{ "info": { "author": "Yu XU", "author_email": "xuyu@genomics.cn", "bugtrack_url": null, "classifiers": [ "Development Status :: 4 - Beta", "Intended Audience :: Developers", "Intended Audience :: Science/Research", "License :: OSI Approved :: GNU General Public License v2 or later (GPLv2+)", "Programming Language :: Python :: 3", "Programming Language :: Python :: 3.4", "Programming Language :: Python :: 3.5", "Programming Language :: Python :: 3.6", "Programming Language :: Python :: 3.7", "Topic :: Scientific/Engineering :: Bio-Informatics" ], "description": "BioUtil\n========\n\nThis is a collection of scripts and modules for bioinfomatics file access\n\nModules, Classes, and Functions\n---------------------------------\n\nxzFile, xzopen()\n access to various compressed files, currently recoganize gzip (.gz), \n bz2(.bz2), and bgzip(.bgz, .b.gz) from samtools package\n\ntsvFile, tsvRecord, tsv\n tab seperated file with named fields, user could also defined some preprocess\n functions for field reading and writing\n\nvcfFile, vcf\n vcf file access, depends on PyVCF_,\n yet provide a convinient and flexable interface\n\nsamFile, sam\n sam file access, based on pysam_. \n pysam_ also provides interface for tabix (random access tsv file with genome positions),\n which could be access from BioUtil.sam\n\nfastqFile, fastaFile:\n fasta/fastq file IO. based on lh3 readfq_.\n\ncachedFasta\n fetch region sequence from large fasta file. 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