Metadata-Version: 1.1
Name: BioUtil
Version: 0.1.0
Summary: Bioinfomatics File access tools
Home-page: https://github.com/sein-tao/pyBioUtil
Author: Yu XU
Author-email: xuyu@genomics.cn
License: GPLv2
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 <https://github.com/jamescasbon/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
        
            .. _pysam: https://github.com/pysam-developers/pysam
        
        faidx
            interface to `pyfaidx <https://github.com/mdshw5/pyfaidx>`_
        
        Dependency
        ------
        
        - Python >= 3.4
        - pysam >= 0.8.2
        - PyVCF >= 0.6.7
        - pyfaidx >= 0.4.7
        
        Change Log
        -------
        
        v0.1.0
            inital release, support xzFile, tsvFile, vcfFile, samFile and faidx
        
        
        Authors
        --------
        Yu XU
        
        Lisense
        --------
        This module is under GPLv2 Lisense 
        
        
            
        
        
Keywords: bioinfomatics fasta vcf bam
Platform: UNKNOWN
Classifier: Development Status :: 4 - Beta
Classifier: Intended Audience :: Developers
Classifier: Intended Audience :: Science/Research
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Classifier: License :: OSI Approved :: GNU General Public License v2 or later (GPLv2+)
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3.4
Classifier: Programming Language :: Python :: 3.5
