Skip to main content

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.
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
experimental, interface to pyfaidx.


Change Log

add logger class
change fasta/fastq Writter methods
add fastqFile, rename fastaReader to cachedFasta
add fastaReader
inital release, support xzFile, tsvFile, vcfFile, samFile and faidx


Yu XU <>


This module is under GPLv2 Lisense

Project details

Download files

Download the file for your platform. If you're not sure which to choose, learn more about installing packages.

Source Distribution

BioUtil-0.4.0.tar.gz (11.6 kB view hashes)

Uploaded source

Built Distribution

BioUtil-0.4.0-py3.6.egg (31.7 kB view hashes)

Uploaded 3 6

Supported by

AWS AWS Cloud computing Datadog Datadog Monitoring Facebook / Instagram Facebook / Instagram PSF Sponsor Fastly Fastly CDN Google Google Object Storage and Download Analytics Huawei Huawei PSF Sponsor Microsoft Microsoft PSF Sponsor NVIDIA NVIDIA PSF Sponsor Pingdom Pingdom Monitoring Salesforce Salesforce PSF Sponsor Sentry Sentry Error logging StatusPage StatusPage Status page