getChromosome

#!/usr/bin/env python
import os
import argparse
import sys

parser = argparse.ArgumentParser()
parser.add_argument("-i", "--multifasta", help="multifasta file")
parser.add_argument("-o", "--output_folder", help="Output folder")
parser.add_argument("-c", "--chromosome", help="Graphics label")
args = parser.parse_args()

multifasta=os.path.realpath(str(args.multifasta))
if not os.path.exists(str(args.output_folder)):
    os.makedirs(str(args.output_folder))
output=os.path.realpath(str(args.output_folder))+"/"
c=str(args.chromosome)

def write_fasta(chrom,fasta_in,output_folder):
    with open(fasta_in, 'r+') as f:
        sys.stdout.flush()
        lines = f.readlines()
        for i in range(0, len(lines)):
            line = lines[i]
            if line[0] == ">":
                print line
                sys.stdout.flush()
                fChr=line.split(" ")[0]
                fChr=fChr[1:]
                if fChr == chrom:
                    print line
                    sys.stdout.flush()
                    seq=str("")
                    s=i
                    code=['N','A','C','T','G']
                    firstbase=lines[s+1][0]
                    f2=open(output_folder+chrom+".fa",'w')
                    f2.write(line)
                    while firstbase in code:
                        s=s + 1
                        seq=seq+lines[s]
                        firstbase=lines[s+1][0]
                    f2.write(seq)
                    print seq
                    sys.stdout.flush()
                    f2.close
                    
write_fasta(c,multifasta,output)