#!/usr/bin/python import argparse parser=argparse.ArgumentParser(description='Convert a sequence-based fasta file into a .cmap physical map format by locating (restriction endonuclease) sequence motifs') parser.add_argument('fasta_file', help='The sequence .fasta file to be converted') parser.add_argument('motif', help='The sequence motif to locate, e.g. ATCGGCTA. Case does not matter.') parser.add_argument('cmap_file', help='Name for output .cmap file') args=parser.parse_args() from Operations.BioNano.FileConverter import FileConverter from Operations.BioNano.FileConverter import FastaFile from Operations.BioNano.FileConverter import Digestor from Operations.BioNano.files import CmapFile from Bio import SeqIO conv=FileConverter(FastaFile(args.fasta_file)) conv.digestor=Digestor(args.motif) with open(args.cmap_file, 'w'): pass conv.output_file=(CmapFile(args.cmap_file)) conv.convert()