Metadata-Version: 1.1
Name: BioUtil
Version: 0.4.0
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_,
            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
        ------------
        
        - Python >= 3.4
        - pysam_ >= 0.8.2
        - PyVCF_ >= 0.6.7
        - pyfaidx_ >= 0.4.7
        
        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 
        
            
        .. _pysam: https://github.com/pysam-developers/pysam
        .. _PyVCF: https://github.com/jamescasbon/PyVCF
        .. _pyfaidx: https://github.com/mdshw5/pyfaidx
        .. _readfq: https://github.com/lh3/readfq
        
        
Keywords: bioinfomatics sequencing fileIO
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
Classifier: Programming Language :: Python :: 3.6
Classifier: Programming Language :: Python :: 3.7
