diff -ruN py-biopython.bak/Makefile py-biopython/Makefile --- py-biopython.bak/Makefile 2010-01-06 08:29:25.000000000 +0800 +++ py-biopython/Makefile 2010-07-01 15:13:26.000000000 +0800 @@ -6,7 +6,7 @@ # PORTNAME= biopython -PORTVERSION= 1.53 +PORTVERSION= 1.54 CATEGORIES= biology python MASTER_SITES= http://www.biopython.org/DIST/ PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} @@ -14,8 +14,7 @@ MAINTAINER= mauricio@arareko.net COMMENT= A collection of Python modules for bioinformatics -BUILD_DEPENDS= ${PYNUMPY} \ - ${PYTHON_SITELIBDIR}/mx/TextTools/__init__.py:${PORTSDIR}/lang/py-mx-base +BUILD_DEPENDS= ${PYNUMPY} RUN_DEPENDS= ${BUILD_DEPENDS} USE_PYTHON= 2.4+ diff -ruN py-biopython.bak/distinfo py-biopython/distinfo --- py-biopython.bak/distinfo 2010-01-06 08:29:25.000000000 +0800 +++ py-biopython/distinfo 2010-07-01 10:38:07.000000000 +0800 @@ -1,3 +1,3 @@ -MD5 (biopython-1.53.tar.gz) = df1004ec64b9b593c0e690c14a20667a -SHA256 (biopython-1.53.tar.gz) = 0db8bf8d37641fdfc6a8aac248de3d8cb4111e55484deb43f67e8d7ad082013f -SIZE (biopython-1.53.tar.gz) = 4284683 +MD5 (biopython-1.54.tar.gz) = d4c4ce5a3e1bb401928ca3dc3d1b08cd +SHA256 (biopython-1.54.tar.gz) = 6f704698d68af75b3601b2a862386682b2317038b8bbaf2eb2ad68c1e1a4dc35 +SIZE (biopython-1.54.tar.gz) = 6445527 diff -ruN py-biopython.bak/pkg-plist py-biopython/pkg-plist --- py-biopython.bak/pkg-plist 2010-01-06 08:29:25.000000000 +0800 +++ py-biopython/pkg-plist 2010-07-01 15:25:17.000000000 +0800 @@ -1,19 +1,3 @@ -%%PYTHON_SITELIBDIR%%/BioSQL/BioSeq.py -%%PYTHON_SITELIBDIR%%/BioSQL/BioSeq.pyc -%%PYTHON_SITELIBDIR%%/BioSQL/BioSeq.pyo -%%PYTHON_SITELIBDIR%%/BioSQL/BioSeqDatabase.py -%%PYTHON_SITELIBDIR%%/BioSQL/BioSeqDatabase.pyc -%%PYTHON_SITELIBDIR%%/BioSQL/BioSeqDatabase.pyo -%%PYTHON_SITELIBDIR%%/BioSQL/DBUtils.py -%%PYTHON_SITELIBDIR%%/BioSQL/DBUtils.pyc -%%PYTHON_SITELIBDIR%%/BioSQL/DBUtils.pyo -%%PYTHON_SITELIBDIR%%/BioSQL/Loader.py -%%PYTHON_SITELIBDIR%%/BioSQL/Loader.pyc -%%PYTHON_SITELIBDIR%%/BioSQL/Loader.pyo -%%PYTHON_SITELIBDIR%%/BioSQL/__init__.py -%%PYTHON_SITELIBDIR%%/BioSQL/__init__.pyc -%%PYTHON_SITELIBDIR%%/BioSQL/__init__.pyo -@dirrm %%PYTHON_SITELIBDIR%%/BioSQL %%PYTHON_SITELIBDIR%%/Bio/Affy/CelFile.py %%PYTHON_SITELIBDIR%%/Bio/Affy/CelFile.pyc %%PYTHON_SITELIBDIR%%/Bio/Affy/CelFile.pyo @@ -189,6 +173,8 @@ %%PYTHON_SITELIBDIR%%/Bio/Entrez/DTDs/HomoloGene.mod.dtd %%PYTHON_SITELIBDIR%%/Bio/Entrez/DTDs/NCBI_Biblio.mod.dtd %%PYTHON_SITELIBDIR%%/Bio/Entrez/DTDs/NCBI_BioSource.mod.dtd +%%PYTHON_SITELIBDIR%%/Bio/Entrez/DTDs/NCBI_BlastOutput.dtd +%%PYTHON_SITELIBDIR%%/Bio/Entrez/DTDs/NCBI_BlastOutput.mod.dtd %%PYTHON_SITELIBDIR%%/Bio/Entrez/DTDs/NCBI_Entity.mod.dtd %%PYTHON_SITELIBDIR%%/Bio/Entrez/DTDs/NCBI_Entrezgene.dtd %%PYTHON_SITELIBDIR%%/Bio/Entrez/DTDs/NCBI_Entrezgene.mod.dtd @@ -219,29 +205,88 @@ %%PYTHON_SITELIBDIR%%/Bio/Entrez/DTDs/PIR_General.mod.dtd %%PYTHON_SITELIBDIR%%/Bio/Entrez/DTDs/PRF_General.mod.dtd 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%%PYTHON_SITELIBDIR%%/Bio/Entrez/DTDs/nlmserials_080101.dtd %%PYTHON_SITELIBDIR%%/Bio/Entrez/DTDs/nlmsharedcatcit_080101.dtd %%PYTHON_SITELIBDIR%%/Bio/Entrez/DTDs/nlmsharedcatcit_090101.dtd +%%PYTHON_SITELIBDIR%%/Bio/Entrez/DTDs/notat.ent +%%PYTHON_SITELIBDIR%%/Bio/Entrez/DTDs/para.ent +%%PYTHON_SITELIBDIR%%/Bio/Entrez/DTDs/phrase.ent +%%PYTHON_SITELIBDIR%%/Bio/Entrez/DTDs/pmc-1.dtd +%%PYTHON_SITELIBDIR%%/Bio/Entrez/DTDs/pubmed_020114.dtd %%PYTHON_SITELIBDIR%%/Bio/Entrez/DTDs/pubmed_080101.dtd %%PYTHON_SITELIBDIR%%/Bio/Entrez/DTDs/pubmed_090101.dtd +%%PYTHON_SITELIBDIR%%/Bio/Entrez/DTDs/pubmed_100101.dtd +%%PYTHON_SITELIBDIR%%/Bio/Entrez/DTDs/references.ent +%%PYTHON_SITELIBDIR%%/Bio/Entrez/DTDs/section.ent %%PYTHON_SITELIBDIR%%/Bio/Entrez/DTDs/taxon.dtd +%%PYTHON_SITELIBDIR%%/Bio/Entrez/DTDs/xmlspecchars.ent %%PYTHON_SITELIBDIR%%/Bio/Entrez/Parser.py %%PYTHON_SITELIBDIR%%/Bio/Entrez/Parser.pyc %%PYTHON_SITELIBDIR%%/Bio/Entrez/Parser.pyo @@ -498,12 +543,12 @@ %%PYTHON_SITELIBDIR%%/Bio/Motif/Parsers/AlignAce.py %%PYTHON_SITELIBDIR%%/Bio/Motif/Parsers/AlignAce.pyc %%PYTHON_SITELIBDIR%%/Bio/Motif/Parsers/AlignAce.pyo -%%PYTHON_SITELIBDIR%%/Bio/Motif/Parsers/MEME.py -%%PYTHON_SITELIBDIR%%/Bio/Motif/Parsers/MEME.pyc -%%PYTHON_SITELIBDIR%%/Bio/Motif/Parsers/MEME.pyo %%PYTHON_SITELIBDIR%%/Bio/Motif/Parsers/MAST.py %%PYTHON_SITELIBDIR%%/Bio/Motif/Parsers/MAST.pyc %%PYTHON_SITELIBDIR%%/Bio/Motif/Parsers/MAST.pyo +%%PYTHON_SITELIBDIR%%/Bio/Motif/Parsers/MEME.py +%%PYTHON_SITELIBDIR%%/Bio/Motif/Parsers/MEME.pyc +%%PYTHON_SITELIBDIR%%/Bio/Motif/Parsers/MEME.pyo %%PYTHON_SITELIBDIR%%/Bio/Motif/Parsers/__init__.py %%PYTHON_SITELIBDIR%%/Bio/Motif/Parsers/__init__.pyc %%PYTHON_SITELIBDIR%%/Bio/Motif/Parsers/__init__.pyo @@ -692,6 +737,36 @@ %%PYTHON_SITELIBDIR%%/Bio/Pathway/__init__.py %%PYTHON_SITELIBDIR%%/Bio/Pathway/__init__.pyc %%PYTHON_SITELIBDIR%%/Bio/Pathway/__init__.pyo +%%PYTHON_SITELIBDIR%%/Bio/Phylo/BaseTree.py +%%PYTHON_SITELIBDIR%%/Bio/Phylo/BaseTree.pyc +%%PYTHON_SITELIBDIR%%/Bio/Phylo/BaseTree.pyo +%%PYTHON_SITELIBDIR%%/Bio/Phylo/Newick.py +%%PYTHON_SITELIBDIR%%/Bio/Phylo/Newick.pyc +%%PYTHON_SITELIBDIR%%/Bio/Phylo/Newick.pyo +%%PYTHON_SITELIBDIR%%/Bio/Phylo/NewickIO.py +%%PYTHON_SITELIBDIR%%/Bio/Phylo/NewickIO.pyc +%%PYTHON_SITELIBDIR%%/Bio/Phylo/NewickIO.pyo +%%PYTHON_SITELIBDIR%%/Bio/Phylo/NexusIO.py +%%PYTHON_SITELIBDIR%%/Bio/Phylo/NexusIO.pyc +%%PYTHON_SITELIBDIR%%/Bio/Phylo/NexusIO.pyo +%%PYTHON_SITELIBDIR%%/Bio/Phylo/PhyloXML.py +%%PYTHON_SITELIBDIR%%/Bio/Phylo/PhyloXML.pyc +%%PYTHON_SITELIBDIR%%/Bio/Phylo/PhyloXML.pyo +%%PYTHON_SITELIBDIR%%/Bio/Phylo/PhyloXMLIO.py +%%PYTHON_SITELIBDIR%%/Bio/Phylo/PhyloXMLIO.pyc +%%PYTHON_SITELIBDIR%%/Bio/Phylo/PhyloXMLIO.pyo +%%PYTHON_SITELIBDIR%%/Bio/Phylo/__init__.py +%%PYTHON_SITELIBDIR%%/Bio/Phylo/__init__.pyc +%%PYTHON_SITELIBDIR%%/Bio/Phylo/__init__.pyo +%%PYTHON_SITELIBDIR%%/Bio/Phylo/_io.py +%%PYTHON_SITELIBDIR%%/Bio/Phylo/_io.pyc +%%PYTHON_SITELIBDIR%%/Bio/Phylo/_io.pyo +%%PYTHON_SITELIBDIR%%/Bio/Phylo/_sugar.py +%%PYTHON_SITELIBDIR%%/Bio/Phylo/_sugar.pyc +%%PYTHON_SITELIBDIR%%/Bio/Phylo/_sugar.pyo +%%PYTHON_SITELIBDIR%%/Bio/Phylo/_utils.py +%%PYTHON_SITELIBDIR%%/Bio/Phylo/_utils.pyc +%%PYTHON_SITELIBDIR%%/Bio/Phylo/_utils.pyo %%PYTHON_SITELIBDIR%%/Bio/PopGen/Async/Local.py %%PYTHON_SITELIBDIR%%/Bio/PopGen/Async/Local.pyc %%PYTHON_SITELIBDIR%%/Bio/PopGen/Async/Local.pyo @@ -710,15 +785,18 @@ %%PYTHON_SITELIBDIR%%/Bio/PopGen/FDist/__init__.py %%PYTHON_SITELIBDIR%%/Bio/PopGen/FDist/__init__.pyc %%PYTHON_SITELIBDIR%%/Bio/PopGen/FDist/__init__.pyo -%%PYTHON_SITELIBDIR%%/Bio/PopGen/GenePop/Utils.py -%%PYTHON_SITELIBDIR%%/Bio/PopGen/GenePop/Utils.pyc -%%PYTHON_SITELIBDIR%%/Bio/PopGen/GenePop/Utils.pyo %%PYTHON_SITELIBDIR%%/Bio/PopGen/GenePop/Controller.py %%PYTHON_SITELIBDIR%%/Bio/PopGen/GenePop/Controller.pyc %%PYTHON_SITELIBDIR%%/Bio/PopGen/GenePop/Controller.pyo %%PYTHON_SITELIBDIR%%/Bio/PopGen/GenePop/EasyController.py %%PYTHON_SITELIBDIR%%/Bio/PopGen/GenePop/EasyController.pyc %%PYTHON_SITELIBDIR%%/Bio/PopGen/GenePop/EasyController.pyo +%%PYTHON_SITELIBDIR%%/Bio/PopGen/GenePop/FileParser.py +%%PYTHON_SITELIBDIR%%/Bio/PopGen/GenePop/FileParser.pyc +%%PYTHON_SITELIBDIR%%/Bio/PopGen/GenePop/FileParser.pyo +%%PYTHON_SITELIBDIR%%/Bio/PopGen/GenePop/Utils.py +%%PYTHON_SITELIBDIR%%/Bio/PopGen/GenePop/Utils.pyc +%%PYTHON_SITELIBDIR%%/Bio/PopGen/GenePop/Utils.pyo %%PYTHON_SITELIBDIR%%/Bio/PopGen/GenePop/__init__.py %%PYTHON_SITELIBDIR%%/Bio/PopGen/GenePop/__init__.pyc %%PYTHON_SITELIBDIR%%/Bio/PopGen/GenePop/__init__.pyo @@ -789,9 +867,6 @@ %%PYTHON_SITELIBDIR%%/Bio/Restriction/__init__.py %%PYTHON_SITELIBDIR%%/Bio/Restriction/__init__.pyc %%PYTHON_SITELIBDIR%%/Bio/Restriction/__init__.pyo -%%PYTHON_SITELIBDIR%%/Bio/SCOP/__init__.py -%%PYTHON_SITELIBDIR%%/Bio/SCOP/__init__.pyc -%%PYTHON_SITELIBDIR%%/Bio/SCOP/__init__.pyo %%PYTHON_SITELIBDIR%%/Bio/SCOP/Cla.py %%PYTHON_SITELIBDIR%%/Bio/SCOP/Cla.pyc %%PYTHON_SITELIBDIR%%/Bio/SCOP/Cla.pyo @@ -810,6 +885,9 @@ %%PYTHON_SITELIBDIR%%/Bio/SCOP/Residues.py %%PYTHON_SITELIBDIR%%/Bio/SCOP/Residues.pyc %%PYTHON_SITELIBDIR%%/Bio/SCOP/Residues.pyo +%%PYTHON_SITELIBDIR%%/Bio/SCOP/__init__.py +%%PYTHON_SITELIBDIR%%/Bio/SCOP/__init__.pyc +%%PYTHON_SITELIBDIR%%/Bio/SCOP/__init__.pyo %%PYTHON_SITELIBDIR%%/Bio/SVDSuperimposer/SVDSuperimposer.py %%PYTHON_SITELIBDIR%%/Bio/SVDSuperimposer/SVDSuperimposer.pyc %%PYTHON_SITELIBDIR%%/Bio/SVDSuperimposer/SVDSuperimposer.pyo @@ -825,12 +903,6 @@ %%PYTHON_SITELIBDIR%%/Bio/SeqFeature.py %%PYTHON_SITELIBDIR%%/Bio/SeqFeature.pyc %%PYTHON_SITELIBDIR%%/Bio/SeqFeature.pyo -%%PYTHON_SITELIBDIR%%/Bio/SeqIO/_convert.py -%%PYTHON_SITELIBDIR%%/Bio/SeqIO/_convert.pyc -%%PYTHON_SITELIBDIR%%/Bio/SeqIO/_convert.pyo -%%PYTHON_SITELIBDIR%%/Bio/SeqIO/_index.py -%%PYTHON_SITELIBDIR%%/Bio/SeqIO/_index.pyc -%%PYTHON_SITELIBDIR%%/Bio/SeqIO/_index.pyo %%PYTHON_SITELIBDIR%%/Bio/SeqIO/AceIO.py %%PYTHON_SITELIBDIR%%/Bio/SeqIO/AceIO.pyc %%PYTHON_SITELIBDIR%%/Bio/SeqIO/AceIO.pyo @@ -855,6 +927,9 @@ %%PYTHON_SITELIBDIR%%/Bio/SeqIO/QualityIO.py %%PYTHON_SITELIBDIR%%/Bio/SeqIO/QualityIO.pyc %%PYTHON_SITELIBDIR%%/Bio/SeqIO/QualityIO.pyo +%%PYTHON_SITELIBDIR%%/Bio/SeqIO/SffIO.py +%%PYTHON_SITELIBDIR%%/Bio/SeqIO/SffIO.pyc +%%PYTHON_SITELIBDIR%%/Bio/SeqIO/SffIO.pyo %%PYTHON_SITELIBDIR%%/Bio/SeqIO/SwissIO.py %%PYTHON_SITELIBDIR%%/Bio/SeqIO/SwissIO.pyc %%PYTHON_SITELIBDIR%%/Bio/SeqIO/SwissIO.pyo @@ -864,6 +939,12 @@ %%PYTHON_SITELIBDIR%%/Bio/SeqIO/__init__.py %%PYTHON_SITELIBDIR%%/Bio/SeqIO/__init__.pyc %%PYTHON_SITELIBDIR%%/Bio/SeqIO/__init__.pyo +%%PYTHON_SITELIBDIR%%/Bio/SeqIO/_convert.py +%%PYTHON_SITELIBDIR%%/Bio/SeqIO/_convert.pyc +%%PYTHON_SITELIBDIR%%/Bio/SeqIO/_convert.pyo +%%PYTHON_SITELIBDIR%%/Bio/SeqIO/_index.py +%%PYTHON_SITELIBDIR%%/Bio/SeqIO/_index.pyc +%%PYTHON_SITELIBDIR%%/Bio/SeqIO/_index.pyo %%PYTHON_SITELIBDIR%%/Bio/SeqRecord.py %%PYTHON_SITELIBDIR%%/Bio/SeqRecord.pyc %%PYTHON_SITELIBDIR%%/Bio/SeqRecord.pyo @@ -897,15 +978,15 @@ %%PYTHON_SITELIBDIR%%/Bio/Sequencing/Ace.py %%PYTHON_SITELIBDIR%%/Bio/Sequencing/Ace.pyc %%PYTHON_SITELIBDIR%%/Bio/Sequencing/Ace.pyo -%%PYTHON_SITELIBDIR%%/Bio/Sequencing/Phd.py -%%PYTHON_SITELIBDIR%%/Bio/Sequencing/Phd.pyc -%%PYTHON_SITELIBDIR%%/Bio/Sequencing/Phd.pyo -%%PYTHON_SITELIBDIR%%/Bio/Sequencing/Applications/__init__.py -%%PYTHON_SITELIBDIR%%/Bio/Sequencing/Applications/__init__.pyc -%%PYTHON_SITELIBDIR%%/Bio/Sequencing/Applications/__init__.pyo %%PYTHON_SITELIBDIR%%/Bio/Sequencing/Applications/_Novoalign.py %%PYTHON_SITELIBDIR%%/Bio/Sequencing/Applications/_Novoalign.pyc %%PYTHON_SITELIBDIR%%/Bio/Sequencing/Applications/_Novoalign.pyo +%%PYTHON_SITELIBDIR%%/Bio/Sequencing/Applications/__init__.py +%%PYTHON_SITELIBDIR%%/Bio/Sequencing/Applications/__init__.pyc +%%PYTHON_SITELIBDIR%%/Bio/Sequencing/Applications/__init__.pyo +%%PYTHON_SITELIBDIR%%/Bio/Sequencing/Phd.py +%%PYTHON_SITELIBDIR%%/Bio/Sequencing/Phd.pyc +%%PYTHON_SITELIBDIR%%/Bio/Sequencing/Phd.pyo %%PYTHON_SITELIBDIR%%/Bio/Sequencing/__init__.py %%PYTHON_SITELIBDIR%%/Bio/Sequencing/__init__.pyc %%PYTHON_SITELIBDIR%%/Bio/Sequencing/__init__.pyo @@ -939,12 +1020,12 @@ %%PYTHON_SITELIBDIR%%/Bio/Translate.py %%PYTHON_SITELIBDIR%%/Bio/Translate.pyc %%PYTHON_SITELIBDIR%%/Bio/Translate.pyo -%%PYTHON_SITELIBDIR%%/Bio/UniGene/__init__.py -%%PYTHON_SITELIBDIR%%/Bio/UniGene/__init__.pyc -%%PYTHON_SITELIBDIR%%/Bio/UniGene/__init__.pyo %%PYTHON_SITELIBDIR%%/Bio/UniGene/UniGene.py %%PYTHON_SITELIBDIR%%/Bio/UniGene/UniGene.pyc %%PYTHON_SITELIBDIR%%/Bio/UniGene/UniGene.pyo +%%PYTHON_SITELIBDIR%%/Bio/UniGene/__init__.py +%%PYTHON_SITELIBDIR%%/Bio/UniGene/__init__.pyc +%%PYTHON_SITELIBDIR%%/Bio/UniGene/__init__.pyo %%PYTHON_SITELIBDIR%%/Bio/Wise/__init__.py %%PYTHON_SITELIBDIR%%/Bio/Wise/__init__.pyc %%PYTHON_SITELIBDIR%%/Bio/Wise/__init__.pyo @@ -981,6 +1062,21 @@ %%PYTHON_SITELIBDIR%%/Bio/utils.py %%PYTHON_SITELIBDIR%%/Bio/utils.pyc %%PYTHON_SITELIBDIR%%/Bio/utils.pyo +%%PYTHON_SITELIBDIR%%/BioSQL/BioSeq.py +%%PYTHON_SITELIBDIR%%/BioSQL/BioSeq.pyc +%%PYTHON_SITELIBDIR%%/BioSQL/BioSeq.pyo +%%PYTHON_SITELIBDIR%%/BioSQL/BioSeqDatabase.py +%%PYTHON_SITELIBDIR%%/BioSQL/BioSeqDatabase.pyc +%%PYTHON_SITELIBDIR%%/BioSQL/BioSeqDatabase.pyo +%%PYTHON_SITELIBDIR%%/BioSQL/DBUtils.py +%%PYTHON_SITELIBDIR%%/BioSQL/DBUtils.pyc +%%PYTHON_SITELIBDIR%%/BioSQL/DBUtils.pyo +%%PYTHON_SITELIBDIR%%/BioSQL/Loader.py +%%PYTHON_SITELIBDIR%%/BioSQL/Loader.pyc +%%PYTHON_SITELIBDIR%%/BioSQL/Loader.pyo +%%PYTHON_SITELIBDIR%%/BioSQL/__init__.py +%%PYTHON_SITELIBDIR%%/BioSQL/__init__.pyc +%%PYTHON_SITELIBDIR%%/BioSQL/__init__.pyo @dirrm %%PYTHON_SITELIBDIR%%/Bio/Affy @dirrm %%PYTHON_SITELIBDIR%%/Bio/Align/Applications @dirrm %%PYTHON_SITELIBDIR%%/Bio/Align @@ -1035,6 +1131,7 @@ @dirrm %%PYTHON_SITELIBDIR%%/Bio/Parsers @dirrm %%PYTHON_SITELIBDIR%%/Bio/Pathway/Rep @dirrm %%PYTHON_SITELIBDIR%%/Bio/Pathway +@dirrm %%PYTHON_SITELIBDIR%%/Bio/Phylo @dirrm %%PYTHON_SITELIBDIR%%/Bio/PopGen/Async @dirrm %%PYTHON_SITELIBDIR%%/Bio/PopGen/FDist @dirrm %%PYTHON_SITELIBDIR%%/Bio/PopGen/GenePop @@ -1056,3 +1153,4 @@ @dirrm %%PYTHON_SITELIBDIR%%/Bio/UniGene @dirrm %%PYTHON_SITELIBDIR%%/Bio/Wise @dirrm %%PYTHON_SITELIBDIR%%/Bio +@dirrm %%PYTHON_SITELIBDIR%%/BioSQL