allpy: d87129162eb4 repeats/test.py

allpy

view repeats/test.py @ 822:d87129162eb4

Implemented & tested new markup API. See #95 1) Sequences, Alignment and Blocks now have two new methods: - add_markup(name, markup_class=optional, **kwargs=optional) - remove_markup(name) name refers to the same name as in aln.markups[name] or sequence[i].name It is now explicitly denied to create markups any other way. 2) Markups now have `remove()` method that means 'release all memory that would not be released otherwised, if we just remove markup from the dictionary'. For sequences markups it removes markup attribute from each monomer. 3) Added necessary del sequence_markup[monomer] method. 4) Many base classes have attribute `kind`; for Alignments and Blocks it is 'alignment', for Sequences it is 'sequence' for AlignmentMarkups it is 'alignment_markup' for SequenceMarkups it is 'sequence_markup'. This attribute is crucial for new alignment construction API. 5) Common stuff for MarkupContainers (Alignments and Sequences) is in MarkupContainerMixin.

author	Daniil Alexeyevsky <dendik@kodomo.fbb.msu.ru>
date	Fri, 15 Jul 2011 16:43:03 +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'))