This is a collection of scripts and modules for bioinfomatics file access

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.

• Python >= 3.4
• pysam >= 0.8.2
• PyVCF >= 0.6.7
• pyfaidx >= 0.4.7

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

Yu XU <[email protected]>

This module is under GPLv2 Lisense