages/Bio/ECell/Record.pyc lib/python${MODPY_VERSION}/site-packages/Bio/ECell/__init__.py lib/python${MODPY_VERSION}/site-packages/Bio/ECell/__init__.pyc lib/python${MODPY_VERSION}/site-packages/Bio/ECell/ecell_format.py lib/python${MODPY_VERSION}/site-packages/Bio/ECell/ecell_format.pyc +lib/python${MODPY_VERSION}/site-packages/Bio/EUtils/ lib/python${MODPY_VERSION}/site-packages/Bio/EUtils/Config.py lib/python${MODPY_VERSION}/site-packages/Bio/EUtils/Config.pyc lib/python${MODPY_VERSION}/site-packages/Bio/EUtils/DBIdsClient.py lib/python${MODPY_VERSION}/site-packages/Bio/EUtils/DBIdsClient.pyc +lib/python${MODPY_VERSION}/site-packages/Bio/EUtils/DTDs/ lib/python${MODPY_VERSION}/site-packages/Bio/EUtils/DTDs/LinkOut.dtd lib/python${MODPY_VERSION}/site-packages/Bio/EUtils/DTDs/LinkOut.py lib/python${MODPY_VERSION}/site-packages/Bio/EUtils/DTDs/LinkOut.pyc @@ -126,6 +141,7 @@ lib/python${MODPY_VERSION}/site-packages/Bio/EUtils/sourcegen.py lib/python${MODPY_VERSION}/site-packages/Bio/EUtils/sourcegen.pyc lib/python${MODPY_VERSION}/site-packages/Bio/EZRetrieve.py lib/python${MODPY_VERSION}/site-packages/Bio/EZRetrieve.pyc +lib/python${MODPY_VERSION}/site-packages/Bio/Emboss/ lib/python${MODPY_VERSION}/site-packages/Bio/Emboss/Applications.py lib/python${MODPY_VERSION}/site-packages/Bio/Emboss/Applications.pyc lib/python${MODPY_VERSION}/site-packages/Bio/Emboss/Primer.py @@ -136,18 +152,22 @@ lib/python${MODPY_VERSION}/site-packages/Bio/Emboss/primer3_format.py lib/python${MODPY_VERSION}/site-packages/Bio/Emboss/primer3_format.pyc lib/python${MODPY_VERSION}/site-packages/Bio/Emboss/primersearch_format.py lib/python${MODPY_VERSION}/site-packages/Bio/Emboss/primersearch_format.pyc +lib/python${MODPY_VERSION}/site-packages/Bio/Encodings/ lib/python${MODPY_VERSION}/site-packages/Bio/Encodings/IUPACEncoding.py lib/python${MODPY_VERSION}/site-packages/Bio/Encodings/IUPACEncoding.pyc lib/python${MODPY_VERSION}/site-packages/Bio/Encodings/__init__.py lib/python${MODPY_VERSION}/site-packages/Bio/Encodings/__init__.pyc +lib/python${MODPY_VERSION}/site-packages/Bio/Enzyme/ lib/python${MODPY_VERSION}/site-packages/Bio/Enzyme/__init__.py lib/python${MODPY_VERSION}/site-packages/Bio/Enzyme/__init__.pyc +lib/python${MODPY_VERSION}/site-packages/Bio/FSSP/ lib/python${MODPY_VERSION}/site-packages/Bio/FSSP/FSSPTools.py lib/python${MODPY_VERSION}/site-packages/Bio/FSSP/FSSPTools.pyc lib/python${MODPY_VERSION}/site-packages/Bio/FSSP/__init__.py lib/python${MODPY_VERSION}/site-packages/Bio/FSSP/__init__.pyc lib/python${MODPY_VERSION}/site-packages/Bio/FSSP/fssp_rec.py lib/python${MODPY_VERSION}/site-packages/Bio/FSSP/fssp_rec.pyc +lib/python${MODPY_VERSION}/site-packages/Bio/Fasta/ lib/python${MODPY_VERSION}/site-packages/Bio/Fasta/FastaAlign.py lib/python${MODPY_VERSION}/site-packages/Bio/Fasta/FastaAlign.pyc lib/python${MODPY_VERSION}/site-packages/Bio/Fasta/__init__.py @@ -158,6 +178,8 @@ lib/python${MODPY_VERSION}/site-packages/Bio/FilteredReader.py lib/python${MODPY_VERSION}/site-packages/Bio/FilteredReader.pyc lib/python${MODPY_VERSION}/site-packages/Bio/FormatIO.py lib/python${MODPY_VERSION}/site-packages/Bio/FormatIO.pyc +lib/python${MODPY_VERSION}/site-packages/Bio/GA/ +lib/python${MODPY_VERSION}/site-packages/Bio/GA/Crossover/ lib/python${MODPY_VERSION}/site-packages/Bio/GA/Crossover/General.py lib/python${MODPY_VERSION}/site-packages/Bio/GA/Crossover/General.pyc lib/python${MODPY_VERSION}/site-packages/Bio/GA/Crossover/GeneralPoint.py @@ -172,6 +194,7 @@ lib/python${MODPY_VERSION}/site-packages/Bio/GA/Crossover/__init__.py lib/python${MODPY_VERSION}/site-packages/Bio/GA/Crossover/__init__.pyc lib/python${MODPY_VERSION}/site-packages/Bio/GA/Evolver.py lib/python${MODPY_VERSION}/site-packages/Bio/GA/Evolver.pyc +lib/python${MODPY_VERSION}/site-packages/Bio/GA/Mutation/ lib/python${MODPY_VERSION}/site-packages/Bio/GA/Mutation/General.py lib/python${MODPY_VERSION}/site-packages/Bio/GA/Mutation/General.pyc lib/python${MODPY_VERSION}/site-packages/Bio/GA/Mutation/Simple.py @@ -180,10 +203,12 @@ lib/python${MODPY_VERSION}/site-packages/Bio/GA/Mutation/__init__.py lib/python${MODPY_VERSION}/site-packages/Bio/GA/Mutation/__init__.pyc lib/python${MODPY_VERSION}/site-packages/Bio/GA/Organism.py lib/python${MODPY_VERSION}/site-packages/Bio/GA/Organism.pyc +lib/python${MODPY_VERSION}/site-packages/Bio/GA/Repair/ lib/python${MODPY_VERSION}/site-packages/Bio/GA/Repair/Stabilizing.py lib/python${MODPY_VERSION}/site-packages/Bio/GA/Repair/Stabilizing.pyc lib/python${MODPY_VERSION}/site-packages/Bio/GA/Repair/__init__.py lib/python${MODPY_VERSION}/site-packages/Bio/GA/Repair/__init__.pyc +lib/python${MODPY_VERSION}/site-packages/Bio/GA/Selection/ lib/python${MODPY_VERSION}/site-packages/Bio/GA/Selection/Abstract.py lib/python${MODPY_VERSION}/site-packages/Bio/GA/Selection/Abstract.pyc lib/python${MODPY_VERSION}/site-packages/Bio/GA/Selection/Diversity.py @@ -196,6 +221,7 @@ lib/python${MODPY_VERSION}/site-packages/Bio/GA/Selection/__init__.py lib/python${MODPY_VERSION}/site-packages/Bio/GA/Selection/__init__.pyc lib/python${MODPY_VERSION}/site-packages/Bio/GA/__init__.py lib/python${MODPY_VERSION}/site-packages/Bio/GA/__init__.pyc +lib/python${MODPY_VERSION}/site-packages/Bio/GFF/ lib/python${MODPY_VERSION}/site-packages/Bio/GFF/GenericTools.py lib/python${MODPY_VERSION}/site-packages/Bio/GFF/GenericTools.pyc lib/python${MODPY_VERSION}/site-packages/Bio/GFF/__init__.py @@ -204,6 +230,7 @@ lib/python${MODPY_VERSION}/site-packages/Bio/GFF/binning.py lib/python${MODPY_VERSION}/site-packages/Bio/GFF/binning.pyc lib/python${MODPY_VERSION}/site-packages/Bio/GFF/easy.py lib/python${MODPY_VERSION}/site-packages/Bio/GFF/easy.pyc +lib/python${MODPY_VERSION}/site-packages/Bio/GenBank/ lib/python${MODPY_VERSION}/site-packages/Bio/GenBank/LocationParser.py lib/python${MODPY_VERSION}/site-packages/Bio/GenBank/LocationParser.pyc lib/python${MODPY_VERSION}/site-packages/Bio/GenBank/Record.py @@ -214,14 +241,17 @@ lib/python${MODPY_VERSION}/site-packages/Bio/GenBank/genbank_format.py lib/python${MODPY_VERSION}/site-packages/Bio/GenBank/genbank_format.pyc lib/python${MODPY_VERSION}/site-packages/Bio/GenBank/utils.py lib/python${MODPY_VERSION}/site-packages/Bio/GenBank/utils.pyc +lib/python${MODPY_VERSION}/site-packages/Bio/Geo/ lib/python${MODPY_VERSION}/site-packages/Bio/Geo/Record.py lib/python${MODPY_VERSION}/site-packages/Bio/Geo/Record.pyc lib/python${MODPY_VERSION}/site-packages/Bio/Geo/__init__.py lib/python${MODPY_VERSION}/site-packages/Bio/Geo/__init__.pyc lib/python${MODPY_VERSION}/site-packages/Bio/Geo/geo_format.py lib/python${MODPY_VERSION}/site-packages/Bio/Geo/geo_format.pyc +lib/python${MODPY_VERSION}/site-packages/Bio/Gobase/ lib/python${MODPY_VERSION}/site-packages/Bio/Gobase/__init__.py lib/python${MODPY_VERSION}/site-packages/Bio/Gobase/__init__.pyc +lib/python${MODPY_VERSION}/site-packages/Bio/Graphics/ lib/python${MODPY_VERSION}/site-packages/Bio/Graphics/BasicChromosome.py lib/python${MODPY_VERSION}/site-packages/Bio/Graphics/BasicChromosome.pyc lib/python${MODPY_VERSION}/site-packages/Bio/Graphics/Comparative.py @@ -232,6 +262,7 @@ lib/python${MODPY_VERSION}/site-packages/Bio/Graphics/Distribution.py lib/python${MODPY_VERSION}/site-packages/Bio/Graphics/Distribution.pyc lib/python${MODPY_VERSION}/site-packages/Bio/Graphics/__init__.py lib/python${MODPY_VERSION}/site-packages/Bio/Graphics/__init__.pyc +lib/python${MODPY_VERSION}/site-packages/Bio/HMM/ lib/python${MODPY_VERSION}/site-packages/Bio/HMM/DynamicProgramming.py lib/python${MODPY_VERSION}/site-packages/Bio/HMM/DynamicProgramming.pyc lib/python${MODPY_VERSION}/site-packages/Bio/HMM/MarkovModel.py @@ -246,38 +277,47 @@ lib/python${MODPY_VERSION}/site-packages/Bio/HotRand.py lib/python${MODPY_VERSION}/site-packages/Bio/HotRand.pyc lib/python${MODPY_VERSION}/site-packages/Bio/Index.py lib/python${MODPY_VERSION}/site-packages/Bio/Index.pyc +lib/python${MODPY_VERSION}/site-packages/Bio/IntelliGenetics/ lib/python${MODPY_VERSION}/site-packages/Bio/IntelliGenetics/Record.py lib/python${MODPY_VERSION}/site-packages/Bio/IntelliGenetics/Record.pyc lib/python${MODPY_VERSION}/site-packages/Bio/IntelliGenetics/__init__.py lib/python${MODPY_VERSION}/site-packages/Bio/IntelliGenetics/__init__.pyc lib/python${MODPY_VERSION}/site-packages/Bio/IntelliGenetics/intelligenetics_format.py lib/python${MODPY_VERSION}/site-packages/Bio/IntelliGenetics/intelligenetics_format.pyc +lib/python${MODPY_VERSION}/site-packages/Bio/InterPro/ lib/python${MODPY_VERSION}/site-packages/Bio/InterPro/__init__.py lib/python${MODPY_VERSION}/site-packages/Bio/InterPro/__init__.pyc +lib/python${MODPY_VERSION}/site-packages/Bio/KDTree/ lib/python${MODPY_VERSION}/site-packages/Bio/KDTree/_KDTree.py lib/python${MODPY_VERSION}/site-packages/Bio/KDTree/_KDTree.pyc lib/python${MODPY_VERSION}/site-packages/Bio/KDTree/__init__.py lib/python${MODPY_VERSION}/site-packages/Bio/KDTree/__init__.pyc +lib/python${MODPY_VERSION}/site-packages/Bio/KEGG/ +lib/python${MODPY_VERSION}/site-packages/Bio/KEGG/Compound/ lib/python${MODPY_VERSION}/site-packages/Bio/KEGG/Compound/__init__.py lib/python${MODPY_VERSION}/site-packages/Bio/KEGG/Compound/__init__.pyc lib/python${MODPY_VERSION}/site-packages/Bio/KEGG/Compound/compound_format.py lib/python${MODPY_VERSION}/site-packages/Bio/KEGG/Compound/compound_format.pyc +lib/python${MODPY_VERSION}/site-packages/Bio/KEGG/Enzyme/ lib/python${MODPY_VERSION}/site-packages/Bio/KEGG/Enzyme/__init__.py lib/python${MODPY_VERSION}/site-packages/Bio/KEGG/Enzyme/__init__.pyc lib/python${MODPY_VERSION}/site-packages/Bio/KEGG/Enzyme/enzyme_format.py lib/python${MODPY_VERSION}/site-packages/Bio/KEGG/Enzyme/enzyme_format.pyc +lib/python${MODPY_VERSION}/site-packages/Bio/KEGG/Map/ lib/python${MODPY_VERSION}/site-packages/Bio/KEGG/Map/__init__.py lib/python${MODPY_VERSION}/site-packages/Bio/KEGG/Map/__init__.pyc lib/python${MODPY_VERSION}/site-packages/Bio/KEGG/Map/map_format.py lib/python${MODPY_VERSION}/site-packages/Bio/KEGG/Map/map_format.pyc lib/python${MODPY_VERSION}/site-packages/Bio/KEGG/__init__.py lib/python${MODPY_VERSION}/site-packages/Bio/KEGG/__init__.pyc +lib/python${MODPY_VERSION}/site-packages/Bio/Kabat/ lib/python${MODPY_VERSION}/site-packages/Bio/Kabat/Record.py lib/python${MODPY_VERSION}/site-packages/Bio/Kabat/Record.pyc lib/python${MODPY_VERSION}/site-packages/Bio/Kabat/__init__.py lib/python${MODPY_VERSION}/site-packages/Bio/Kabat/__init__.pyc lib/python${MODPY_VERSION}/site-packages/Bio/Kabat/kabat_format.py lib/python${MODPY_VERSION}/site-packages/Bio/Kabat/kabat_format.pyc +lib/python${MODPY_VERSION}/site-packages/Bio/LocusLink/ lib/python${MODPY_VERSION}/site-packages/Bio/LocusLink/__init__.py lib/python${MODPY_VERSION}/site-packages/Bio/LocusLink/__init__.pyc lib/python${MODPY_VERSION}/site-packages/Bio/LocusLink/locus_format.py @@ -292,6 +332,7 @@ lib/python${MODPY_VERSION}/site-packages/Bio/MarkupEditor.py lib/python${MODPY_VERSION}/site-packages/Bio/MarkupEditor.pyc lib/python${MODPY_VERSION}/site-packages/Bio/MaxEntropy.py lib/python${MODPY_VERSION}/site-packages/Bio/MaxEntropy.pyc +lib/python${MODPY_VERSION}/site-packages/Bio/Medline/ lib/python${MODPY_VERSION}/site-packages/Bio/Medline/NLMMedlineXML.py lib/python${MODPY_VERSION}/site-packages/Bio/Medline/NLMMedlineXML.pyc lib/python${MODPY_VERSION}/site-packages/Bio/Medline/__init__.py @@ -302,6 +343,7 @@ lib/python${MODPY_VERSION}/site-packages/Bio/Medline/nlmmedline_010319_format.py lib/python${MODPY_VERSION}/site-packages/Bio/Medline/nlmmedline_010319_format.pyc lib/python${MODPY_VERSION}/site-packages/Bio/Medline/nlmmedline_011101_format.py lib/python${MODPY_VERSION}/site-packages/Bio/Medline/nlmmedline_011101_format.pyc +lib/python${MODPY_VERSION}/site-packages/Bio/MetaTool/ lib/python${MODPY_VERSION}/site-packages/Bio/MetaTool/Input.py lib/python${MODPY_VERSION}/site-packages/Bio/MetaTool/Input.pyc lib/python${MODPY_VERSION}/site-packages/Bio/MetaTool/Record.py @@ -310,6 +352,7 @@ lib/python${MODPY_VERSION}/site-packages/Bio/MetaTool/__init__.py lib/python${MODPY_VERSION}/site-packages/Bio/MetaTool/__init__.pyc lib/python${MODPY_VERSION}/site-packages/Bio/MetaTool/metatool_format.py lib/python${MODPY_VERSION}/site-packages/Bio/MetaTool/metatool_format.pyc +lib/python${MODPY_VERSION}/site-packages/Bio/Mindy/ lib/python${MODPY_VERSION}/site-packages/Bio/Mindy/BaseDB.py lib/python${MODPY_VERSION}/site-packages/Bio/Mindy/BaseDB.pyc lib/python${MODPY_VERSION}/site-packages/Bio/Mindy/BerkeleyDB.py @@ -326,6 +369,7 @@ lib/python${MODPY_VERSION}/site-packages/Bio/Mindy/__init__.py lib/python${MODPY_VERSION}/site-packages/Bio/Mindy/__init__.pyc lib/python${MODPY_VERSION}/site-packages/Bio/Mindy/compression.py lib/python${MODPY_VERSION}/site-packages/Bio/Mindy/compression.pyc +lib/python${MODPY_VERSION}/site-packages/Bio/MultiProc/ lib/python${MODPY_VERSION}/site-packages/Bio/MultiProc/Scheduler.py lib/python${MODPY_VERSION}/site-packages/Bio/MultiProc/Scheduler.pyc lib/python${MODPY_VERSION}/site-packages/Bio/MultiProc/Task.py @@ -334,6 +378,7 @@ lib/python${MODPY_VERSION}/site-packages/Bio/MultiProc/__init__.py lib/python${MODPY_VERSION}/site-packages/Bio/MultiProc/__init__.pyc lib/python${MODPY_VERSION}/site-packages/Bio/MultiProc/copen.py lib/python${MODPY_VERSION}/site-packages/Bio/MultiProc/copen.pyc +lib/python${MODPY_VERSION}/site-packages/Bio/NBRF/ lib/python${MODPY_VERSION}/site-packages/Bio/NBRF/Record.py lib/python${MODPY_VERSION}/site-packages/Bio/NBRF/Record.pyc lib/python${MODPY_VERSION}/site-packages/Bio/NBRF/ValSeq.py @@ -342,6 +387,7 @@ lib/python${MODPY_VERSION}/site-packages/Bio/NBRF/__init__.py lib/python${MODPY_VERSION}/site-packages/Bio/NBRF/__init__.pyc lib/python${MODPY_VERSION}/site-packages/Bio/NBRF/nbrf_format.py lib/python${MODPY_VERSION}/site-packages/Bio/NBRF/nbrf_format.pyc +lib/python${MODPY_VERSION}/site-packages/Bio/NMR/ lib/python${MODPY_VERSION}/site-packages/Bio/NMR/NOEtools.py lib/python${MODPY_VERSION}/site-packages/Bio/NMR/NOEtools.pyc lib/python${MODPY_VERSION}/site-packages/Bio/NMR/__init__.py @@ -350,16 +396,20 @@ lib/python${MODPY_VERSION}/site-packages/Bio/NMR/xpktools.py lib/python${MODPY_VERSION}/site-packages/Bio/NMR/xpktools.pyc lib/python${MODPY_VERSION}/site-packages/Bio/NaiveBayes.py lib/python${MODPY_VERSION}/site-packages/Bio/NaiveBayes.pyc +lib/python${MODPY_VERSION}/site-packages/Bio/Ndb/ lib/python${MODPY_VERSION}/site-packages/Bio/Ndb/__init__.py lib/python${MODPY_VERSION}/site-packages/Bio/Ndb/__init__.pyc lib/python${MODPY_VERSION}/site-packages/Bio/NetCatch.py lib/python${MODPY_VERSION}/site-packages/Bio/NetCatch.pyc +lib/python${MODPY_VERSION}/site-packages/Bio/NeuralNetwork/ +lib/python${MODPY_VERSION}/site-packages/Bio/NeuralNetwork/BackPropagation/ lib/python${MODPY_VERSION}/site-packages/Bio/NeuralNetwork/BackPropagation/Layer.py lib/python${MODPY_VERSION}/site-packages/Bio/NeuralNetwork/BackPropagation/Layer.pyc lib/python${MODPY_VERSION}/site-packages/Bio/NeuralNetwork/BackPropagation/Network.py lib/python${MODPY_VERSION}/site-packages/Bio/NeuralNetwork/BackPropagation/Network.pyc lib/python${MODPY_VERSION}/site-packages/Bio/NeuralNetwork/BackPropagation/__init__.py lib/python${MODPY_VERSION}/site-packages/Bio/NeuralNetwork/BackPropagation/__init__.pyc +lib/python${MODPY_VERSION}/site-packages/Bio/NeuralNetwork/Gene/ lib/python${MODPY_VERSION}/site-packages/Bio/NeuralNetwork/Gene/Motif.py lib/python${MODPY_VERSION}/site-packages/Bio/NeuralNetwork/Gene/Motif.pyc lib/python${MODPY_VERSION}/site-packages/Bio/NeuralNetwork/Gene/Pattern.py @@ -376,6 +426,7 @@ lib/python${MODPY_VERSION}/site-packages/Bio/NeuralNetwork/Training.py lib/python${MODPY_VERSION}/site-packages/Bio/NeuralNetwork/Training.pyc lib/python${MODPY_VERSION}/site-packages/Bio/NeuralNetwork/__init__.py lib/python${MODPY_VERSION}/site-packages/Bio/NeuralNetwork/__init__.pyc +lib/python${MODPY_VERSION}/site-packages/Bio/PDB/ lib/python${MODPY_VERSION}/site-packages/Bio/PDB/Atom.py lib/python${MODPY_VERSION}/site-packages/Bio/PDB/Atom.pyc lib/python${MODPY_VERSION}/site-packages/Bio/PDB/Chain.py @@ -410,15 +461,19 @@ lib/python${MODPY_VERSION}/site-packages/Bio/PDB/StructureBuilder.py lib/python${MODPY_VERSION}/site-packages/Bio/PDB/StructureBuilder.pyc lib/python${MODPY_VERSION}/site-packages/Bio/PDB/__init__.py lib/python${MODPY_VERSION}/site-packages/Bio/PDB/__init__.pyc +lib/python${MODPY_VERSION}/site-packages/Bio/PDB/mmCIF/ lib/python${MODPY_VERSION}/site-packages/Bio/PDB/mmCIF/MMCIFlex.so lib/python${MODPY_VERSION}/site-packages/Bio/PDB/mmCIF/__init__.py lib/python${MODPY_VERSION}/site-packages/Bio/PDB/mmCIF/__init__.pyc lib/python${MODPY_VERSION}/site-packages/Bio/ParserSupport.py lib/python${MODPY_VERSION}/site-packages/Bio/ParserSupport.pyc +lib/python${MODPY_VERSION}/site-packages/Bio/Parsers/ lib/python${MODPY_VERSION}/site-packages/Bio/Parsers/__init__.py lib/python${MODPY_VERSION}/site-packages/Bio/Parsers/__init__.pyc lib/python${MODPY_VERSION}/site-packages/Bio/Parsers/spark.py lib/python${MODPY_VERSION}/site-packages/Bio/Parsers/spark.pyc +lib/python${MODPY_VERSION}/site-packages/Bio/Pathway/ +lib/python${MODPY_VERSION}/site-packages/Bio/Pathway/Rep/ lib/python${MODPY_VERSION}/site-packages/Bio/Pathway/Rep/Graph.py lib/python${MODPY_VERSION}/site-packages/Bio/Pathway/Rep/Graph.pyc lib/python${MODPY_VERSION}/site-packages/Bio/Pathway/Rep/HashSet.py @@ -431,6 +486,7 @@ lib/python${MODPY_VERSION}/site-packages/Bio/Pathway/__init__.py lib/python${MODPY_VERSION}/site-packages/Bio/Pathway/__init__.pyc lib/python${MODPY_VERSION}/site-packages/Bio/PropertyManager.py lib/python${MODPY_VERSION}/site-packages/Bio/PropertyManager.pyc +lib/python${MODPY_VERSION}/site-packages/Bio/Prosite/ lib/python${MODPY_VERSION}/site-packages/Bio/Prosite/Pattern.py lib/python${MODPY_VERSION}/site-packages/Bio/Prosite/Pattern.pyc lib/python${MODPY_VERSION}/site-packages/Bio/Prosite/Prodoc.py @@ -439,6 +495,7 @@ lib/python${MODPY_VERSION}/site-packages/Bio/Prosite/__init__.py lib/python${MODPY_VERSION}/site-packages/Bio/Prosite/__init__.pyc lib/python${MODPY_VERSION}/site-packages/Bio/PubMed.py lib/python${MODPY_VERSION}/site-packages/Bio/PubMed.pyc +lib/python${MODPY_VERSION}/site-packages/Bio/Rebase/ lib/python${MODPY_VERSION}/site-packages/Bio/Rebase/Rebase.py lib/python${MODPY_VERSION}/site-packages/Bio/Rebase/Rebase.pyc lib/python${MODPY_VERSION}/site-packages/Bio/Rebase/__init__.py @@ -447,6 +504,7 @@ lib/python${MODPY_VERSION}/site-packages/Bio/RecordFile.py lib/python${MODPY_VERSION}/site-packages/Bio/RecordFile.pyc lib/python${MODPY_VERSION}/site-packages/Bio/ReseekFile.py lib/python${MODPY_VERSION}/site-packages/Bio/ReseekFile.pyc +lib/python${MODPY_VERSION}/site-packages/Bio/SCOP/ lib/python${MODPY_VERSION}/site-packages/Bio/SCOP/Cla.py lib/python${MODPY_VERSION}/site-packages/Bio/SCOP/Cla.pyc lib/python${MODPY_VERSION}/site-packages/Bio/SCOP/Des.py @@ -463,6 +521,7 @@ lib/python${MODPY_VERSION}/site-packages/Bio/SCOP/Residues.py lib/python${MODPY_VERSION}/site-packages/Bio/SCOP/Residues.pyc lib/python${MODPY_VERSION}/site-packages/Bio/SCOP/__init__.py lib/python${MODPY_VERSION}/site-packages/Bio/SCOP/__init__.pyc +lib/python${MODPY_VERSION}/site-packages/Bio/SCOP/tests/ lib/python${MODPY_VERSION}/site-packages/Bio/SCOP/tests/__init__.py lib/python${MODPY_VERSION}/site-packages/Bio/SCOP/tests/__init__.pyc lib/python${MODPY_VERSION}/site-packages/Bio/SCOP/tests/testCla.py @@ -481,12 +540,14 @@ lib/python${MODPY_VERSION}/site-packages/Bio/SCOP/tests/testScop.py lib/python${MODPY_VERSION}/site-packages/Bio/SCOP/tests/testScop.pyc lib/python${MODPY_VERSION}/site-packages/Bio/SGMLExtractor.py lib/python${MODPY_VERSION}/site-packages/Bio/SGMLExtractor.pyc +lib/python${MODPY_VERSION}/site-packages/Bio/SVDSuperimposer/ lib/python${MODPY_VERSION}/site-packages/Bio/SVDSuperimposer/SVDSuperimposer.py lib/python${MODPY_VERSION}/site-packages/Bio/SVDSuperimposer/SVDSuperimposer.pyc lib/python${MODPY_VERSION}/site-packages/Bio/SVDSuperimposer/__init__.py lib/python${MODPY_VERSION}/site-packages/Bio/SVDSuperimposer/__init__.pyc lib/python${MODPY_VERSION}/site-packages/Bio/SVM.py lib/python${MODPY_VERSION}/site-packages/Bio/SVM.pyc +lib/python${MODPY_VERSION}/site-packages/Bio/Saf/ lib/python${MODPY_VERSION}/site-packages/Bio/Saf/Record.py lib/python${MODPY_VERSION}/site-packages/Bio/Saf/Record.pyc lib/python${MODPY_VERSION}/site-packages/Bio/Saf/__init__.py @@ -499,6 +560,7 @@ lib/python${MODPY_VERSION}/site-packages/Bio/Seq.py lib/python${MODPY_VERSION}/site-packages/Bio/Seq.pyc lib/python${MODPY_VERSION}/site-packages/Bio/SeqFeature.py lib/python${MODPY_VERSION}/site-packages/Bio/SeqFeature.pyc +lib/python${MODPY_VERSION}/site-packages/Bio/SeqIO/ lib/python${MODPY_VERSION}/site-packages/Bio/SeqIO/FASTA.py lib/python${MODPY_VERSION}/site-packages/Bio/SeqIO/FASTA.pyc lib/python${MODPY_VERSION}/site-packages/Bio/SeqIO/__init__.py @@ -507,6 +569,7 @@ lib/python${MODPY_VERSION}/site-packages/Bio/SeqIO/generic.py lib/python${MODPY_VERSION}/site-packages/Bio/SeqIO/generic.pyc lib/python${MODPY_VERSION}/site-packages/Bio/SeqRecord.py lib/python${MODPY_VERSION}/site-packages/Bio/SeqRecord.pyc +lib/python${MODPY_VERSION}/site-packages/Bio/SeqUtils/ lib/python${MODPY_VERSION}/site-packages/Bio/SeqUtils/CodonUsage.py lib/python${MODPY_VERSION}/site-packages/Bio/SeqUtils/CodonUsage.pyc lib/python${MODPY_VERSION}/site-packages/Bio/SeqUtils/CodonUsageIndices.py @@ -519,6 +582,7 @@ lib/python${MODPY_VERSION}/site-packages/Bio/SeqUtils/ProtParamData.py lib/python${MODPY_VERSION}/site-packages/Bio/SeqUtils/ProtParamData.pyc lib/python${MODPY_VERSION}/site-packages/Bio/SeqUtils/__init__.py lib/python${MODPY_VERSION}/site-packages/Bio/SeqUtils/__init__.pyc +lib/python${MODPY_VERSION}/site-packages/Bio/Sequencing/ lib/python${MODPY_VERSION}/site-packages/Bio/Sequencing/Ace.py lib/python${MODPY_VERSION}/site-packages/Bio/Sequencing/Ace.pyc lib/python${MODPY_VERSION}/site-packages/Bio/Sequencing/Phd.py @@ -529,12 +593,14 @@ lib/python${MODPY_VERSION}/site-packages/Bio/Std.py lib/python${MODPY_VERSION}/site-packages/Bio/Std.pyc lib/python${MODPY_VERSION}/site-packages/Bio/StdHandler.py lib/python${MODPY_VERSION}/site-packages/Bio/StdHandler.pyc +lib/python${MODPY_VERSION}/site-packages/Bio/SubsMat/ lib/python${MODPY_VERSION}/site-packages/Bio/SubsMat/FreqTable.py lib/python${MODPY_VERSION}/site-packages/Bio/SubsMat/FreqTable.pyc lib/python${MODPY_VERSION}/site-packages/Bio/SubsMat/MatrixInfo.py lib/python${MODPY_VERSION}/site-packages/Bio/SubsMat/MatrixInfo.pyc lib/python${MODPY_VERSION}/site-packages/Bio/SubsMat/__init__.py lib/python${MODPY_VERSION}/site-packages/Bio/SubsMat/__init__.pyc +lib/python${MODPY_VERSION}/site-packages/Bio/SwissProt/ lib/python${MODPY_VERSION}/site-packages/Bio/SwissProt/KeyWList.py lib/python${MODPY_VERSION}/site-packages/Bio/SwissProt/KeyWList.pyc lib/python${MODPY_VERSION}/site-packages/Bio/SwissProt/SProt.py @@ -545,8 +611,10 @@ lib/python${MODPY_VERSION}/site-packages/Bio/Transcribe.py lib/python${MODPY_VERSION}/site-packages/Bio/Transcribe.pyc lib/python${MODPY_VERSION}/site-packages/Bio/Translate.py lib/python${MODPY_VERSION}/site-packages/Bio/Translate.pyc +lib/python${MODPY_VERSION}/site-packages/Bio/UniGene/ lib/python${MODPY_VERSION}/site-packages/Bio/UniGene/__init__.py lib/python${MODPY_VERSION}/site-packages/Bio/UniGene/__init__.pyc +lib/python${MODPY_VERSION}/site-packages/Bio/WWW/ lib/python${MODPY_VERSION}/site-packages/Bio/WWW/ExPASy.py lib/python${MODPY_VERSION}/site-packages/Bio/WWW/ExPASy.pyc lib/python${MODPY_VERSION}/site-packages/Bio/WWW/InterPro.py @@ -557,6 +625,7 @@ lib/python${MODPY_VERSION}/site-packages/Bio/WWW/SCOP.py lib/python${MODPY_VERSION}/site-packages/Bio/WWW/SCOP.pyc lib/python${MODPY_VERSION}/site-packages/Bio/WWW/__init__.py lib/python${MODPY_VERSION}/site-packages/Bio/WWW/__init__.pyc +lib/python${MODPY_VERSION}/site-packages/Bio/Wise/ lib/python${MODPY_VERSION}/site-packages/Bio/Wise/__init__.py lib/python${MODPY_VERSION}/site-packages/Bio/Wise/__init__.pyc lib/python${MODPY_VERSION}/site-packages/Bio/Wise/dnal.py @@ -569,10 +638,13 @@ lib/python${MODPY_VERSION}/site-packages/Bio/__init__.py lib/python${MODPY_VERSION}/site-packages/Bio/__init__.pyc lib/python${MODPY_VERSION}/site-packages/Bio/biblio.py lib/python${MODPY_VERSION}/site-packages/Bio/biblio.pyc +lib/python${MODPY_VERSION}/site-packages/Bio/builders/ +lib/python${MODPY_VERSION}/site-packages/Bio/builders/Search/ lib/python${MODPY_VERSION}/site-packages/Bio/builders/Search/__init__.py lib/python${MODPY_VERSION}/site-packages/Bio/builders/Search/__init__.pyc lib/python${MODPY_VERSION}/site-packages/Bio/builders/Search/search.py lib/python${MODPY_VERSION}/site-packages/Bio/builders/Search/search.pyc +lib/python${MODPY_VERSION}/site-packages/Bio/builders/SeqRecord/ lib/python${MODPY_VERSION}/site-packages/Bio/builders/SeqRecord/__init__.py lib/python${MODPY_VERSION}/site-packages/Bio/builders/SeqRecord/__init__.pyc lib/python${MODPY_VERSION}/site-packages/Bio/builders/SeqRecord/sequence.py @@ -585,6 +657,7 @@ lib/python${MODPY_VERSION}/site-packages/Bio/cdistance.so lib/python${MODPY_VERSION}/site-packages/Bio/ckMeans.so lib/python${MODPY_VERSION}/site-packages/Bio/clistfns.so lib/python${MODPY_VERSION}/site-packages/Bio/cmathfns.so +lib/python${MODPY_VERSION}/site-packages/Bio/config/ lib/python${MODPY_VERSION}/site-packages/Bio/config/DBRegistry.py lib/python${MODPY_VERSION}/site-packages/Bio/config/DBRegistry.pyc lib/python${MODPY_VERSION}/site-packages/Bio/config/FormatRegistry.py @@ -603,6 +676,7 @@ lib/python${MODPY_VERSION}/site-packages/Bio/cpairwise2.so lib/python${MODPY_VERSION}/site-packages/Bio/crc.py lib/python${MODPY_VERSION}/site-packages/Bio/crc.pyc lib/python${MODPY_VERSION}/site-packages/Bio/cstringfns.so +lib/python${MODPY_VERSION}/site-packages/Bio/dbdefs/ lib/python${MODPY_VERSION}/site-packages/Bio/dbdefs/__init__.py lib/python${MODPY_VERSION}/site-packages/Bio/dbdefs/__init__.pyc lib/python${MODPY_VERSION}/site-packages/Bio/dbdefs/_support.py @@ -623,8 +697,10 @@ lib/python${MODPY_VERSION}/site-packages/Bio/dbdefs/swissprot.py lib/python${MODPY_VERSION}/site-packages/Bio/dbdefs/swissprot.pyc lib/python${MODPY_VERSION}/site-packages/Bio/distance.py lib/python${MODPY_VERSION}/site-packages/Bio/distance.pyc +lib/python${MODPY_VERSION}/site-packages/Bio/expressions/ lib/python${MODPY_VERSION}/site-packages/Bio/expressions/__init__.py lib/python${MODPY_VERSION}/site-packages/Bio/expressions/__init__.pyc +lib/python${MODPY_VERSION}/site-packages/Bio/expressions/blast/ lib/python${MODPY_VERSION}/site-packages/Bio/expressions/blast/__init__.py lib/python${MODPY_VERSION}/site-packages/Bio/expressions/blast/__init__.pyc lib/python${MODPY_VERSION}/site-packages/Bio/expressions/blast/ncbiblast.py @@ -633,6 +709,7 @@ lib/python${MODPY_VERSION}/site-packages/Bio/expressions/blast/wublast.py lib/python${MODPY_VERSION}/site-packages/Bio/expressions/blast/wublast.pyc lib/python${MODPY_VERSION}/site-packages/Bio/expressions/blocks.py lib/python${MODPY_VERSION}/site-packages/Bio/expressions/blocks.pyc +lib/python${MODPY_VERSION}/site-packages/Bio/expressions/embl/ lib/python${MODPY_VERSION}/site-packages/Bio/expressions/embl/__init__.py lib/python${MODPY_VERSION}/site-packages/Bio/expressions/embl/__init__.pyc lib/python${MODPY_VERSION}/site-packages/Bio/expressions/embl/embl65.py @@ -643,6 +720,7 @@ lib/python${MODPY_VERSION}/site-packages/Bio/expressions/genbank.py lib/python${MODPY_VERSION}/site-packages/Bio/expressions/genbank.pyc lib/python${MODPY_VERSION}/site-packages/Bio/expressions/hmmpfam.py lib/python${MODPY_VERSION}/site-packages/Bio/expressions/hmmpfam.pyc +lib/python${MODPY_VERSION}/site-packages/Bio/expressions/swissprot/ lib/python${MODPY_VERSION}/site-packages/Bio/expressions/swissprot/__init__.py lib/python${MODPY_VERSION}/site-packages/Bio/expressions/swissprot/__init__.pyc lib/python${MODPY_VERSION}/site-packages/Bio/expressions/swissprot/speclist.py @@ -651,6 +729,7 @@ lib/python${MODPY_VERSION}/site-packages/Bio/expressions/swissprot/sprot38.py lib/python${MODPY_VERSION}/site-packages/Bio/expressions/swissprot/sprot38.pyc lib/python${MODPY_VERSION}/site-packages/Bio/expressions/swissprot/sprot40.py lib/python${MODPY_VERSION}/site-packages/Bio/expressions/swissprot/sprot40.pyc +lib/python${MODPY_VERSION}/site-packages/Bio/formatdefs/ lib/python${MODPY_VERSION}/site-packages/Bio/formatdefs/__init__.py lib/python${MODPY_VERSION}/site-packages/Bio/formatdefs/__init__.pyc lib/python${MODPY_VERSION}/site-packages/Bio/formatdefs/embl.py @@ -684,6 +763,8 @@ lib/python${MODPY_VERSION}/site-packages/Bio/triefind.py lib/python${MODPY_VERSION}/site-packages/Bio/triefind.pyc lib/python${MODPY_VERSION}/site-packages/Bio/utils.py lib/python${MODPY_VERSION}/site-packages/Bio/utils.pyc +lib/python${MODPY_VERSION}/site-packages/Bio/writers/ +lib/python${MODPY_VERSION}/site-packages/Bio/writers/SeqRecord/ lib/python${MODPY_VERSION}/site-packages/Bio/writers/SeqRecord/__init__.py lib/python${MODPY_VERSION}/site-packages/Bio/writers/SeqRecord/__init__.pyc lib/python${MODPY_VERSION}/site-packages/Bio/writers/SeqRecord/empty.py @@ -694,6 +775,7 @@ lib/python${MODPY_VERSION}/site-packages/Bio/writers/__init__.py lib/python${MODPY_VERSION}/site-packages/Bio/writers/__init__.pyc lib/python${MODPY_VERSION}/site-packages/Bio/xkMeans.py lib/python${MODPY_VERSION}/site-packages/Bio/xkMeans.pyc +lib/python${MODPY_VERSION}/site-packages/BioSQL/ lib/python${MODPY_VERSION}/site-packages/BioSQL/BioSeq.py lib/python${MODPY_VERSION}/site-packages/BioSQL/BioSeq.pyc lib/python${MODPY_VERSION}/site-packages/BioSQL/BioSeqDatabase.py @@ -704,6 +786,7 @@ lib/python${MODPY_VERSION}/site-packages/BioSQL/Loader.py lib/python${MODPY_VERSION}/site-packages/BioSQL/Loader.pyc lib/python${MODPY_VERSION}/site-packages/BioSQL/__init__.py lib/python${MODPY_VERSION}/site-packages/BioSQL/__init__.pyc +lib/python${MODPY_VERSION}/site-packages/Martel/ lib/python${MODPY_VERSION}/site-packages/Martel/Dispatch.py lib/python${MODPY_VERSION}/site-packages/Martel/Dispatch.pyc lib/python${MODPY_VERSION}/site-packages/Martel/Expression.py @@ -734,12 +817,16 @@ lib/python${MODPY_VERSION}/site-packages/Martel/optimize.py lib/python${MODPY_VERSION}/site-packages/Martel/optimize.pyc @comment lib/python${MODPY_VERSION}/site-packages/Martel/setup.py @comment lib/python${MODPY_VERSION}/site-packages/Martel/setup.pyc +share/examples/py-biopython/ +share/examples/py-biopython/Amino/ share/examples/py-biopython/Amino/aster.pro share/examples/py-biopython/Amino/loveliesbleeding.pro share/examples/py-biopython/Amino/rose.pro share/examples/py-biopython/Amino/rosemary.pro +share/examples/py-biopython/BioSQL/ share/examples/py-biopython/BioSQL/biosqldb-mysql.sql share/examples/py-biopython/BioSQL/biosqldb-pg.sql +share/examples/py-biopython/Blast/ share/examples/py-biopython/Blast/README share/examples/py-biopython/Blast/bt001 share/examples/py-biopython/Blast/bt002 @@ -810,35 +897,45 @@ share/examples/py-biopython/Blast/bt067 share/examples/py-biopython/Blast/bt068 share/examples/py-biopython/Blast/bt069 share/examples/py-biopython/Blast/bt070 +share/examples/py-biopython/CDD/ share/examples/py-biopython/CDD/pfam00035.htm share/examples/py-biopython/CDD/pfam01356.htm share/examples/py-biopython/CDD/pfam02903.htm share/examples/py-biopython/CDD/smart00499.htm share/examples/py-biopython/CDD/smart00505.htm +share/examples/py-biopython/Clustalw/ share/examples/py-biopython/Clustalw/cw02.aln share/examples/py-biopython/Clustalw/opuntia.aln +share/examples/py-biopython/CodonUsage/ share/examples/py-biopython/CodonUsage/.DS_Store share/examples/py-biopython/CodonUsage/HighlyExpressedGenes.txt +share/examples/py-biopython/ECell/ share/examples/py-biopython/ECell/sample.txt +share/examples/py-biopython/Emboss/ share/examples/py-biopython/Emboss/bac_find.primer3 share/examples/py-biopython/Emboss/bac_find.psearch share/examples/py-biopython/Emboss/cds_forward.primer3 share/examples/py-biopython/Emboss/cds_reverse.primer3 share/examples/py-biopython/Emboss/short.primer3 +share/examples/py-biopython/Enzymes/ share/examples/py-biopython/Enzymes/lactate.txt share/examples/py-biopython/Enzymes/lipoprotein.txt share/examples/py-biopython/Enzymes/proline.txt share/examples/py-biopython/Enzymes/valine.txt +share/examples/py-biopython/FSSP/ share/examples/py-biopython/FSSP/1cnv.fssp +share/examples/py-biopython/Fasta/ share/examples/py-biopython/Fasta/README share/examples/py-biopython/Fasta/f001 share/examples/py-biopython/Fasta/f002 share/examples/py-biopython/Fasta/fa01 +share/examples/py-biopython/GFF/ share/examples/py-biopython/GFF/NC_001422.gbk share/examples/py-biopython/GFF/NC_001802.fna share/examples/py-biopython/GFF/NC_001802lc.fna share/examples/py-biopython/GFF/NC_001802x.fna share/examples/py-biopython/GFF/multi.fna +share/examples/py-biopython/GenBank/ share/examples/py-biopython/GenBank/NT_019265.gb share/examples/py-biopython/GenBank/arab1.gb share/examples/py-biopython/GenBank/blank_seq.gb @@ -852,11 +949,13 @@ share/examples/py-biopython/GenBank/one_of.gb share/examples/py-biopython/GenBank/origin_line.gb share/examples/py-biopython/GenBank/pri1.gb share/examples/py-biopython/GenBank/protein_refseq.gb +share/examples/py-biopython/Geo/ share/examples/py-biopython/Geo/GSE16.txt share/examples/py-biopython/Geo/GSM645.txt share/examples/py-biopython/Geo/GSM691.txt share/examples/py-biopython/Geo/GSM700.txt share/examples/py-biopython/Geo/GSM804.txt +share/examples/py-biopython/Gobase/ share/examples/py-biopython/Gobase/E15449.htm share/examples/py-biopython/Gobase/E15449.txt share/examples/py-biopython/Gobase/G405967.htm @@ -869,32 +968,39 @@ share/examples/py-biopython/Gobase/P6513764.htm share/examples/py-biopython/Gobase/Pt6513764.txt share/examples/py-biopython/Gobase/S4323016.htm share/examples/py-biopython/Gobase/S4323016.txt +share/examples/py-biopython/Graphics/ share/examples/py-biopython/Graphics/README +share/examples/py-biopython/IntelliGenetics/ share/examples/py-biopython/IntelliGenetics/TAT_mase-nuc.txt share/examples/py-biopython/IntelliGenetics/TAT_mase_nuc.txt share/examples/py-biopython/IntelliGenetics/VIF_mase-pro.txt share/examples/py-biopython/IntelliGenetics/vpu_nucaligned.txt +share/examples/py-biopython/InterPro/ share/examples/py-biopython/InterPro/IPR001064.htm share/examples/py-biopython/InterPro/IPR001171.htm share/examples/py-biopython/InterPro/IPR001391.htm share/examples/py-biopython/InterPro/IPR001442.htm share/examples/py-biopython/InterPro/IPR001571.htm +share/examples/py-biopython/KEGG/ share/examples/py-biopython/KEGG/compound.irregular share/examples/py-biopython/KEGG/compound.sample share/examples/py-biopython/KEGG/enzyme.irregular share/examples/py-biopython/KEGG/enzyme.sample share/examples/py-biopython/KEGG/map00950.rea +share/examples/py-biopython/Kabat/ share/examples/py-biopython/Kabat/k000245.txt share/examples/py-biopython/Kabat/k000255.txt share/examples/py-biopython/Kabat/k000347.txt share/examples/py-biopython/Kabat/k000397.txt share/examples/py-biopython/Kabat/k000456.txt +share/examples/py-biopython/LocusLink/ share/examples/py-biopython/LocusLink/LL_block share/examples/py-biopython/LocusLink/Locus14789.htm share/examples/py-biopython/LocusLink/Locus16590.htm share/examples/py-biopython/LocusLink/Locus2523.htm share/examples/py-biopython/LocusLink/Locus5797.htm share/examples/py-biopython/LocusLink/Locus6373.htm +share/examples/py-biopython/MetaTool/ share/examples/py-biopython/MetaTool/Example3.txt share/examples/py-biopython/MetaTool/Example4.txt share/examples/py-biopython/MetaTool/Example6.txt @@ -920,10 +1026,12 @@ share/examples/py-biopython/MetaTool/example2.txt share/examples/py-biopython/MetaTool/meta.out share/examples/py-biopython/MetaTool/meta2.out share/examples/py-biopython/MetaTool/meta9.out +share/examples/py-biopython/NBRF/ share/examples/py-biopython/NBRF/B_nuc.pir share/examples/py-biopython/NBRF/Cw_prot.pir share/examples/py-biopython/NBRF/DMA_nuc.pir share/examples/py-biopython/NBRF/DMB_prot.pir +share/examples/py-biopython/Ndb/ share/examples/py-biopython/Ndb/AH0014.htm share/examples/py-biopython/Ndb/PD0072.htm share/examples/py-biopython/Ndb/PD0080.htm @@ -934,9 +1042,11 @@ share/examples/py-biopython/Ndb/PR0007.htm share/examples/py-biopython/Ndb/TRNA05.htm share/examples/py-biopython/Ndb/URX035.htm share/examples/py-biopython/Ndb/ZHF026.htm +share/examples/py-biopython/NeuralNetwork/ share/examples/py-biopython/NeuralNetwork/enolase.fasta share/examples/py-biopython/NeuralNetwork/patternio.txt share/examples/py-biopython/NeuralNetwork/repeat.fasta +share/examples/py-biopython/Nucleic/ share/examples/py-biopython/Nucleic/centaurea.nu share/examples/py-biopython/Nucleic/elderberry.nu share/examples/py-biopython/Nucleic/lavender.nu @@ -944,7 +1054,10 @@ share/examples/py-biopython/Nucleic/lupine.nu share/examples/py-biopython/Nucleic/phlox.nu share/examples/py-biopython/Nucleic/sweetpea.nu share/examples/py-biopython/Nucleic/wisteria.nu +share/examples/py-biopython/PDB/ share/examples/py-biopython/PDB/a_structure.pdb +share/examples/py-biopython/Prosite/ +share/examples/py-biopython/Prosite/Doc/ share/examples/py-biopython/Prosite/Doc/pdoc00100.htm share/examples/py-biopython/Prosite/Doc/pdoc00100.txt share/examples/py-biopython/Prosite/Doc/pdoc00113.htm @@ -985,6 +1098,7 @@ share/examples/py-biopython/Prosite/ps00488.txt share/examples/py-biopython/Prosite/ps00546.txt share/examples/py-biopython/Prosite/ps00812.txt share/examples/py-biopython/Prosite/ps01213.txt +share/examples/py-biopython/Rebase/ share/examples/py-biopython/Rebase/bamii.htm share/examples/py-biopython/Rebase/bamii.txt share/examples/py-biopython/Rebase/cac81.htm @@ -997,16 +1111,20 @@ share/examples/py-biopython/Rebase/pvuii.htm share/examples/py-biopython/Rebase/pvuii.txt share/examples/py-biopython/Rebase/taqi.htm share/examples/py-biopython/Rebase/taqi.txt +share/examples/py-biopython/Registry/ share/examples/py-biopython/Registry/EDD_RAT.dat share/examples/py-biopython/Registry/bt001 share/examples/py-biopython/Registry/seqs.fasta +share/examples/py-biopython/Saf/ share/examples/py-biopython/Saf/saf1.txt +share/examples/py-biopython/SubsMat/ share/examples/py-biopython/SubsMat/aaDistrib.txt share/examples/py-biopython/SubsMat/acc_rep_mat.pik share/examples/py-biopython/SubsMat/protein_count.txt share/examples/py-biopython/SubsMat/protein_freq.txt share/examples/py-biopython/SubsMat/redAADistrib.txt share/examples/py-biopython/SubsMat/redAltAADistrib.txt +share/examples/py-biopython/SwissProt/ share/examples/py-biopython/SwissProt/README share/examples/py-biopython/SwissProt/kw001 share/examples/py-biopython/SwissProt/kw002 @@ -1024,6 +1142,7 @@ share/examples/py-biopython/SwissProt/sp011 share/examples/py-biopython/SwissProt/sp012 share/examples/py-biopython/SwissProt/sp013 share/examples/py-biopython/SwissProt/sp014 +share/examples/py-biopython/UniGene/ share/examples/py-biopython/UniGene/Bt145.htm share/examples/py-biopython/UniGene/Bt59.htm share/examples/py-biopython/UniGene/Dr00010.htm @@ -1036,6 +1155,7 @@ share/examples/py-biopython/UniGene/Mm28919.htm share/examples/py-biopython/UniGene/Mm421.htm share/examples/py-biopython/UniGene/Rn20.htm share/examples/py-biopython/UniGene/Rn35.htm +share/examples/py-biopython/WIT/ share/examples/py-biopython/WIT/ec2137.htm share/examples/py-biopython/WIT/ec2137.txt share/examples/py-biopython/WIT/ec2214.htm @@ -1056,11 +1176,13 @@ share/examples/py-biopython/WIT/ec4416.htm share/examples/py-biopython/WIT/ec4416.txt share/examples/py-biopython/WIT/ec6344.htm share/examples/py-biopython/WIT/ec6344.txt +share/examples/py-biopython/Wise/ share/examples/py-biopython/Wise/human_114_g01_exons.fna_01 share/examples/py-biopython/Wise/human_114_g02_exons.fna_01 share/examples/py-biopython/dump share/examples/py-biopython/martel_support.py share/examples/py-biopython/martel_support.pyc +share/examples/py-biopython/output/ share/examples/py-biopython/output/test_BioSQL share/examples/py-biopython/output/test_Cluster share/examples/py-biopython/output/test_CodonUsage @@ -1295,125 +1417,3 @@ share/examples/py-biopython/unittest.py share/examples/py-biopython/unittest.pyc share/examples/py-biopython/unittestgui.py share/examples/py-biopython/unittestgui.pyc -@dirrm share/examples/py-biopython/output -@dirrm share/examples/py-biopython/Wise -@dirrm share/examples/py-biopython/WIT -@dirrm share/examples/py-biopython/UniGene -@dirrm share/examples/py-biopython/SwissProt -@dirrm share/examples/py-biopython/SubsMat -@dirrm share/examples/py-biopython/Saf -@dirrm share/examples/py-biopython/Registry -@dirrm share/examples/py-biopython/Rebase -@dirrm share/examples/py-biopython/Prosite/Doc -@dirrm share/examples/py-biopython/Prosite -@dirrm share/examples/py-biopython/PDB -@dirrm share/examples/py-biopython/Nucleic -@dirrm share/examples/py-biopython/NeuralNetwork -@dirrm share/examples/py-biopython/Ndb -@dirrm share/examples/py-biopython/NBRF -@dirrm share/examples/py-biopython/MetaTool -@dirrm share/examples/py-biopython/LocusLink -@dirrm share/examples/py-biopython/Kabat -@dirrm share/examples/py-biopython/KEGG -@dirrm share/examples/py-biopython/InterPro -@dirrm share/examples/py-biopython/IntelliGenetics -@dirrm share/examples/py-biopython/Graphics -@dirrm share/examples/py-biopython/Gobase -@dirrm share/examples/py-biopython/Geo -@dirrm share/examples/py-biopython/GenBank -@dirrm share/examples/py-biopython/GFF -@dirrm share/examples/py-biopython/Fasta -@dirrm share/examples/py-biopython/FSSP -@dirrm share/examples/py-biopython/Enzymes -@dirrm share/examples/py-biopython/Emboss -@dirrm share/examples/py-biopython/ECell -@dirrm share/examples/py-biopython/CodonUsage -@dirrm share/examples/py-biopython/Clustalw -@dirrm share/examples/py-biopython/CDD -@dirrm share/examples/py-biopython/Blast -@dirrm share/examples/py-biopython/BioSQL -@dirrm share/examples/py-biopython/Amino -@dirrm share/examples/py-biopython -@dirrm lib/python${MODPY_VERSION}/site-packages/Martel -@dirrm lib/python${MODPY_VERSION}/site-packages/BioSQL -@dirrm lib/python${MODPY_VERSION}/site-packages/Bio/writers/SeqRecord -@dirrm lib/python${MODPY_VERSION}/site-packages/Bio/writers -@dirrm lib/python${MODPY_VERSION}/site-packages/Bio/formatdefs -@dirrm lib/python${MODPY_VERSION}/site-packages/Bio/expressions/swissprot -@dirrm lib/python${MODPY_VERSION}/site-packages/Bio/expressions/embl -@dirrm lib/python${MODPY_VERSION}/site-packages/Bio/expressions/blast -@dirrm lib/python${MODPY_VERSION}/site-packages/Bio/expressions -@dirrm lib/python${MODPY_VERSION}/site-packages/Bio/dbdefs -@dirrm lib/python${MODPY_VERSION}/site-packages/Bio/config -@dirrm lib/python${MODPY_VERSION}/site-packages/Bio/builders/SeqRecord -@dirrm lib/python${MODPY_VERSION}/site-packages/Bio/builders/Search -@dirrm lib/python${MODPY_VERSION}/site-packages/Bio/builders -@dirrm lib/python${MODPY_VERSION}/site-packages/Bio/Wise -@dirrm lib/python${MODPY_VERSION}/site-packages/Bio/WWW -@dirrm lib/python${MODPY_VERSION}/site-packages/Bio/UniGene -@dirrm lib/python${MODPY_VERSION}/site-packages/Bio/SwissProt -@dirrm lib/python${MODPY_VERSION}/site-packages/Bio/SubsMat -@dirrm lib/python${MODPY_VERSION}/site-packages/Bio/Sequencing -@dirrm lib/python${MODPY_VERSION}/site-packages/Bio/SeqUtils -@dirrm lib/python${MODPY_VERSION}/site-packages/Bio/SeqIO -@dirrm lib/python${MODPY_VERSION}/site-packages/Bio/Saf -@dirrm lib/python${MODPY_VERSION}/site-packages/Bio/SVDSuperimposer -@dirrm lib/python${MODPY_VERSION}/site-packages/Bio/SCOP/tests -@dirrm lib/python${MODPY_VERSION}/site-packages/Bio/SCOP -@dirrm lib/python${MODPY_VERSION}/site-packages/Bio/Rebase -@dirrm lib/python${MODPY_VERSION}/site-packages/Bio/Prosite -@dirrm lib/python${MODPY_VERSION}/site-packages/Bio/Pathway/Rep -@dirrm lib/python${MODPY_VERSION}/site-packages/Bio/Pathway -@dirrm lib/python${MODPY_VERSION}/site-packages/Bio/Parsers -@dirrm lib/python${MODPY_VERSION}/site-packages/Bio/PDB/mmCIF -@dirrm lib/python${MODPY_VERSION}/site-packages/Bio/PDB -@dirrm lib/python${MODPY_VERSION}/site-packages/Bio/NeuralNetwork/Gene -@dirrm lib/python${MODPY_VERSION}/site-packages/Bio/NeuralNetwork/BackPropagation -@dirrm lib/python${MODPY_VERSION}/site-packages/Bio/NeuralNetwork -@dirrm lib/python${MODPY_VERSION}/site-packages/Bio/Ndb -@dirrm lib/python${MODPY_VERSION}/site-packages/Bio/NMR -@dirrm lib/python${MODPY_VERSION}/site-packages/Bio/NBRF -@dirrm lib/python${MODPY_VERSION}/site-packages/Bio/MultiProc -@dirrm lib/python${MODPY_VERSION}/site-packages/Bio/Mindy -@dirrm lib/python${MODPY_VERSION}/site-packages/Bio/MetaTool -@dirrm lib/python${MODPY_VERSION}/site-packages/Bio/Medline -@dirrm lib/python${MODPY_VERSION}/site-packages/Bio/LocusLink -@dirrm lib/python${MODPY_VERSION}/site-packages/Bio/Kabat -@dirrm lib/python${MODPY_VERSION}/site-packages/Bio/KEGG/Map -@dirrm lib/python${MODPY_VERSION}/site-packages/Bio/KEGG/Enzyme -@dirrm lib/python${MODPY_VERSION}/site-packages/Bio/KEGG/Compound -@dirrm lib/python${MODPY_VERSION}/site-packages/Bio/KEGG -@dirrm lib/python${MODPY_VERSION}/site-packages/Bio/KDTree -@dirrm lib/python${MODPY_VERSION}/site-packages/Bio/InterPro -@dirrm lib/python${MODPY_VERSION}/site-packages/Bio/IntelliGenetics -@dirrm lib/python${MODPY_VERSION}/site-packages/Bio/HMM -@dirrm lib/python${MODPY_VERSION}/site-packages/Bio/Graphics -@dirrm lib/python${MODPY_VERSION}/site-packages/Bio/Gobase -@dirrm lib/python${MODPY_VERSION}/site-packages/Bio/Geo -@dirrm lib/python${MODPY_VERSION}/site-packages/Bio/GenBank -@dirrm lib/python${MODPY_VERSION}/site-packages/Bio/GFF -@dirrm lib/python${MODPY_VERSION}/site-packages/Bio/GA/Selection -@dirrm lib/python${MODPY_VERSION}/site-packages/Bio/GA/Repair -@dirrm lib/python${MODPY_VERSION}/site-packages/Bio/GA/Mutation -@dirrm lib/python${MODPY_VERSION}/site-packages/Bio/GA/Crossover -@dirrm lib/python${MODPY_VERSION}/site-packages/Bio/GA -@dirrm lib/python${MODPY_VERSION}/site-packages/Bio/Fasta -@dirrm lib/python${MODPY_VERSION}/site-packages/Bio/FSSP -@dirrm lib/python${MODPY_VERSION}/site-packages/Bio/Enzyme -@dirrm lib/python${MODPY_VERSION}/site-packages/Bio/Encodings -@dirrm lib/python${MODPY_VERSION}/site-packages/Bio/Emboss -@dirrm lib/python${MODPY_VERSION}/site-packages/Bio/EUtils/DTDs -@dirrm lib/python${MODPY_VERSION}/site-packages/Bio/EUtils -@dirrm lib/python${MODPY_VERSION}/site-packages/Bio/ECell -@dirrm lib/python${MODPY_VERSION}/site-packages/Bio/Data -@dirrm lib/python${MODPY_VERSION}/site-packages/Bio/Crystal -@dirrm lib/python${MODPY_VERSION}/site-packages/Bio/Cluster -@dirrm lib/python${MODPY_VERSION}/site-packages/Bio/Clustalw -@dirrm lib/python${MODPY_VERSION}/site-packages/Bio/CDD -@dirrm lib/python${MODPY_VERSION}/site-packages/Bio/Blast -@dirrm lib/python${MODPY_VERSION}/site-packages/Bio/Application -@dirrm lib/python${MODPY_VERSION}/site-packages/Bio/Alphabet -@dirrm lib/python${MODPY_VERSION}/site-packages/Bio/AlignAce -@dirrm lib/python${MODPY_VERSION}/site-packages/Bio/Align -@dirrm lib/python${MODPY_VERSION}/site-packages/Bio/Ais -@dirrm lib/python${MODPY_VERSION}/site-packages/Bio