Mercurial > repos > xuebing > sharplabtool

comparison tools/maf/maf_reverse_complement.py @ 0:9071e359b9a3

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author xuebing
date Fri, 09 Mar 2012 19:37:19 -0500
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-1:000000000000 0:9071e359b9a3
1 #!/usr/bin/env python
2
3 """
4 Reads a MAF file. Produces a MAF file containing
5 the reverse complement for each block in the source file.
6
7 usage: %prog input_maf_file output_maf_file
8 """
9 #Dan Blankenberg
10 from galaxy import eggs
11 import pkg_resources; pkg_resources.require( "bx-python" )
12 import bx.align.maf
13 from galaxy.tools.util import maf_utilities
14 import sys
15
16 assert sys.version_info[:2] >= ( 2, 4 )
17
18 def __main__():
19 #Parse Command Line
20 input_file = sys.argv.pop( 1 )
21 output_file = sys.argv.pop( 1 )
22 species = maf_utilities.parse_species_option( sys.argv.pop( 1 ) )
23
24 try:
25 maf_writer = bx.align.maf.Writer( open( output_file, 'w' ) )
26 except:
27 print sys.stderr, "Unable to open output file"
28 sys.exit()
29 try:
30 count = 0
31 for count, maf in enumerate( bx.align.maf.Reader( open( input_file ) ) ):
32 maf = maf.reverse_complement()
33 if species:
34 maf = maf.limit_to_species( species )
35 maf_writer.write( maf )
36 except:
37 print >>sys.stderr, "Your MAF file appears to be malformed."
38 sys.exit()
39 print "%i regions were reverse complemented." % count
40 maf_writer.close()
41
42 if __name__ == "__main__": __main__()