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| author | yuri <yuri@FreeBSD.org> | 2018-10-19 10:05:37 +0800 |
|---|---|---|
| committer | yuri <yuri@FreeBSD.org> | 2018-10-19 10:05:37 +0800 |
| commit | 62395aa53dbe3aa5903dc1f3c70b5223b2ab2d3f (patch) | |
| tree | d5897f498a81440f8a618133371e3255e3e893b0 /biology | |
| parent | cb34c34a0a6aac0615e73f361eea6084884272ca (diff) | |
| download | freebsd-ports-gnome-62395aa53dbe3aa5903dc1f3c70b5223b2ab2d3f.tar.gz freebsd-ports-gnome-62395aa53dbe3aa5903dc1f3c70b5223b2ab2d3f.tar.zst freebsd-ports-gnome-62395aa53dbe3aa5903dc1f3c70b5223b2ab2d3f.zip | |
New port: biology/py-pyfaidx: Efficient pythonic random access to fasta subsequences
Diffstat (limited to 'biology')
| -rw-r--r-- | biology/Makefile | 1 | ||||
| -rw-r--r-- | biology/py-pyfaidx/Makefile | 21 | ||||
| -rw-r--r-- | biology/py-pyfaidx/distinfo | 3 | ||||
| -rw-r--r-- | biology/py-pyfaidx/pkg-descr | 13 |
4 files changed, 38 insertions, 0 deletions
diff --git a/biology/Makefile b/biology/Makefile index 57778a520b56..520042420826 100644 --- a/biology/Makefile +++ b/biology/Makefile @@ -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 diff --git a/biology/py-pyfaidx/Makefile b/biology/py-pyfaidx/Makefile new file mode 100644 index 000000000000..7f97f9c4fc3d --- /dev/null +++ b/biology/py-pyfaidx/Makefile @@ -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> diff --git a/biology/py-pyfaidx/distinfo b/biology/py-pyfaidx/distinfo new file mode 100644 index 000000000000..9229e09ed11f --- /dev/null +++ b/biology/py-pyfaidx/distinfo @@ -0,0 +1,3 @@ +TIMESTAMP = 1539913803 +SHA256 (pyfaidx-0.5.5.1.tar.gz) = d216924c901f39d445e13e574583442cd09f67424e13c2d33a5aacdfd367d39d +SIZE (pyfaidx-0.5.5.1.tar.gz) = 30205 diff --git a/biology/py-pyfaidx/pkg-descr b/biology/py-pyfaidx/pkg-descr new file mode 100644 index 000000000000..7bbfc03d6bf1 --- /dev/null +++ b/biology/py-pyfaidx/pkg-descr @@ -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 |