svn commit: r482399 - in head/biology: . py-pyfaidx
Yuri Victorovich
yuri at FreeBSD.org
Fri Oct 19 02:05:39 UTC 2018
Author: yuri
Date: Fri Oct 19 02:05:37 2018
New Revision: 482399
URL: https://svnweb.freebsd.org/changeset/ports/482399
Log:
New port: biology/py-pyfaidx: Efficient pythonic random access to fasta subsequences
Added:
head/biology/py-pyfaidx/
head/biology/py-pyfaidx/Makefile (contents, props changed)
head/biology/py-pyfaidx/distinfo (contents, props changed)
head/biology/py-pyfaidx/pkg-descr (contents, props changed)
Modified:
head/biology/Makefile
Modified: head/biology/Makefile
==============================================================================
--- head/biology/Makefile Fri Oct 19 02:03:40 2018 (r482398)
+++ head/biology/Makefile Fri Oct 19 02:05:37 2018 (r482399)
@@ -109,6 +109,7 @@
SUBDIR += py-macs2
SUBDIR += py-orange3-bioinformatics
SUBDIR += py-orange3-single-cell
+ SUBDIR += py-pyfaidx
SUBDIR += py-pysam
SUBDIR += pycogent
SUBDIR += pyfasta
Added: head/biology/py-pyfaidx/Makefile
==============================================================================
--- /dev/null 00:00:00 1970 (empty, because file is newly added)
+++ head/biology/py-pyfaidx/Makefile Fri Oct 19 02:05:37 2018 (r482399)
@@ -0,0 +1,21 @@
+# $FreeBSD$
+
+PORTNAME= pyfaidx
+DISTVERSION= 0.5.5.1
+CATEGORIES= biology python
+MASTER_SITES= CHEESESHOP
+PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX}
+
+MAINTAINER= yuri at FreeBSD.org
+COMMENT= Efficient pythonic random access to fasta subsequences
+
+LICENSE= BSD3CLAUSE
+
+RUN_DEPENDS= ${PYTHON_PKGNAMEPREFIX}six>0:devel/py-six@${PY_FLAVOR}
+
+USES= python
+USE_PYTHON= distutils concurrent autoplist
+
+NO_ARCH= yes
+
+.include <bsd.port.mk>
Added: head/biology/py-pyfaidx/distinfo
==============================================================================
--- /dev/null 00:00:00 1970 (empty, because file is newly added)
+++ head/biology/py-pyfaidx/distinfo Fri Oct 19 02:05:37 2018 (r482399)
@@ -0,0 +1,3 @@
+TIMESTAMP = 1539913803
+SHA256 (pyfaidx-0.5.5.1.tar.gz) = d216924c901f39d445e13e574583442cd09f67424e13c2d33a5aacdfd367d39d
+SIZE (pyfaidx-0.5.5.1.tar.gz) = 30205
Added: head/biology/py-pyfaidx/pkg-descr
==============================================================================
--- /dev/null 00:00:00 1970 (empty, because file is newly added)
+++ head/biology/py-pyfaidx/pkg-descr Fri Oct 19 02:05:37 2018 (r482399)
@@ -0,0 +1,13 @@
+FASTA is a format to exchange generic information, partial or of the entire
+organism.
+
+A function "faidx" (FAsta InDeX) creates a small flat index file ".fai" allowing
+for fast random access to any subsequence in the indexed FASTA file, while
+loading a minimal amount of the file in to memory. This python module implements
+pure Python classes for indexing, retrieval, and in-place modification of FASTA
+files using a samtools compatible index. The pyfaidx module is API compatible
+with the pygr seqdb module. A command-line script "faidx" is installed alongside
+the pyfaidx module, and facilitates complex manipulation of FASTA files without
+any programming knowledge.
+
+WWW: https://github.com/mdshw5/pyfaidx
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