get_ren_hic_contacts.py

import argparse
from contact import Contacts

def main():
    args = parse_arguments()

    contacts = Contacts(build = args.assembly,
                        chromosome = args.chromosome,
                        resolution = args.resolution)

    contacts.get_raw_contacts_from_ren_hic_file(hic_file = args.hic)

    contacts.write_contacts_to_file(outfile = args.raw_contacts, fmt = "%1f")

    contacts.ice_raw_contacts(raw_contacts_file = args.raw_contacts,
                              bias_file = args.biases,
                              iterations = args.iterations,
                              hicorrector_path = args.hicorrector)

    contacts.write_contacts_to_file(outfile = args.iced, fmt = "%1f")

    contacts.truncate_to_median_diagonal_value()

    contacts.write_contacts_to_file(outfile = args.output, fmt = "%1f")


def parse_arguments():
    parser = argparse.ArgumentParser(
        description = 'Generates an ICEd matrix of intra- or ' +
                'interchromosomal contacts from a Ren lab Hi-C file.')

    parser.add_argument('--hic',
                        metavar = "FILE",
                        action = "store",
                        help = "The input Hi-C file.")

    parser.add_argument('--raw_contacts',
                        metavar = "FILE",
                        action = "store",
                        help = "An intermediate file of raw (un-ICEd) " + 
                               "contacts.")

    parser.add_argument('--biases',
                        metavar = "FILE",
                        action = "store",
                        help = "An intermediate file of biases generated by " +
                               "hicorrector.")

    parser.add_argument('--iced',
                        metavar = "FILE",
                        action = "store",
                        help = "An intermediate file of ICEd contacts.")

    parser.add_argument('-o', '--output',
                        metavar = "FILE",
                        action = "store",
                        help = "The output ICEd and scaled contacts file.")

    parser.add_argument('--assembly',
                        metavar = "ASSEMBLY",
                        action = "store",
                        choices = ["mm9", "mm10", "hg19"],
                        default = "mm9",
                        help = "The genome assembly. (default mm9)")

    parser.add_argument('--chromosome',
                        metavar = "CHROM",
                        action = "store",
                        help = "The chromosome of interest. Input 'genome' " +
                               "for an interchromosomal matrix.")

    parser.add_argument('--resolution',
                        metavar = 'INT',
                        type = int,
                        action = 'store',
                        default = 1000000,
                        help = "Contact matrix resolution in bp. (default 1000000 = 1 Mb)")

    parser.add_argument('--hicorrector',
                        metavar = "FILE",
                        action = 'store',
                        default = "/mnt/new-storage/Software/hicorrector/1.2/bin/ic",
                        help = "Path to hicorrector ic. (default /mnt/new-storage/Software/hicorrector/1.2/bin/ic)")

    parser.add_argument('--iterations',
                        metavar = 'INT',
                        type = int,
                        action = 'store',
                        default = 100,
                        help = "Number of ICE iterations (default 100)")

    return parser.parse_args()


if __name__ == "__main__":
    main()