GC_bias.py

import sys,os
import random
import string
from math import log,exp
from optparse import OptionParser
import getopt
import time
def main():
    usage = """%prog -i <file> -g <GC_file> -b <name_sort_sam file> -o <out_fastq> -m <mode> -k <y/n>

GC v1.0.1
Author: Yuchao Xia	
Description: accord GC content to filter paired-end reads from name sorted simulate bam file.
	"""
    parser = OptionParser(usage)
    parser.add_option("-i", "--inFile", dest="inFile", help="A reference fasta file.",metavar="FILE")
    parser.add_option("-g","--GC",dest='input_GC',help='GC_function file,splited by \t,the filst col is GC content',metavar="FILE")
    parser.add_option("-b","--bam",dest='input_sam',help='the name sorted sam/bam format file generated by ART ',metavar="FILE")
    parser.add_option('-o','--output',dest='output',help='output fastq file',metavar="file")
    parser.add_option('-k','--keepsam',dest='keepsam',help='generate sam file',metavar='y/n')
    parser.add_option('-m','--mode',dest='mode',help='the function of GC content',metavar='int')
    (opts, args) = parser.parse_args()
    if opts.keepsam is None:
        keepsam='n'
    else:
        keepsam=opts.keepsam
    if opts.input_GC is None:
        input_GC='GC_content.txt'
    else:
        input_GC=opts.input_GC
    if int(opts.mode)==1:
        cmd='python GC_v1.0.1.py -i '+opts.inFile+' -g '+input_GC+' -b '+opts.input_sam+' -o '+opts.output+' -k '+keepsam+' -m '+opts.mode
    elif int(opts.mode)==2:
        cmd='python GC_v1.0.2.py -i '+opts.inFile+' -g '+input_GC+' -b '+opts.input_sam+' -o '+opts.output+' -k '+keepsam+' -m '+opts.mode
    elif int(opts.mode)==2:
        cmd='python GC_v1.0.3.py -i '+opts.inFile+' -g '+input_GC+' -b '+opts.input_sam+' -o '+opts.output+' -k '+keepsam+' -m '+opts.mode
    else:
        cmd='python GC_v1.0.4.py -i '+opts.inFile+' -g '+input_GC+' -b '+opts.input_sam+' -o '+opts.output+' -k '+keepsam+' -m '+opts.mode
    os.system(cmd)
if __name__ == "__main__":
    main()