Date: Fri, 19 Oct 2018 02:05:37 +0000 (UTC) From: Yuri Victorovich <yuri@FreeBSD.org> To: ports-committers@freebsd.org, svn-ports-all@freebsd.org, svn-ports-head@freebsd.org Subject: svn commit: r482399 - in head/biology: . py-pyfaidx Message-ID: <201810190205.w9J25bbJ077839@repo.freebsd.org>
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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@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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