#!/opt/Python/2.7.3/bin/python import sys from collections import defaultdict import numpy as np import re import os import argparse from Bio import SeqIO def usage(): test="name" message=''' python CircosConf.py --input circos.config --output pipe.conf ''' print message def fasta_id(fastafile): fastaid = defaultdict(str) for record in SeqIO.parse(fastafile,"fasta"): fastaid[record.id] = 1 return fastaid def readtable(infile): data = defaultdict(str) with open (infile, 'r') as filehd: for line in filehd: line = line.rstrip() if len(line) > 2: unit = re.split(r'\t',line) if not data.has_key(unit[0]): data[unit[0]] = unit[1] return data def main(): parser = argparse.ArgumentParser() parser.add_argument('-i', '--input') parser.add_argument('-o', '--output') parser.add_argument('-v', dest='verbose', action='store_true') args = parser.parse_args() try: len(args.input) > 0 except: usage() sys.exit(2) if __name__ == '__main__': main()