allpy: 3bdcee61356d repeats/test.py

allpy

view repeats/test.py @ 668:3bdcee61356d

blocks3d/www: fix log-file caused bug of building r2w was configured to use /tmp/blocks3d-www-build.log. It caused build error if this file has been creted by other user. Log-file path was changed to ./output/blocks3d-www-build.log Makefile was changed to create ./output directory before running r2w

author	boris (kodomo) <bnagaev@gmail.com>
date	Fri, 01 Jul 2011 10:32:37 +0400
parents	6070ac379ec8
children

line source

1 import sys

2 import pprint

4 from repeat_joiner import Interval, RepeatJoiner

6 rj = RepeatJoiner()

7 for line in open(sys.argv[1]):

8 line = line.strip()

9 if line:

10 c1, c2, from1, to1, from2, to2, ori1, ori2 = line.split()[:8]

11 if c1 == 'DNA_1':

12 continue # first line

13 ori1 = True if int(ori1) == 1 else False

14 ori2 = True if int(ori2) == 1 else False

15 from1 = int(from1)

16 to1 = int(to1) + 1

17 from2 = int(from2)

18 to2 = int(to2) + 1

20 r1 = Interval(rj, c1, from1, to1, ori1)

21 r2 = Interval(rj, c2, from2, to2, ori2)

22 Interval.pair(r1, r2)

24 rj.build_groups()

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)

31 prev = set()

32 for interval in interval_group:

33 if interval.tuple() in prev:

34 continue

35 prev.add(interval.tuple())

36 print "%i\t%s" % (i, str(interval).replace(' ', '\t'))