bx-python is a python library and associated set of scripts to allow for rapid

implementation of genome scale analyses. The library contains a variety of
useful modules, but the particular strengths are:

Classes for reading and working with genome-scale multiple local alignments
(in MAF, AXT, and LAV formats). Generic data structure for indexing on disk
files that contain blocks of data associated with intervals on various
sequences (used, for example, to provide random access to individual
alignments in huge files; optomized for use over network filesystems).
Data structures for working with intervals on sequences:
 * "Binned bitsets" which act just like chromosome sized bit arrays,
   but lazily allocate regions and allow large blocks of all set or
   all unset bits to be stored compactly
 * "Intersecter" for performing fast intersection tests that preserve
   both query and target intervals and associated annotation

WWW: https://github.com/bxlab/bx-python

PR:		218757
Submitted by:	Yuri Victorovich <yuri@rawbw.com>

4 files changed, 47 insertions, 0 deletions

diff --git a/biology/Makefile b/biology/Makefile
index 85155f710443..6732768052c0 100644
--- a/biology/Makefile
+++ b/biology/Makefile
@@ -83,6 +83,7 @@
     SUBDIR += psi88
     SUBDIR += py-biom-format
     SUBDIR += py-biopython
+    SUBDIR += py-bx-python
     SUBDIR += py-pysam
     SUBDIR += pycogent
     SUBDIR += pyfasta
diff --git a/biology/py-bx-python/Makefile b/biology/py-bx-python/Makefile
new file mode 100644
index 000000000000..89ccb9749a3e
--- /dev/null
+++ b/biology/py-bx-python/Makefile
@@ -0,0 +1,26 @@
+# Created by: Yuri Victorovich <yuri@rawbw.com>
+# $FreeBSD$
+
+PORTNAME=	bx-python
+PORTVERSION=	0.7.4
+DISTVERSIONPREFIX=	v
+CATEGORIES=	biology python
+PKGNAMEPREFIX=	${PYTHON_PKGNAMEPREFIX}
+
+MAINTAINER=	yuri@rawbw.com
+COMMENT=	Python module for reading, manipulating and writing genomic data sets
+
+LICENSE=	MIT
+LICENSE_FILE=	${WRKSRC}/LICENSE
+
+BUILD_DEPENDS=	${PYNUMPY} \
+		${PYTHON_PKGNAMEPREFIX}python-lzo>0:archivers/py-python-lzo
+RUN_DEPENDS:=	${BUILD_DEPENDS}
+
+USE_GITHUB=	yes
+GH_ACCOUNT=	bxlab
+
+USES=		compiler python
+USE_PYTHON=	autoplist distutils
+
+.include <bsd.port.mk>
diff --git a/biology/py-bx-python/distinfo b/biology/py-bx-python/distinfo
new file mode 100644
index 000000000000..65e3ff91b1fd
--- /dev/null
+++ b/biology/py-bx-python/distinfo
@@ -0,0 +1,3 @@
+TIMESTAMP = 1492586227
+SHA256 (bxlab-bx-python-v0.7.4_GH0.tar.gz) = 1066d1e56d062d0661f23c19942eb757bd7ab7cb8bc7d89a72fdc3931c995cb4
+SIZE (bxlab-bx-python-v0.7.4_GH0.tar.gz) = 2277893
diff --git a/biology/py-bx-python/pkg-descr b/biology/py-bx-python/pkg-descr
new file mode 100644
index 000000000000..b5bab083ebcc
--- /dev/null
+++ b/biology/py-bx-python/pkg-descr
@@ -0,0 +1,17 @@
+bx-python is a python library and associated set of scripts to allow for rapid
+implementation of genome scale analyses. The library contains a variety of
+useful modules, but the particular strengths are:
+
+Classes for reading and working with genome-scale multiple local alignments
+(in MAF, AXT, and LAV formats). Generic data structure for indexing on disk
+files that contain blocks of data associated with intervals on various
+sequences (used, for example, to provide random access to individual
+alignments in huge files; optomized for use over network filesystems).
+Data structures for working with intervals on sequences:
+ * "Binned bitsets" which act just like chromosome sized bit arrays,
+   but lazily allocate regions and allow large blocks of all set or
+   all unset bits to be stored compactly
+ * "Intersecter" for performing fast intersection tests that preserve
+   both query and target intervals and associated annotation
+
+WWW: https://github.com/bxlab/bx-python