For making Hi-C Box and GRAAL play nice together

remap_hetero_fragments.py

#!/usr/bin/env python

## Read two GRAALy files and produce a new, improved
## hetero_contacts table using different indices.
## It's complicated.

import sys

INFO_CONTIGS_FILE = "info_contigs.txt"
FRAGMENTS_HETERO_FILE = "fragments_hetero_contacts.txt"

contig_to_offset = {}

with open(INFO_CONTIGS_FILE, 'r') as contigs,\
     open(FRAGMENTS_HETERO_FILE, 'r') as contacts:
    # Store the offset for each contig, as given in INFO_CONTIGS_FILE
    for line in contigs:
        if line.startswith("contig"):
            # header line
            continue
        fields = line.strip().split()
        contig = fields[0]
        offset = int(fields[3])
        if contig in contig_to_offset:
            sys.stderr.write("weird, contig %s is already in dict\n" % contig)
            continue
        contig_to_offset[contig] = offset

    # For each line of FRAGMENTS_HETERO_FILE, find the id
    # corresponding to the offset/contig in columns 1 and 2,
    # and the id corresponding to the offset/contig in columns
    # 3 and 4. Output the first id, the second id, and the
    # original count from column 5.
    for line in contacts:
        fields = line.strip().split()
        count = fields[4]
        contig1 = fields[1]
        offset1 = int(fields[0])
        id1 = str(contig_to_offset[contig1] + offset1)
        contig2 = fields[3]
        offset2 = int(fields[2])
        id2 = str(contig_to_offset[contig2] + offset2)
        sys.stdout.write("%s\t%s\t%s\n" % (id1, id2, count))