allpy: ee2c10aa74b8 repeats/test.py

allpy

view repeats/test.py @ 610:ee2c10aa74b8

paired_cores/score.py: change method of score evaluation Boundary positions of blocks are not considered. Columns represented with one sequence or pure gap columns are not considered. Calculate weighted average of number of connected components in columns. Weight of column = l / sum(l) (l = number of sequnces representing column)

author	boris (kodomo) <bnagaev@gmail.com>
date	Tue, 05 Apr 2011 23:11:41 +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'))