PyCogent is a software library for genomic biology. It is a fully integrated

and thoroughly tested framework for: controlling third-party applications;
devising workflows; querying databases; conducting novel probabilistic
analyses of biological sequence evolution; and generating publication quality
graphics. It is distinguished by many unique built-in capabilities (such as
true codon alignment) and the frequent addition of entirely new methods for
the analysis of genomic data.

WWW:	http://pycogent.sourceforge.net/

PR:		ports/135863
Submitted by:	Wen Heping <wenheping at gmail.com>

5 files changed, 887 insertions, 0 deletions

diff --git a/biology/Makefile b/biology/Makefile
index 20a3d819973d..1f6c6de10713 100644
--- a/biology/Makefile
+++ b/biology/Makefile
@@ -75,6 +75,7 @@
     SUBDIR += protomol
     SUBDIR += psi88
     SUBDIR += py-biopython
+    SUBDIR += pycogent
     SUBDIR += pymol
     SUBDIR += rasmol
     SUBDIR += recombine
diff --git a/biology/pycogent/Makefile b/biology/pycogent/Makefile
new file mode 100644
index 000000000000..4b8348554b0d
--- /dev/null
+++ b/biology/pycogent/Makefile
@@ -0,0 +1,28 @@
+# New ports collection makefile for:	pycogent
+# Date created:		20 June, 2009
+# Whom:			Wen Heping <wenheping@gmail.com>
+#
+# $FreeBSD$
+#
+
+PORTNAME=	pycogent
+PORTVERSION=	1.3.1
+CATEGORIES=	biology python
+MASTER_SITES=	SF
+DISTNAME=	PyCogent-${PORTVERSION}
+EXTRACT_SUFX=	.tgz
+
+MAINTAINER=	wenheping@gmail.com
+COMMENT=	A toolkit for statistical analysis of biological sequences
+
+BUILD_DEPENDS=	${PYNUMPY} \
+		${LOCALBASE}/bin/cython:${PORTSDIR}/lang/cython \
+		${LOCALBASE}/bin/sphinx-build:${PORTSDIR}/textproc/py-sphinx \
+		${PYTHON_PKGNAMEPREFIX}sqlalchemy>=0.5:${PORTSDIR}/databases/py-sqlalchemy
+RUN_DEPENDS=	${BUILD_DEPENDS}
+
+USE_PYTHON=		yes
+USE_PYDISTUTILS=	yes
+PYDISTUTILS_PKGNAME=	cogent
+
+.include <bsd.port.mk>
diff --git a/biology/pycogent/distinfo b/biology/pycogent/distinfo
new file mode 100644
index 000000000000..09398220a025
--- /dev/null
+++ b/biology/pycogent/distinfo
@@ -0,0 +1,3 @@
+MD5 (PyCogent-1.3.1.tgz) = 4cc108a69e5ffd343508db4615514b74
+SHA256 (PyCogent-1.3.1.tgz) = 56636a2aeee464968056458f8384262f874cdac12b89a43c4c3e5d88582a7fc6
+SIZE (PyCogent-1.3.1.tgz) = 2062874
diff --git a/biology/pycogent/pkg-descr b/biology/pycogent/pkg-descr
new file mode 100644
index 000000000000..600342b93248
--- /dev/null
+++ b/biology/pycogent/pkg-descr
@@ -0,0 +1,9 @@
+PyCogent is a software library for genomic biology. It is a fully integrated
+and thoroughly tested framework for: controlling third-party applications;
+devising workflows; querying databases; conducting novel probabilistic
+analyses of biological sequence evolution; and generating publication quality
+graphics. It is distinguished by many unique built-in capabilities (such as
+true codon alignment) and the frequent addition of entirely new methods for
+the analysis of genomic data.
+
+WWW:	http://pycogent.sourceforge.net/
diff --git a/biology/pycogent/pkg-plist b/biology/pycogent/pkg-plist
new file mode 100644
index 000000000000..a1bc29f1f35d
--- /dev/null
+++ b/biology/pycogent/pkg-plist
@@ -0,0 +1,846 @@
+%%PYTHON_SITELIBDIR%%/cogent/__init__.py
+%%PYTHON_SITELIBDIR%%/cogent/__init__.pyc
+%%PYTHON_SITELIBDIR%%/cogent/__init__.pyo
+%%PYTHON_SITELIBDIR%%/cogent/align/__init__.py
+%%PYTHON_SITELIBDIR%%/cogent/align/__init__.pyc
+%%PYTHON_SITELIBDIR%%/cogent/align/__init__.pyo
+%%PYTHON_SITELIBDIR%%/cogent/align/_compare.so
+%%PYTHON_SITELIBDIR%%/cogent/align/_pairwise_pogs.so
+%%PYTHON_SITELIBDIR%%/cogent/align/_pairwise_seqs.so
+%%PYTHON_SITELIBDIR%%/cogent/align/algorithm.py
+%%PYTHON_SITELIBDIR%%/cogent/align/algorithm.pyc
+%%PYTHON_SITELIBDIR%%/cogent/align/algorithm.pyo
+%%PYTHON_SITELIBDIR%%/cogent/align/align.py
+%%PYTHON_SITELIBDIR%%/cogent/align/align.pyc
+%%PYTHON_SITELIBDIR%%/cogent/align/align.pyo
+%%PYTHON_SITELIBDIR%%/cogent/align/dp_calculation.py
+%%PYTHON_SITELIBDIR%%/cogent/align/dp_calculation.pyc
+%%PYTHON_SITELIBDIR%%/cogent/align/dp_calculation.pyo
+%%PYTHON_SITELIBDIR%%/cogent/align/indel_model.py
+%%PYTHON_SITELIBDIR%%/cogent/align/indel_model.pyc
+%%PYTHON_SITELIBDIR%%/cogent/align/indel_model.pyo
+%%PYTHON_SITELIBDIR%%/cogent/align/indel_positions.py
+%%PYTHON_SITELIBDIR%%/cogent/align/indel_positions.pyc
+%%PYTHON_SITELIBDIR%%/cogent/align/indel_positions.pyo
+%%PYTHON_SITELIBDIR%%/cogent/align/pairwise.py
+%%PYTHON_SITELIBDIR%%/cogent/align/pairwise.pyc
+%%PYTHON_SITELIBDIR%%/cogent/align/pairwise.pyo
+%%PYTHON_SITELIBDIR%%/cogent/align/partial_order_graph.py
+%%PYTHON_SITELIBDIR%%/cogent/align/partial_order_graph.pyc
+%%PYTHON_SITELIBDIR%%/cogent/align/partial_order_graph.pyo
+%%PYTHON_SITELIBDIR%%/cogent/align/progressive.py
+%%PYTHON_SITELIBDIR%%/cogent/align/progressive.pyc
+%%PYTHON_SITELIBDIR%%/cogent/align/progressive.pyo
+%%PYTHON_SITELIBDIR%%/cogent/align/pycompare.py
+%%PYTHON_SITELIBDIR%%/cogent/align/pycompare.pyc
+%%PYTHON_SITELIBDIR%%/cogent/align/pycompare.pyo
+%%PYTHON_SITELIBDIR%%/cogent/align/traceback.py
+%%PYTHON_SITELIBDIR%%/cogent/align/traceback.pyc
+%%PYTHON_SITELIBDIR%%/cogent/align/traceback.pyo
+%%PYTHON_SITELIBDIR%%/cogent/align/weights/__init__.py
+%%PYTHON_SITELIBDIR%%/cogent/align/weights/__init__.pyc
+%%PYTHON_SITELIBDIR%%/cogent/align/weights/__init__.pyo
+%%PYTHON_SITELIBDIR%%/cogent/align/weights/methods.py
+%%PYTHON_SITELIBDIR%%/cogent/align/weights/methods.pyc
+%%PYTHON_SITELIBDIR%%/cogent/align/weights/methods.pyo
+%%PYTHON_SITELIBDIR%%/cogent/align/weights/util.py
+%%PYTHON_SITELIBDIR%%/cogent/align/weights/util.pyc
+%%PYTHON_SITELIBDIR%%/cogent/align/weights/util.pyo
+%%PYTHON_SITELIBDIR%%/cogent/app/__init__.py
+%%PYTHON_SITELIBDIR%%/cogent/app/__init__.pyc
+%%PYTHON_SITELIBDIR%%/cogent/app/__init__.pyo
+%%PYTHON_SITELIBDIR%%/cogent/app/blast.py
+%%PYTHON_SITELIBDIR%%/cogent/app/blast.pyc
+%%PYTHON_SITELIBDIR%%/cogent/app/blast.pyo
+%%PYTHON_SITELIBDIR%%/cogent/app/carnac.py
+%%PYTHON_SITELIBDIR%%/cogent/app/carnac.pyc
+%%PYTHON_SITELIBDIR%%/cogent/app/carnac.pyo
+%%PYTHON_SITELIBDIR%%/cogent/app/cd_hit.py
+%%PYTHON_SITELIBDIR%%/cogent/app/cd_hit.pyc
+%%PYTHON_SITELIBDIR%%/cogent/app/cd_hit.pyo
+%%PYTHON_SITELIBDIR%%/cogent/app/clearcut.py
+%%PYTHON_SITELIBDIR%%/cogent/app/clearcut.pyc
+%%PYTHON_SITELIBDIR%%/cogent/app/clearcut.pyo
+%%PYTHON_SITELIBDIR%%/cogent/app/clustalw.py
+%%PYTHON_SITELIBDIR%%/cogent/app/clustalw.pyc
+%%PYTHON_SITELIBDIR%%/cogent/app/clustalw.pyo
+%%PYTHON_SITELIBDIR%%/cogent/app/cmfinder.py
+%%PYTHON_SITELIBDIR%%/cogent/app/cmfinder.pyc
+%%PYTHON_SITELIBDIR%%/cogent/app/cmfinder.pyo
+%%PYTHON_SITELIBDIR%%/cogent/app/comrna.py
+%%PYTHON_SITELIBDIR%%/cogent/app/comrna.pyc
+%%PYTHON_SITELIBDIR%%/cogent/app/comrna.pyo
+%%PYTHON_SITELIBDIR%%/cogent/app/consan.py
+%%PYTHON_SITELIBDIR%%/cogent/app/consan.pyc
+%%PYTHON_SITELIBDIR%%/cogent/app/consan.pyo
+%%PYTHON_SITELIBDIR%%/cogent/app/contrafold.py
+%%PYTHON_SITELIBDIR%%/cogent/app/contrafold.pyc
+%%PYTHON_SITELIBDIR%%/cogent/app/contrafold.pyo
+%%PYTHON_SITELIBDIR%%/cogent/app/cove.py
+%%PYTHON_SITELIBDIR%%/cogent/app/cove.pyc
+%%PYTHON_SITELIBDIR%%/cogent/app/cove.pyo
+%%PYTHON_SITELIBDIR%%/cogent/app/dialign.py
+%%PYTHON_SITELIBDIR%%/cogent/app/dialign.pyc
+%%PYTHON_SITELIBDIR%%/cogent/app/dialign.pyo
+%%PYTHON_SITELIBDIR%%/cogent/app/dotur.py
+%%PYTHON_SITELIBDIR%%/cogent/app/dotur.pyc
+%%PYTHON_SITELIBDIR%%/cogent/app/dotur.pyo
+%%PYTHON_SITELIBDIR%%/cogent/app/dynalign.py
+%%PYTHON_SITELIBDIR%%/cogent/app/dynalign.pyc
+%%PYTHON_SITELIBDIR%%/cogent/app/dynalign.pyo
+%%PYTHON_SITELIBDIR%%/cogent/app/fasttree.py
+%%PYTHON_SITELIBDIR%%/cogent/app/fasttree.pyc
+%%PYTHON_SITELIBDIR%%/cogent/app/fasttree.pyo
+%%PYTHON_SITELIBDIR%%/cogent/app/fasttree_v1.py
+%%PYTHON_SITELIBDIR%%/cogent/app/fasttree_v1.pyc
+%%PYTHON_SITELIBDIR%%/cogent/app/fasttree_v1.pyo
+%%PYTHON_SITELIBDIR%%/cogent/app/foldalign.py
+%%PYTHON_SITELIBDIR%%/cogent/app/foldalign.pyc
+%%PYTHON_SITELIBDIR%%/cogent/app/foldalign.pyo
+%%PYTHON_SITELIBDIR%%/cogent/app/gctmpca.py
+%%PYTHON_SITELIBDIR%%/cogent/app/gctmpca.pyc
+%%PYTHON_SITELIBDIR%%/cogent/app/gctmpca.pyo
+%%PYTHON_SITELIBDIR%%/cogent/app/ilm.py
+%%PYTHON_SITELIBDIR%%/cogent/app/ilm.pyc
+%%PYTHON_SITELIBDIR%%/cogent/app/ilm.pyo
+%%PYTHON_SITELIBDIR%%/cogent/app/infernal.py
+%%PYTHON_SITELIBDIR%%/cogent/app/infernal.pyc
+%%PYTHON_SITELIBDIR%%/cogent/app/infernal.pyo
+%%PYTHON_SITELIBDIR%%/cogent/app/knetfold.py
+%%PYTHON_SITELIBDIR%%/cogent/app/knetfold.pyc
+%%PYTHON_SITELIBDIR%%/cogent/app/knetfold.pyo
+%%PYTHON_SITELIBDIR%%/cogent/app/lagan.py
+%%PYTHON_SITELIBDIR%%/cogent/app/lagan.pyc
+%%PYTHON_SITELIBDIR%%/cogent/app/lagan.pyo
+%%PYTHON_SITELIBDIR%%/cogent/app/mafft.py
+%%PYTHON_SITELIBDIR%%/cogent/app/mafft.pyc
+%%PYTHON_SITELIBDIR%%/cogent/app/mafft.pyo
+%%PYTHON_SITELIBDIR%%/cogent/app/mfold.py
+%%PYTHON_SITELIBDIR%%/cogent/app/mfold.pyc
+%%PYTHON_SITELIBDIR%%/cogent/app/mfold.pyo
+%%PYTHON_SITELIBDIR%%/cogent/app/muscle.py
+%%PYTHON_SITELIBDIR%%/cogent/app/muscle.pyc
+%%PYTHON_SITELIBDIR%%/cogent/app/muscle.pyo
+%%PYTHON_SITELIBDIR%%/cogent/app/nupack.py
+%%PYTHON_SITELIBDIR%%/cogent/app/nupack.pyc
+%%PYTHON_SITELIBDIR%%/cogent/app/nupack.pyo
+%%PYTHON_SITELIBDIR%%/cogent/app/parameters.py
+%%PYTHON_SITELIBDIR%%/cogent/app/parameters.pyc
+%%PYTHON_SITELIBDIR%%/cogent/app/parameters.pyo
+%%PYTHON_SITELIBDIR%%/cogent/app/pfold.py
+%%PYTHON_SITELIBDIR%%/cogent/app/pfold.pyc
+%%PYTHON_SITELIBDIR%%/cogent/app/pfold.pyo
+%%PYTHON_SITELIBDIR%%/cogent/app/pknotsrg.py
+%%PYTHON_SITELIBDIR%%/cogent/app/pknotsrg.pyc
+%%PYTHON_SITELIBDIR%%/cogent/app/pknotsrg.pyo
+%%PYTHON_SITELIBDIR%%/cogent/app/raxml.py
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+%%PYTHON_SITELIBDIR%%/cogent/app/raxml.pyo
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+%%PYTHON_SITELIBDIR%%/cogent/app/util.pyc
+%%PYTHON_SITELIBDIR%%/cogent/app/util.pyo
+%%PYTHON_SITELIBDIR%%/cogent/app/vienna_package.py
+%%PYTHON_SITELIBDIR%%/cogent/app/vienna_package.pyc
+%%PYTHON_SITELIBDIR%%/cogent/app/vienna_package.pyo
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+%%PYTHON_SITELIBDIR%%/cogent/cluster/UPGMA.pyc
+%%PYTHON_SITELIBDIR%%/cogent/cluster/UPGMA.pyo
+%%PYTHON_SITELIBDIR%%/cogent/cluster/__init__.py
+%%PYTHON_SITELIBDIR%%/cogent/cluster/__init__.pyc
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+%%PYTHON_SITELIBDIR%%/cogent/db/ensembl/genome.pyc
+%%PYTHON_SITELIBDIR%%/cogent/db/ensembl/genome.pyo
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+%%PYTHON_SITELIBDIR%%/cogent/db/ensembl/host.pyo
+%%PYTHON_SITELIBDIR%%/cogent/db/ensembl/name.py
+%%PYTHON_SITELIBDIR%%/cogent/db/ensembl/name.pyc
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