PKG-INFO

Metadata-Version: 1.1
Name: MethylPurify
Version: 2.0-20141116
Summary: Methylation subclone detection
Home-page: UNKNOWN
Author: Xiaoqi Zheng
Author-email: zheng.shnu@gmail.com
License: UNKNOWN
Description: 
        MethylPurify_v2
        ------------------
        
        This script is used for predicting subclone purity.
        
        
        Get Dependent data
        ````````````````````
        Get the version of genome fasta that you mapped your fastqs, 
        we support hg18 and hg19 genome fasta now, take hg19 as an example
        
        .. code:: python
           
             ## use built-in script
             cd methylpurify/db
             bash genome.sh hg19
        
        
        Get Dependent software
        ````````````````````````
        * `samtools <http://samtools.sourceforge.net>`_, version 0.2.0
        * `numpy <http://www.numpy.org>`_, version 1.8.2
        * `pyfasta`, version 0.5.2
        
        Easy to start 
        `````````````````````
        Input: BAM file, this should be mapped with BSMap with -R option
        * `BSMap <https://code.google.com/p/bsmap/>`_
        
        Currently, we only support hg19 and hg18 genome index mapped BAM file.
        
        If your fastq mapping is done with hg19 index, use following command:
        
        .. code:: python
        
              MethylPurify -f input.bam -b 300 -c 10 -s 50 -i methylpurify/db/CGI_hg19_slop1000.bed -g /path/to/hg19.fa --cnv
        
        
        The results would be placed into *input* folder: alpha1.pred, MethylProfile.bed
        
        
        Options
        ````````````````
        * -f: input BAM file
        * -c: coverage level
        * -b: genome bin size
        * -s: sampling times
        * -g: species genome fasta file
        * -i: CG island specified, can use methylpurify/db/CGI_hg19_slop1000.bed for hg19, methylpurify/db/CGI_hg18_slop1000.bed for hg18
        * --cnv: use cnv data or not, only available for hg19, for other assembly, do not use this
        
        
        
Keywords: genomics methylation cancer
Platform: UNKNOWN
Classifier: Development Status :: 4 - Beta
Classifier: Environment :: Console
Classifier: Intended Audience :: Science/Research
Classifier: License :: OSI Approved :: Python Software Foundation License
Classifier: Operating System :: MacOS :: MacOS X
Classifier: Operating System :: POSIX :: Linux
Classifier: Operating System :: Unix
Classifier: Operating System :: POSIX
Classifier: Programming Language :: Python :: 2.6
Classifier: Programming Language :: Python :: 2.7