fix_ligm_locations.py

import sys
import re

rev_gr_re = re.compile(r'([0-9]+)>{1}')
correct = lambda s: rev_gr_re.sub(r'>\1',s) + '\n'

if len(sys.argv) == 3:
    ip = open(sys.argv[1],'r')
    op = open(sys.argv[2],'w')
else:
    raise Exception, "Must supply an input and output file."

for line in ip:
    if line.startswith('FT ') and len(line[:20].split()) == 2:
        line = line.rstrip()
        corrected_lines = [line]
        while line[-1] == ',':
            line = ip.next().rstrip()
            corrected_lines += [line]
        corrected_lines = map(correct,corrected_lines)
        op.write(''.join(corrected_lines))  # newlines are added in "correct" lambda fn
    else:
        op.write(line)

ip.close()
op.close()