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[pkgsrc/trunk]: pkgsrc py-biopython: initial commit

details:   https://anonhg.NetBSD.org/pkgsrc/rev/fe4d2ce75941
branches:  trunk
changeset: 337674:fe4d2ce75941
user:      brook <brook%pkgsrc.org@localhost>
date:      Fri Aug 09 21:52:34 2019 +0000

description:
py-biopython: initial commit

The Biopython package contains high-quality, reusable modules and
scripts written in Python to make it as easy as possible to use Python
for bioinformatics.  The Biopython includes the follwing: the ability
to parse bioinformatics files into python utilizable data structures,
including support for the formats such as Blast output, Clustalw,
FASTA, GenBank, PubMed and Medicine, various Expasy files, SCOP,
Rebase, UniGene, and SwissProt.

diffstat:

 biology/Makefile              |     3 +-
 biology/py-biopython/DESCR    |     7 +
 biology/py-biopython/Makefile |    24 +
 biology/py-biopython/PLIST    |  1262 +++++++++++++++++++++++++++++++++++++++++
 biology/py-biopython/distinfo |     6 +
 doc/CHANGES-2019              |     3 +-
 6 files changed, 1303 insertions(+), 2 deletions(-)

diffs (truncated from 1346 to 300 lines):

diff -r 99014e24be93 -r fe4d2ce75941 biology/Makefile
--- a/biology/Makefile  Fri Aug 09 20:56:19 2019 +0000
+++ b/biology/Makefile  Fri Aug 09 21:52:34 2019 +0000
@@ -1,4 +1,4 @@
-# $NetBSD: Makefile,v 1.54 2019/05/10 16:20:22 bacon Exp $
+# $NetBSD: Makefile,v 1.55 2019/08/09 21:52:34 brook Exp $
 #
 
 COMMENT=       Software for the biological sciences
@@ -43,6 +43,7 @@
 SUBDIR+=       primer3
 SUBDIR+=       profit
 SUBDIR+=       puzzle
+SUBDIR+=       py-biopython
 SUBDIR+=       py-mol
 SUBDIR+=       py-pydicom
 SUBDIR+=       rasmol
diff -r 99014e24be93 -r fe4d2ce75941 biology/py-biopython/DESCR
--- /dev/null   Thu Jan 01 00:00:00 1970 +0000
+++ b/biology/py-biopython/DESCR        Fri Aug 09 21:52:34 2019 +0000
@@ -0,0 +1,7 @@
+The Biopython package contains high-quality, reusable modules and
+scripts written in Python to make it as easy as possible to use Python
+for bioinformatics.  The Biopython includes the follwing: the ability
+to parse bioinformatics files into python utilizable data structures,
+including support for the formats such as Blast output, Clustalw,
+FASTA, GenBank, PubMed and Medicine, various Expasy files, SCOP,
+Rebase, UniGene, and SwissProt.
diff -r 99014e24be93 -r fe4d2ce75941 biology/py-biopython/Makefile
--- /dev/null   Thu Jan 01 00:00:00 1970 +0000
+++ b/biology/py-biopython/Makefile     Fri Aug 09 21:52:34 2019 +0000
@@ -0,0 +1,24 @@
+# $NetBSD: Makefile,v 1.1 2019/08/09 21:52:34 brook Exp $
+
+DISTNAME=      biopython-1.74
+PKGNAME=       ${PYPKGPREFIX}-${DISTNAME}
+CATEGORIES=    biology
+MASTER_SITES=  http://biopython.org/DIST/
+
+MAINTAINER=    pkgsrc-users%NetBSD.org@localhost
+HOMEPAGE=      http://biopython.org/
+COMMENT=       Python libraries for computational molecular biology
+LICENSE=       biopython-license
+
+USE_TOOLS+=    pax
+
+INSTALLATION_DIRS+=    share/doc/biopython share/examples/biopython
+
+post-install:
+       ${INSTALL_DATA} ${WRKSRC}/README.rst ${DESTDIR}${PREFIX}/share/doc/biopython
+       ${INSTALL_DATA} ${WRKSRC}/Doc/Tutorial.pdf ${DESTDIR}${PREFIX}/share/doc/biopython
+       cd ${WRKSRC}/Doc/examples && ${PAX} -rw . ${DESTDIR}${PREFIX}/share/examples/biopython
+
+.include "../../lang/python/egg.mk"
+.include "../../math/py-numpy/buildlink3.mk"
+.include "../../mk/bsd.pkg.mk"
diff -r 99014e24be93 -r fe4d2ce75941 biology/py-biopython/PLIST
--- /dev/null   Thu Jan 01 00:00:00 1970 +0000
+++ b/biology/py-biopython/PLIST        Fri Aug 09 21:52:34 2019 +0000
@@ -0,0 +1,1262 @@
+@comment $NetBSD: PLIST,v 1.1 2019/08/09 21:52:34 brook Exp $
+${PYSITELIB}/${EGG_INFODIR}/PKG-INFO
+${PYSITELIB}/${EGG_INFODIR}/SOURCES.txt
+${PYSITELIB}/${EGG_INFODIR}/dependency_links.txt
+${PYSITELIB}/${EGG_INFODIR}/requires.txt
+${PYSITELIB}/${EGG_INFODIR}/top_level.txt
+${PYSITELIB}/Bio/Affy/CelFile.py
+${PYSITELIB}/Bio/Affy/CelFile.pyc
+${PYSITELIB}/Bio/Affy/CelFile.pyo
+${PYSITELIB}/Bio/Affy/__init__.py
+${PYSITELIB}/Bio/Affy/__init__.pyc
+${PYSITELIB}/Bio/Affy/__init__.pyo
+${PYSITELIB}/Bio/Align/AlignInfo.py
+${PYSITELIB}/Bio/Align/AlignInfo.pyc
+${PYSITELIB}/Bio/Align/AlignInfo.pyo
+${PYSITELIB}/Bio/Align/Applications/_ClustalOmega.py
+${PYSITELIB}/Bio/Align/Applications/_ClustalOmega.pyc
+${PYSITELIB}/Bio/Align/Applications/_ClustalOmega.pyo
+${PYSITELIB}/Bio/Align/Applications/_Clustalw.py
+${PYSITELIB}/Bio/Align/Applications/_Clustalw.pyc
+${PYSITELIB}/Bio/Align/Applications/_Clustalw.pyo
+${PYSITELIB}/Bio/Align/Applications/_Dialign.py
+${PYSITELIB}/Bio/Align/Applications/_Dialign.pyc
+${PYSITELIB}/Bio/Align/Applications/_Dialign.pyo
+${PYSITELIB}/Bio/Align/Applications/_MSAProbs.py
+${PYSITELIB}/Bio/Align/Applications/_MSAProbs.pyc
+${PYSITELIB}/Bio/Align/Applications/_MSAProbs.pyo
+${PYSITELIB}/Bio/Align/Applications/_Mafft.py
+${PYSITELIB}/Bio/Align/Applications/_Mafft.pyc
+${PYSITELIB}/Bio/Align/Applications/_Mafft.pyo
+${PYSITELIB}/Bio/Align/Applications/_Muscle.py
+${PYSITELIB}/Bio/Align/Applications/_Muscle.pyc
+${PYSITELIB}/Bio/Align/Applications/_Muscle.pyo
+${PYSITELIB}/Bio/Align/Applications/_Prank.py
+${PYSITELIB}/Bio/Align/Applications/_Prank.pyc
+${PYSITELIB}/Bio/Align/Applications/_Prank.pyo
+${PYSITELIB}/Bio/Align/Applications/_Probcons.py
+${PYSITELIB}/Bio/Align/Applications/_Probcons.pyc
+${PYSITELIB}/Bio/Align/Applications/_Probcons.pyo
+${PYSITELIB}/Bio/Align/Applications/_TCoffee.py
+${PYSITELIB}/Bio/Align/Applications/_TCoffee.pyc
+${PYSITELIB}/Bio/Align/Applications/_TCoffee.pyo
+${PYSITELIB}/Bio/Align/Applications/__init__.py
+${PYSITELIB}/Bio/Align/Applications/__init__.pyc
+${PYSITELIB}/Bio/Align/Applications/__init__.pyo
+${PYSITELIB}/Bio/Align/__init__.py
+${PYSITELIB}/Bio/Align/__init__.pyc
+${PYSITELIB}/Bio/Align/__init__.pyo
+${PYSITELIB}/Bio/Align/_aligners.c
+${PYSITELIB}/Bio/Align/_aligners.so
+${PYSITELIB}/Bio/AlignIO/ClustalIO.py
+${PYSITELIB}/Bio/AlignIO/ClustalIO.pyc
+${PYSITELIB}/Bio/AlignIO/ClustalIO.pyo
+${PYSITELIB}/Bio/AlignIO/EmbossIO.py
+${PYSITELIB}/Bio/AlignIO/EmbossIO.pyc
+${PYSITELIB}/Bio/AlignIO/EmbossIO.pyo
+${PYSITELIB}/Bio/AlignIO/FastaIO.py
+${PYSITELIB}/Bio/AlignIO/FastaIO.pyc
+${PYSITELIB}/Bio/AlignIO/FastaIO.pyo
+${PYSITELIB}/Bio/AlignIO/Interfaces.py
+${PYSITELIB}/Bio/AlignIO/Interfaces.pyc
+${PYSITELIB}/Bio/AlignIO/Interfaces.pyo
+${PYSITELIB}/Bio/AlignIO/MafIO.py
+${PYSITELIB}/Bio/AlignIO/MafIO.pyc
+${PYSITELIB}/Bio/AlignIO/MafIO.pyo
+${PYSITELIB}/Bio/AlignIO/MauveIO.py
+${PYSITELIB}/Bio/AlignIO/MauveIO.pyc
+${PYSITELIB}/Bio/AlignIO/MauveIO.pyo
+${PYSITELIB}/Bio/AlignIO/NexusIO.py
+${PYSITELIB}/Bio/AlignIO/NexusIO.pyc
+${PYSITELIB}/Bio/AlignIO/NexusIO.pyo
+${PYSITELIB}/Bio/AlignIO/PhylipIO.py
+${PYSITELIB}/Bio/AlignIO/PhylipIO.pyc
+${PYSITELIB}/Bio/AlignIO/PhylipIO.pyo
+${PYSITELIB}/Bio/AlignIO/StockholmIO.py
+${PYSITELIB}/Bio/AlignIO/StockholmIO.pyc
+${PYSITELIB}/Bio/AlignIO/StockholmIO.pyo
+${PYSITELIB}/Bio/AlignIO/__init__.py
+${PYSITELIB}/Bio/AlignIO/__init__.pyc
+${PYSITELIB}/Bio/AlignIO/__init__.pyo
+${PYSITELIB}/Bio/Alphabet/IUPAC.py
+${PYSITELIB}/Bio/Alphabet/IUPAC.pyc
+${PYSITELIB}/Bio/Alphabet/IUPAC.pyo
+${PYSITELIB}/Bio/Alphabet/Reduced.py
+${PYSITELIB}/Bio/Alphabet/Reduced.pyc
+${PYSITELIB}/Bio/Alphabet/Reduced.pyo
+${PYSITELIB}/Bio/Alphabet/__init__.py
+${PYSITELIB}/Bio/Alphabet/__init__.pyc
+${PYSITELIB}/Bio/Alphabet/__init__.pyo
+${PYSITELIB}/Bio/Application/__init__.py
+${PYSITELIB}/Bio/Application/__init__.pyc
+${PYSITELIB}/Bio/Application/__init__.pyo
+${PYSITELIB}/Bio/Blast/Applications.py
+${PYSITELIB}/Bio/Blast/Applications.pyc
+${PYSITELIB}/Bio/Blast/Applications.pyo
+${PYSITELIB}/Bio/Blast/NCBIWWW.py
+${PYSITELIB}/Bio/Blast/NCBIWWW.pyc
+${PYSITELIB}/Bio/Blast/NCBIWWW.pyo
+${PYSITELIB}/Bio/Blast/NCBIXML.py
+${PYSITELIB}/Bio/Blast/NCBIXML.pyc
+${PYSITELIB}/Bio/Blast/NCBIXML.pyo
+${PYSITELIB}/Bio/Blast/ParseBlastTable.py
+${PYSITELIB}/Bio/Blast/ParseBlastTable.pyc
+${PYSITELIB}/Bio/Blast/ParseBlastTable.pyo
+${PYSITELIB}/Bio/Blast/Record.py
+${PYSITELIB}/Bio/Blast/Record.pyc
+${PYSITELIB}/Bio/Blast/Record.pyo
+${PYSITELIB}/Bio/Blast/__init__.py
+${PYSITELIB}/Bio/Blast/__init__.pyc
+${PYSITELIB}/Bio/Blast/__init__.pyo
+${PYSITELIB}/Bio/CAPS/__init__.py
+${PYSITELIB}/Bio/CAPS/__init__.pyc
+${PYSITELIB}/Bio/CAPS/__init__.pyo
+${PYSITELIB}/Bio/Cluster/__init__.py
+${PYSITELIB}/Bio/Cluster/__init__.pyc
+${PYSITELIB}/Bio/Cluster/__init__.pyo
+${PYSITELIB}/Bio/Cluster/_cluster.so
+${PYSITELIB}/Bio/Cluster/cluster.c
+${PYSITELIB}/Bio/Cluster/cluster.h
+${PYSITELIB}/Bio/Cluster/clustermodule.c
+${PYSITELIB}/Bio/Compass/__init__.py
+${PYSITELIB}/Bio/Compass/__init__.pyc
+${PYSITELIB}/Bio/Compass/__init__.pyo
+${PYSITELIB}/Bio/Crystal/__init__.py
+${PYSITELIB}/Bio/Crystal/__init__.pyc
+${PYSITELIB}/Bio/Crystal/__init__.pyo
+${PYSITELIB}/Bio/Data/CodonTable.py
+${PYSITELIB}/Bio/Data/CodonTable.pyc
+${PYSITELIB}/Bio/Data/CodonTable.pyo
+${PYSITELIB}/Bio/Data/IUPACData.py
+${PYSITELIB}/Bio/Data/IUPACData.pyc
+${PYSITELIB}/Bio/Data/IUPACData.pyo
+${PYSITELIB}/Bio/Data/SCOPData.py
+${PYSITELIB}/Bio/Data/SCOPData.pyc
+${PYSITELIB}/Bio/Data/SCOPData.pyo
+${PYSITELIB}/Bio/Data/__init__.py
+${PYSITELIB}/Bio/Data/__init__.pyc
+${PYSITELIB}/Bio/Data/__init__.pyo
+${PYSITELIB}/Bio/Emboss/Applications.py
+${PYSITELIB}/Bio/Emboss/Applications.pyc
+${PYSITELIB}/Bio/Emboss/Applications.pyo
+${PYSITELIB}/Bio/Emboss/Primer3.py
+${PYSITELIB}/Bio/Emboss/Primer3.pyc
+${PYSITELIB}/Bio/Emboss/Primer3.pyo
+${PYSITELIB}/Bio/Emboss/PrimerSearch.py
+${PYSITELIB}/Bio/Emboss/PrimerSearch.pyc
+${PYSITELIB}/Bio/Emboss/PrimerSearch.pyo
+${PYSITELIB}/Bio/Emboss/__init__.py
+${PYSITELIB}/Bio/Emboss/__init__.pyc
+${PYSITELIB}/Bio/Emboss/__init__.pyo
+${PYSITELIB}/Bio/Entrez/DTDs/Docsum_3_0.dtd
+${PYSITELIB}/Bio/Entrez/DTDs/Docsum_3_0.mod.dtd
+${PYSITELIB}/Bio/Entrez/DTDs/Docsum_3_1.dtd
+${PYSITELIB}/Bio/Entrez/DTDs/Docsum_3_1.mod.dtd
+${PYSITELIB}/Bio/Entrez/DTDs/Docsum_3_2.dtd
+${PYSITELIB}/Bio/Entrez/DTDs/Docsum_3_2.mod.dtd
+${PYSITELIB}/Bio/Entrez/DTDs/Docsum_3_3.dtd
+${PYSITELIB}/Bio/Entrez/DTDs/Docsum_3_3.mod.dtd
+${PYSITELIB}/Bio/Entrez/DTDs/Docsum_3_4.dtd
+${PYSITELIB}/Bio/Entrez/DTDs/Docsum_3_4.mod.dtd
+${PYSITELIB}/Bio/Entrez/DTDs/EMBL_General.dtd
+${PYSITELIB}/Bio/Entrez/DTDs/EMBL_General.mod.dtd
+${PYSITELIB}/Bio/Entrez/DTDs/GenBank_General.dtd
+${PYSITELIB}/Bio/Entrez/DTDs/GenBank_General.mod.dtd
+${PYSITELIB}/Bio/Entrez/DTDs/HomoloGene.dtd
+${PYSITELIB}/Bio/Entrez/DTDs/HomoloGene.mod.dtd
+${PYSITELIB}/Bio/Entrez/DTDs/INSD_INSDSeq.dtd
+${PYSITELIB}/Bio/Entrez/DTDs/INSD_INSDSeq.mod.dtd
+${PYSITELIB}/Bio/Entrez/DTDs/MMDB.dtd
+${PYSITELIB}/Bio/Entrez/DTDs/MMDB.mod.dtd
+${PYSITELIB}/Bio/Entrez/DTDs/MMDB_Chemical_graph.dtd
+${PYSITELIB}/Bio/Entrez/DTDs/MMDB_Chemical_graph.mod.dtd
+${PYSITELIB}/Bio/Entrez/DTDs/MMDB_Features.dtd
+${PYSITELIB}/Bio/Entrez/DTDs/MMDB_Features.mod.dtd
+${PYSITELIB}/Bio/Entrez/DTDs/MMDB_Structural_model.dtd
+${PYSITELIB}/Bio/Entrez/DTDs/MMDB_Structural_model.mod.dtd
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+${PYSITELIB}/Bio/Entrez/DTDs/NCBI_Access.mod.dtd
+${PYSITELIB}/Bio/Entrez/DTDs/NCBI_Biblio.dtd
+${PYSITELIB}/Bio/Entrez/DTDs/NCBI_Biblio.mod.dtd
+${PYSITELIB}/Bio/Entrez/DTDs/NCBI_BioSource.dtd
+${PYSITELIB}/Bio/Entrez/DTDs/NCBI_BioSource.mod.dtd
+${PYSITELIB}/Bio/Entrez/DTDs/NCBI_BioTree.dtd
+${PYSITELIB}/Bio/Entrez/DTDs/NCBI_BioTree.mod.dtd
+${PYSITELIB}/Bio/Entrez/DTDs/NCBI_Blast4.dtd
+${PYSITELIB}/Bio/Entrez/DTDs/NCBI_Blast4.mod.dtd
+${PYSITELIB}/Bio/Entrez/DTDs/NCBI_BlastDL.dtd
+${PYSITELIB}/Bio/Entrez/DTDs/NCBI_BlastDL.mod.dtd
+${PYSITELIB}/Bio/Entrez/DTDs/NCBI_BlastOutput.dtd
+${PYSITELIB}/Bio/Entrez/DTDs/NCBI_BlastOutput.mod.dtd
+${PYSITELIB}/Bio/Entrez/DTDs/NCBI_Cdd.dtd
+${PYSITELIB}/Bio/Entrez/DTDs/NCBI_Cdd.mod.dtd
+${PYSITELIB}/Bio/Entrez/DTDs/NCBI_Cn3d.dtd
+${PYSITELIB}/Bio/Entrez/DTDs/NCBI_Cn3d.mod.dtd
+${PYSITELIB}/Bio/Entrez/DTDs/NCBI_Entity.mod.dtd
+${PYSITELIB}/Bio/Entrez/DTDs/NCBI_Entrez2.dtd
+${PYSITELIB}/Bio/Entrez/DTDs/NCBI_Entrez2.mod.dtd
+${PYSITELIB}/Bio/Entrez/DTDs/NCBI_Entrezgene.dtd
+${PYSITELIB}/Bio/Entrez/DTDs/NCBI_Entrezgene.mod.dtd
+${PYSITELIB}/Bio/Entrez/DTDs/NCBI_FeatDef.dtd
+${PYSITELIB}/Bio/Entrez/DTDs/NCBI_FeatDef.mod.dtd
+${PYSITELIB}/Bio/Entrez/DTDs/NCBI_GBSeq.dtd
+${PYSITELIB}/Bio/Entrez/DTDs/NCBI_GBSeq.mod.dtd
+${PYSITELIB}/Bio/Entrez/DTDs/NCBI_Gene.dtd
+${PYSITELIB}/Bio/Entrez/DTDs/NCBI_Gene.mod.dtd
+${PYSITELIB}/Bio/Entrez/DTDs/NCBI_General.dtd
+${PYSITELIB}/Bio/Entrez/DTDs/NCBI_General.mod.dtd
+${PYSITELIB}/Bio/Entrez/DTDs/NCBI_ID1Access.dtd
+${PYSITELIB}/Bio/Entrez/DTDs/NCBI_ID1Access.mod.dtd
+${PYSITELIB}/Bio/Entrez/DTDs/NCBI_ID2Access.dtd
+${PYSITELIB}/Bio/Entrez/DTDs/NCBI_ID2Access.mod.dtd
+${PYSITELIB}/Bio/Entrez/DTDs/NCBI_MedArchive.dtd
+${PYSITELIB}/Bio/Entrez/DTDs/NCBI_MedArchive.mod.dtd
+${PYSITELIB}/Bio/Entrez/DTDs/NCBI_Medlars.dtd
+${PYSITELIB}/Bio/Entrez/DTDs/NCBI_Medlars.mod.dtd
+${PYSITELIB}/Bio/Entrez/DTDs/NCBI_Medline.dtd
+${PYSITELIB}/Bio/Entrez/DTDs/NCBI_Medline.mod.dtd
+${PYSITELIB}/Bio/Entrez/DTDs/NCBI_Mim.dtd
+${PYSITELIB}/Bio/Entrez/DTDs/NCBI_Mim.mod.dtd
+${PYSITELIB}/Bio/Entrez/DTDs/NCBI_Mime.dtd
+${PYSITELIB}/Bio/Entrez/DTDs/NCBI_Mime.mod.dtd
+${PYSITELIB}/Bio/Entrez/DTDs/NCBI_ObjPrt.dtd
+${PYSITELIB}/Bio/Entrez/DTDs/NCBI_ObjPrt.mod.dtd
+${PYSITELIB}/Bio/Entrez/DTDs/NCBI_Organism.dtd
+${PYSITELIB}/Bio/Entrez/DTDs/NCBI_Organism.mod.dtd
+${PYSITELIB}/Bio/Entrez/DTDs/NCBI_PCAssay.dtd
+${PYSITELIB}/Bio/Entrez/DTDs/NCBI_PCAssay.mod.dtd
+${PYSITELIB}/Bio/Entrez/DTDs/NCBI_PCSubstance.dtd
+${PYSITELIB}/Bio/Entrez/DTDs/NCBI_PCSubstance.mod.dtd
+${PYSITELIB}/Bio/Entrez/DTDs/NCBI_Project.dtd
+${PYSITELIB}/Bio/Entrez/DTDs/NCBI_Project.mod.dtd
+${PYSITELIB}/Bio/Entrez/DTDs/NCBI_Protein.dtd
+${PYSITELIB}/Bio/Entrez/DTDs/NCBI_Protein.mod.dtd
+${PYSITELIB}/Bio/Entrez/DTDs/NCBI_Pub.dtd
+${PYSITELIB}/Bio/Entrez/DTDs/NCBI_Pub.mod.dtd
+${PYSITELIB}/Bio/Entrez/DTDs/NCBI_PubMed.dtd
+${PYSITELIB}/Bio/Entrez/DTDs/NCBI_PubMed.mod.dtd
+${PYSITELIB}/Bio/Entrez/DTDs/NCBI_RNA.dtd
+${PYSITELIB}/Bio/Entrez/DTDs/NCBI_RNA.mod.dtd
+${PYSITELIB}/Bio/Entrez/DTDs/NCBI_Remap.dtd
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