Add py-biopython, is a collection of Python packages and modules created

by the Biopython Project, intended to provide the basis for building
bioinformatics applications in the Python language.

PR:		ports/20260
Submitted by:	Johann Visagie <johann@egenetics.com>

6 files changed, 166 insertions, 0 deletions

diff --git a/biology/Makefile b/biology/Makefile
index 3142d00711f9..6508ab53e363 100644
--- a/biology/Makefile
+++ b/biology/Makefile
@@ -18,6 +18,7 @@
     SUBDIR += platon
     SUBDIR += povchem
     SUBDIR += psi88
+    SUBDIR += py-biopython
     SUBDIR += rasmol
     SUBDIR += seaview
     SUBDIR += sim4
diff --git a/biology/py-biopython/Makefile b/biology/py-biopython/Makefile
new file mode 100644
index 000000000000..22c806cd1e81
--- /dev/null
+++ b/biology/py-biopython/Makefile
@@ -0,0 +1,27 @@
+# New ports collection makefile for:	py-biopython
+# Date created:		28 July 2000
+# Whom:	      		Johann Visagie <johann@egenetics.com>
+#
+# $FreeBSD$
+#
+
+PORTNAME=	biopython
+PORTVERSION=	0.90.d01
+CATEGORIES=	biology python
+MASTER_SITES=	http://www.biopython.org/Download/
+PKGNAMEPREFIX=	py-
+DISTNAME=	biopython-0.90-d01
+
+MAINTAINER=	johann@egenetics.com
+
+BUILD_DEPENDS=	python:${PORTSDIR}/lang/python \
+		${LOCALBASE}/lib/python1.5/site-packages/Numeric/Numeric.py:${PORTSDIR}/math/numpy \
+		${LOCALBASE}/lib/python1.5/site-packages/distutils/core.py:${PORTSDIR}/misc/py-distutils
+
+do-build:
+	@(cd ${WRKSRC}; ${SETENV} ${MAKE_ENV} python setup.py build)
+
+do-install:
+	@(cd ${WRKSRC}; ${SETENV} ${MAKE_ENV} python setup.py install)
+
+.include <bsd.port.mk>
diff --git a/biology/py-biopython/distinfo b/biology/py-biopython/distinfo
new file mode 100644
index 000000000000..e9642bb363e2
--- /dev/null
+++ b/biology/py-biopython/distinfo
@@ -0,0 +1 @@
+MD5 (biopython-0.90-d01.tar.gz) = 14ccfee8ca4f42ea963a2205b2c631c1
diff --git a/biology/py-biopython/pkg-comment b/biology/py-biopython/pkg-comment
new file mode 100644
index 000000000000..0310e64fb4a0
--- /dev/null
+++ b/biology/py-biopython/pkg-comment
@@ -0,0 +1 @@
+A collection of Python modules for bioinformatics
diff --git a/biology/py-biopython/pkg-descr b/biology/py-biopython/pkg-descr
new file mode 100644
index 000000000000..2216005d2351
--- /dev/null
+++ b/biology/py-biopython/pkg-descr
@@ -0,0 +1,12 @@
+The Biopython Project is an international association of developers of freely
+available Python tools for use in areas of computational molecular biology
+such as bioinformatics and genomics.
+
+Biopython is a collection of Python packages and modules created by the
+Biopython Project, intended to provide the basis for building bioinformatics
+applications in the Python language.  It is currently in developer's
+(pre-alpha) release.  Caveat emptor.
+
+WWW: http://www.biopython.org/
+
+-- Johann Visagie <johann@egenetics.com>
diff --git a/biology/py-biopython/pkg-plist b/biology/py-biopython/pkg-plist
new file mode 100644
index 000000000000..ecf8f2ae927d
--- /dev/null
+++ b/biology/py-biopython/pkg-plist
@@ -0,0 +1,124 @@
+lib/python1.5/site-packages/Bio/__init__.py
+lib/python1.5/site-packages/Bio/ParserSupport.py
+lib/python1.5/site-packages/Bio/Seq.py
+lib/python1.5/site-packages/Bio/Index.py
+lib/python1.5/site-packages/Bio/PropertyManager.py
+lib/python1.5/site-packages/Bio/File.py
+lib/python1.5/site-packages/Bio/Sequence.py
+lib/python1.5/site-packages/Bio/utils.py
+lib/python1.5/site-packages/Bio/SeqRecord.py
+lib/python1.5/site-packages/Bio/SwissProt/__init__.py
+lib/python1.5/site-packages/Bio/SwissProt/KeyWList.py
+lib/python1.5/site-packages/Bio/SwissProt/SProt.py
+lib/python1.5/site-packages/Bio/Blast/__init__.py
+lib/python1.5/site-packages/Bio/Blast/NCBIWWW.py
+lib/python1.5/site-packages/Bio/Blast/Record.py
+lib/python1.5/site-packages/Bio/Blast/NCBIStandalone.py
+lib/python1.5/site-packages/Bio/Enzyme/__init__.py
+lib/python1.5/site-packages/Bio/Enzyme/Enzyme.py
+lib/python1.5/site-packages/Bio/Fasta/__init__.py
+lib/python1.5/site-packages/Bio/Fasta/Fasta.py
+lib/python1.5/site-packages/Bio/PDB/__init__.py
+lib/python1.5/site-packages/Bio/Prosite/__init__.py
+lib/python1.5/site-packages/Bio/Prosite/Prosite.py
+lib/python1.5/site-packages/Bio/Prosite/Pattern.py
+lib/python1.5/site-packages/Bio/Prosite/Prodoc.py
+lib/python1.5/site-packages/Bio/Medline/Medline.py
+lib/python1.5/site-packages/Bio/Medline/PubMed.py
+lib/python1.5/site-packages/Bio/Medline/__init__.py
+lib/python1.5/site-packages/Bio/Data/IUPACData.py
+lib/python1.5/site-packages/Bio/Data/__init__.py
+lib/python1.5/site-packages/Bio/Data/CodonTable.py
+lib/python1.5/site-packages/Bio/Entrez/__init__.py
+lib/python1.5/site-packages/Bio/Tools/mathfns.py
+lib/python1.5/site-packages/Bio/Tools/__init__.py
+lib/python1.5/site-packages/Bio/Tools/Transcribe.py
+lib/python1.5/site-packages/Bio/Tools/listfns.py
+lib/python1.5/site-packages/Bio/Tools/stringfns.py
+lib/python1.5/site-packages/Bio/Tools/Translate.py
+lib/python1.5/site-packages/Bio/Tools/Classification/__init__.py
+lib/python1.5/site-packages/Bio/Tools/Classification/NaiveBayes.py
+lib/python1.5/site-packages/Bio/Tools/Classification/SVM.py
+lib/python1.5/site-packages/Bio/Tools/Classification/kNN.py
+lib/python1.5/site-packages/Bio/WWW/__init__.py
+lib/python1.5/site-packages/Bio/WWW/NCBI.py
+lib/python1.5/site-packages/Bio/WWW/ExPASy.py
+lib/python1.5/site-packages/Bio/WWW/SCOP.py
+lib/python1.5/site-packages/Bio/Alphabet/__init__.py
+lib/python1.5/site-packages/Bio/Alphabet/IUPAC.py
+lib/python1.5/site-packages/Bio/Encodings/IUPACEncoding.py
+lib/python1.5/site-packages/Bio/Encodings/__init__.py
+lib/python1.5/site-packages/Bio/SeqIO/__init__.py
+lib/python1.5/site-packages/Bio/SeqIO/FASTA.py
+lib/python1.5/site-packages/Bio/PDB/__init__.pyc
+lib/python1.5/site-packages/Bio/WWW/__init__.pyc
+lib/python1.5/site-packages/Bio/WWW/NCBI.pyc
+lib/python1.5/site-packages/Bio/WWW/ExPASy.pyc
+lib/python1.5/site-packages/Bio/WWW/SCOP.pyc
+lib/python1.5/site-packages/Bio/Data/IUPACData.pyc
+lib/python1.5/site-packages/Bio/Data/__init__.pyc
+lib/python1.5/site-packages/Bio/Data/CodonTable.pyc
+lib/python1.5/site-packages/Bio/Encodings/IUPACEncoding.pyc
+lib/python1.5/site-packages/Bio/Encodings/__init__.pyc
+lib/python1.5/site-packages/Bio/__init__.pyc
+lib/python1.5/site-packages/Bio/Blast/__init__.pyc
+lib/python1.5/site-packages/Bio/Blast/NCBIWWW.pyc
+lib/python1.5/site-packages/Bio/Blast/Record.pyc
+lib/python1.5/site-packages/Bio/Blast/NCBIStandalone.pyc
+lib/python1.5/site-packages/Bio/SeqIO/__init__.pyc
+lib/python1.5/site-packages/Bio/SeqIO/FASTA.pyc
+lib/python1.5/site-packages/Bio/ParserSupport.pyc
+lib/python1.5/site-packages/Bio/Medline/Medline.pyc
+lib/python1.5/site-packages/Bio/Medline/PubMed.pyc
+lib/python1.5/site-packages/Bio/Medline/__init__.pyc
+lib/python1.5/site-packages/Bio/Tools/mathfns.pyc
+lib/python1.5/site-packages/Bio/Tools/__init__.pyc
+lib/python1.5/site-packages/Bio/Tools/Transcribe.pyc
+lib/python1.5/site-packages/Bio/Tools/listfns.pyc
+lib/python1.5/site-packages/Bio/Tools/stringfns.pyc
+lib/python1.5/site-packages/Bio/Tools/Translate.pyc
+lib/python1.5/site-packages/Bio/Tools/Classification/__init__.pyc
+lib/python1.5/site-packages/Bio/Tools/Classification/NaiveBayes.pyc
+lib/python1.5/site-packages/Bio/Tools/Classification/SVM.pyc
+lib/python1.5/site-packages/Bio/Tools/Classification/kNN.pyc
+lib/python1.5/site-packages/Bio/Seq.pyc
+lib/python1.5/site-packages/Bio/Index.pyc
+lib/python1.5/site-packages/Bio/SwissProt/__init__.pyc
+lib/python1.5/site-packages/Bio/SwissProt/KeyWList.pyc
+lib/python1.5/site-packages/Bio/SwissProt/SProt.pyc
+lib/python1.5/site-packages/Bio/Fasta/__init__.pyc
+lib/python1.5/site-packages/Bio/Fasta/Fasta.pyc
+lib/python1.5/site-packages/Bio/Alphabet/__init__.pyc
+lib/python1.5/site-packages/Bio/Alphabet/IUPAC.pyc
+lib/python1.5/site-packages/Bio/PropertyManager.pyc
+lib/python1.5/site-packages/Bio/File.pyc
+lib/python1.5/site-packages/Bio/Sequence.pyc
+lib/python1.5/site-packages/Bio/utils.pyc
+lib/python1.5/site-packages/Bio/Entrez/__init__.pyc
+lib/python1.5/site-packages/Bio/Enzyme/__init__.pyc
+lib/python1.5/site-packages/Bio/Enzyme/Enzyme.pyc
+lib/python1.5/site-packages/Bio/SeqRecord.pyc
+lib/python1.5/site-packages/Bio/Prosite/__init__.pyc
+lib/python1.5/site-packages/Bio/Prosite/Prosite.pyc
+lib/python1.5/site-packages/Bio/Prosite/Pattern.pyc
+lib/python1.5/site-packages/Bio/Prosite/Prodoc.pyc
+lib/python1.5/site-packages/Bio/Tools/Classification/cSVM.so
+lib/python1.5/site-packages/Bio/Tools/clistfns.so
+lib/python1.5/site-packages/Bio/Tools/cmathfns.so
+lib/python1.5/site-packages/Bio/Tools/cstringfns.so
+@dirrm lib/python1.5/site-packages/Bio/WWW
+@dirrm lib/python1.5/site-packages/Bio/Tools/Classification
+@dirrm lib/python1.5/site-packages/Bio/Tools
+@dirrm lib/python1.5/site-packages/Bio/SwissProt
+@dirrm lib/python1.5/site-packages/Bio/SeqIO
+@dirrm lib/python1.5/site-packages/Bio/Prosite
+@dirrm lib/python1.5/site-packages/Bio/PDB
+@dirrm lib/python1.5/site-packages/Bio/Medline
+@dirrm lib/python1.5/site-packages/Bio/Fasta
+@dirrm lib/python1.5/site-packages/Bio/Enzyme
+@dirrm lib/python1.5/site-packages/Bio/Entrez
+@dirrm lib/python1.5/site-packages/Bio/Encodings
+@dirrm lib/python1.5/site-packages/Bio/Data
+@dirrm lib/python1.5/site-packages/Bio/Blast
+@dirrm lib/python1.5/site-packages/Bio/Alphabet
+@dirrm lib/python1.5/site-packages/Bio