view repeats/test.py @ 715:2c3bd08e1f1d
pair_cores: add required option for output file with classes of homology
* method blocks_to_homology() of structure.AlignmentMixin was used (see #58)
* other output files are now optional
* command line option -y corresponds output homology file
author |
boris <bnagaev@gmail.com> |
date |
Fri, 08 Jul 2011 00:23:51 +0200 |
parents |
6070ac379ec8 |
children |
|
line source
4 from repeat_joiner import Interval, RepeatJoiner
7 for line in open(sys.argv[1]):
10 c1, c2, from1, to1, from2, to2, ori1, ori2 = line.split()[:8]
13 ori1 = True if int(ori1) == 1 else False
14 ori2 = True if int(ori2) == 1 else False
20 r1 = Interval(rj, c1, from1, to1, ori1)
21 r2 = Interval(rj, c2, from2, to2, ori2)
25 rj.interval_groups.sort(key=lambda g: len(g), reverse=True)
28 print "group\tchr\tchr_from\tchr_to\tgroup_from\tgroup_to\tori\tgroup_ori"
29 for i, interval_group in enumerate(rj.interval_groups):
30 interval_group.sort(key=lambda i: i.group_start)
32 for interval in interval_group:
33 if interval.tuple() in prev:
35 prev.add(interval.tuple())
36 print "%i\t%s" % (i, str(interval).replace(' ', '\t'))