Metadata-Version: 1.0
Name: CellMethy
Version: 1.2.0
Summary: Identifying focal full methylation of cell subpopulation and inferring fraction
Home-page: https://github.com/pypa/CellMethyproject
Author: Fang Wang
Author-email: wangfang@ems.hrbmu.edu.cn
License: Harbin Medical University, Python Software Foundation License
Description: CellMethy_v1
        
        DNA methylation patterns within a cell population from individual somatic tissues are highly heterogeneous and polymorphic. We developed CellMethy method to quantify fraction of focal full methylation of cell subpopulation (FMC fraction) and identify fully methylated regions of cell subpopulation (CellMethy) based on single base resolution DNA methylation data. 
        This script is used for infering fraction of focal full methylation cell subpopulation.
                
        
        ***************
        Easy to start:
        ***************
        
        Inputfile: File sepearated by "\\t" after bismark processed including read id, strand, chromosome, position of CpGc and methylation state (Z or z).
        
        The result would be placed into input folder:  outputfile.
        
        If your fastq mapping is done with bismark and extracted methylation state, use following command:
                
                ::
                
                     python CellMethy.py -f inputfile -o outputfile
        
        Options:
        ^^^^^^^^
        
                -f: The file name of input file after bismark processed, include five columns: read ID, strand, chromosome, position of CpG and methylation states Z (methylated) or z (unmethylated) separated by '\\t'.
            
                -c: Lowest coverage cutoff in each bin, default is 10.
                
                -b: number of CpGs in each bin, default is 5.
            
                -o: The file name of output file showing full methylation of cell subpopulation, include five columns: chromosome, start, end, FMC fraction, and CpGs number in the region separated by "\\t".
                
        examples:
        """"""""" 
                
                ::
                         
                     cd ~/CellMethy-*.*.*
                     python ./CellMethy/bin/CellMethy.py -f ./data/data_file -b5 -c 10 -o myoutput 
        
            
        How to get Input file
        ^^^^^^^^^^^^^^^^^^^^^^^^^^
        If you have fastq data, you can mapping with bismark tools.
        
        examples:
        """""""""
                
                ::
                        
                     bismark ./referenceGenome --bowtie2 test.fastq -o test.sam   
                     bismark_methylation_extractor -s --comprehensive test.sam
          
          
        The output file named "CpG_context_test.txt" is inputfile of  CellMethy.
        The format of  CellMethy inputfile  include read id, strand, chromosome, position of CpGc and methylation state (Z or z) separated by '\\t'.
        
                
                ::
                        
                    Read1	+	chr21	9827508	Z
                    Read1	-	chr21	9827503	z
                    Read1	-	chr21	9827484	z
                    Read2	+	chr21	9827434	Z
                    Read2	+	chr21	9827454	Z
                    Read2	-	chr21	9827483	z
          
          
        
Keywords: CellMethy setuptools development
Platform: UNKNOWN
Classifier: Development Status :: 3 - Alpha
Classifier: Intended Audience :: Science/Research
Classifier: Topic :: Software Development :: Build Tools
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
