{ "info": { "author": "Xiaoqi Zheng", "author_email": "zheng.shnu@gmail.com", "bugtrack_url": null, "classifiers": [ "Development Status :: 4 - Beta", "Environment :: Console", "Intended Audience :: Science/Research", "License :: OSI Approved :: Python Software Foundation License", "Operating System :: MacOS :: MacOS X", "Operating System :: POSIX", "Operating System :: POSIX :: Linux", "Operating System :: Unix", "Programming Language :: Python :: 2.6", "Programming Language :: Python :: 2.7" ], "description": "MethylPurify_v2\n------------------\n\nThis script is used for predicting subclone purity.\n\n\nGet Dependent data\n````````````````````\nGet the version of genome fasta that you mapped your fastqs, \nwe support hg18 and hg19 genome fasta now, take hg19 as an example\n\n.. code:: python\n \n ## use built-in script\n cd methylpurify/db\n bash genome.sh hg19\n\n\nGet Dependent software\n````````````````````````\n* `samtools `_, version 0.2.0\n* `numpy `_, version 1.8.2\n* `pyfasta`, version 0.5.2\n\nEasy to start \n`````````````````````\nInput: BAM file, this should be mapped with BSMap with -R option\n* `BSMap `_\n\nCurrently, we only support hg19 and hg18 genome index mapped BAM file.\n\nIf your fastq mapping is done with hg19 index, use following command:\n\n.. code:: python\n\n MethylPurify -f input.bam -b 300 -c 10 -s 50 -i methylpurify/db/CGI_hg19_slop1000.bed -g /path/to/hg19.fa --cnv\n\n\nThe results would be placed into *input* folder: alpha1.pred, MethylProfile.bed\n\n\nOptions\n````````````````\n* -f: input BAM file\n* -c: coverage level\n* -b: genome bin size\n* -s: sampling times\n* -g: species genome fasta file\n* -i: CG island specified, can use methylpurify/db/CGI_hg19_slop1000.bed for hg19, methylpurify/db/CGI_hg18_slop1000.bed for hg18\n* --cnv: use cnv data or not, only available for hg19, for other assembly, do not use this", "description_content_type": null, "docs_url": null, "download_url": "UNKNOWN", "downloads": { "last_day": -1, 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