Bioinfomatics File access tools
Project description
BioUtil
========
This is a collection of scripts and modules for bioinfomatics file access
Modules, Classes, and Functions
-------
xzFile, xzopen()
access to various compressed files, currently recoganize gzip (.gz),
bz2(.bz2), and bgzip(.bgz, .b.gz) from samtools package
tsvFile, tsvRecord, tsv
tab seperated file with named fields, user could also defined some preprocess
functions for field reading and writing
vcfFile, vcf
vcf file access, depends on PyVCF_,
yet provide a convinient and flexable interface
samFile, sam
sam file access, based on pysam_.
pysam_ also provides interface for tabix (random access tsv file with genome positions),
which could be access from BioUtil.sam
fastaReader
fetch region sequence from large fasta file. This module is based on faidx
through pysam_ pysam.FastaFile.
faidx
experimental, interface to pyfaidx_.
Dependency
------
- Python >= 3.4
- pysam_ >= 0.8.2
- PyVCF_ >= 0.6.7
- pyfaidx_ >= 0.4.7
Change Log
-------
v0.1.1
add fastaReader
v0.1.0
inital release, support xzFile, tsvFile, vcfFile, samFile and faidx
Authors
--------
Yu XU
Lisense
--------
This module is under GPLv2 Lisense
.. _pysam: https://github.com/pysam-developers/pysam
.. _PyVCF: https://github.com/jamescasbon/PyVCF
.. _pyfaidx: https://github.com/mdshw5/pyfaidx
========
This is a collection of scripts and modules for bioinfomatics file access
Modules, Classes, and Functions
-------
xzFile, xzopen()
access to various compressed files, currently recoganize gzip (.gz),
bz2(.bz2), and bgzip(.bgz, .b.gz) from samtools package
tsvFile, tsvRecord, tsv
tab seperated file with named fields, user could also defined some preprocess
functions for field reading and writing
vcfFile, vcf
vcf file access, depends on PyVCF_,
yet provide a convinient and flexable interface
samFile, sam
sam file access, based on pysam_.
pysam_ also provides interface for tabix (random access tsv file with genome positions),
which could be access from BioUtil.sam
fastaReader
fetch region sequence from large fasta file. This module is based on faidx
through pysam_ pysam.FastaFile.
faidx
experimental, interface to pyfaidx_.
Dependency
------
- Python >= 3.4
- pysam_ >= 0.8.2
- PyVCF_ >= 0.6.7
- pyfaidx_ >= 0.4.7
Change Log
-------
v0.1.1
add fastaReader
v0.1.0
inital release, support xzFile, tsvFile, vcfFile, samFile and faidx
Authors
--------
Yu XU
Lisense
--------
This module is under GPLv2 Lisense
.. _pysam: https://github.com/pysam-developers/pysam
.. _PyVCF: https://github.com/jamescasbon/PyVCF
.. _pyfaidx: https://github.com/mdshw5/pyfaidx
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