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maf_gc_content.py @ 3

リビジョン 3, 0.6 KB (コミッタ: kohda, 14 年前)
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行番号
1	#!/usr/bin/python2.6
2
3	"""
4	Read a MAF from standard input and print average GC content of each alignment
5
6	usage: %prog < maf > out
7	"""
8
9	from __future__ import division
10
11	import sys
12
13	from bx.align import maf
14
15
16	def __main__():
17
18	maf_reader = maf.Reader( sys.stdin )
19
20	for m in maf_reader:
21	gc = 0
22	bases = 0
23	for c in m.components:
24	gc += c.text.count( 'G' )
25	gc += c.text.count( 'C' )
26	gc += c.text.count( 'g' )
27	gc += c.text.count( 'c' )
28	bases += ( len( c.text ) - c.text.count( '-' ) )
29
30	print gc / bases
31
32	if __name__ == "__main__": __main__()

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