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Port details
py-bx-python Python module for reading, manipulating and writing genomic data sets
0.7.4 biology on this many watch lists=0 search for ports that depend on this port Find issues related to this port Report an issue related to this port
Maintainer: yuri@rawbw.com search for ports maintained by this maintainer
Port Added: 06 May 2017 06:28:34
Also Listed In: python
License: MIT
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
SVNWeb : Homepage : PortsMon
    Pseudo-pkg-plist information, but much better, from make generate-plist
    Expand this list (3 items)
  1. /usr/local/share/licenses/py27-bx-python-0.7.4/catalog.mk
  2. /usr/local/share/licenses/py27-bx-python-0.7.4/LICENSE
  3. /usr/local/share/licenses/py27-bx-python-0.7.4/MIT
  4. Collapse this list.

To install the port: cd /usr/ports/biology/py-bx-python/ && make install clean
To add the package: pkg install py27-bx-python

PKGNAME: py27-bx-python

distinfo:

TIMESTAMP = 1492586227
SHA256 (bxlab-bx-python-v0.7.4_GH0.tar.gz) = 1066d1e56d062d0661f23c19942eb757bd7ab7cb8bc7d89a72fdc3931c995cb4
SIZE (bxlab-bx-python-v0.7.4_GH0.tar.gz) = 2277893


NOTE: FreshPorts displays only information on required and default dependencies. Optional dependencies are not covered.

Build dependencies:
  1. numeric.py : math/py-numpy
  2. py27-python-lzo>0 : archivers/py-python-lzo
  3. py27-setuptools>0 : devel/py27-setuptools
  4. python2.7 : lang/python27
Runtime dependencies:
  1. numeric.py : math/py-numpy
  2. py27-python-lzo>0 : archivers/py-python-lzo
  3. py27-setuptools>0 : devel/py27-setuptools
  4. python2.7 : lang/python27
There are no ports dependent upon this port

Configuration Options
     No options to configure

USES:
compiler python

Master Sites:
  1. https://codeload.github.com/bxlab/bx-python/tar.gz/v0.7.4?dummy=/

Number of commits found: 1

Commit History - (may be incomplete: see SVNWeb link above for full details)
DateByDescription
06 May 2017 06:07:04
Original commit files touched by this commit  0.7.4
Revision:440232
miwi search for other commits by this committer
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>

Number of commits found: 1

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