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Bioinfomatics File access tools

Project description

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
fastqFile, fastaFile:
fasta/fastq file IO. based on lh3 readfq.
cachedFasta
fetch region sequence from large fasta file. This module is based on faidx through pysam pysam.FastaFile. from v0.1.2: old name fastaReader is deprecated as misleading with fastaFile reader
faidx
experimental, interface to pyfaidx.

Dependency

Change Log

v0.4
add logger class
v0.3
change fasta/fastq Writter methods
v0.2
add fastqFile, rename fastaReader to cachedFasta
v0.1.1
add fastaReader
v0.1.0
inital release, support xzFile, tsvFile, vcfFile, samFile and faidx

Authors

Yu XU <xuyu@genomics.cn>

Lisense

This module is under GPLv2 Lisense

Project details


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