allpy: d9a3e99ae19b repeats/test.py

allpy

view repeats/test.py @ 666:d9a3e99ae19b

blocks3d/www: mark conservative columns inside blocks Previously letters were marked if column is conservative over all sequences of alignment. Currently it was changed to conservatism over block including this letter. Additional attribute storing conservatism of columns inside block was added to block. This caused all colors of blocks to be changed.

author	boris <bnagaev@gmail.com>
date	Fri, 01 Jul 2011 03:21:08 +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'))