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maf_count.py

リビジョン 3, 1.5 KB (コミッタ: kohda, 15 年前)
Install Unix tools http://hannonlab.cshl.edu/galaxy_unix_tools/galaxy.html

行番号
1	#!/usr/bin/python2.6
2
3	"""
4	Read a MAF from standard input and print counts of alignments, bases, or
5	columns.
6
7	usage: %prog [options]
8	-c, --cols: count alignment columns rather than number of alignments
9	-b, --bases: count bases in first species rather than number of alignments
10	-s, --skip=N: when counting bases, skip this base
11	-e, --each: print a count for each alignment rather than whole file
12	-r, --ref=N: reference sequence (first by default, 0..n)
13	"""
14
15	from bx.cookbook import doc_optparse
16	import sys
17
18	import bx.align.maf
19
20	def __main__():
21
22	options, args = doc_optparse.parse( __doc__ )
23
24	try:
25	if options.cols: action = "cols"
26	elif options.bases: action = "bases"
27	else: action = "aligns"
28	print_each = bool( options.each )
29	if options.ref: ref = int( options.ref )
30	else: ref = 0
31	if options.skip: skip = options.skip
32	else: skip = None
33	except:
34	doc_optparse.exit()
35
36	maf_reader = bx.align.maf.Reader( sys.stdin )
37
38	count = 0
39
40	for m in maf_reader:
41
42	if action == "aligns":
43	count += 1
44	elif action == "cols":
45	count += m.text_size
46	elif action == "bases":
47	if skip:
48	count += ( m.components[ref].size - m.components[ref].text.count( skip ) )
49	else:
50	count += m.components[ref].size
51
52	if print_each:
53	print count
54	count = 0
55
56	if not print_each: print count
57
58	if __name__ == "__main__": __main__()

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