Mercurial > repos > xuebing > sharplabtool

comparison tools/maf/maf_thread_for_species.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 Read a maf file and write out a new maf with only blocks having all of
5 the passed in species, after dropping any other species and removing columns
6 containing only gaps. This will attempt to fuse together any blocks
7 which are adjacent after the unwanted species have been dropped.
8
9 usage: %prog input_maf output_maf species1,species2
10 """
11 #Dan Blankenberg
12 import sys
13 from galaxy import eggs
14 import pkg_resources; pkg_resources.require( "bx-python" )
15 import bx.align.maf
16
17 from bx.align.tools.thread import *
18 from bx.align.tools.fuse import *
19
20 def main():
21 input_file = sys.argv.pop( 1 )
22 output_file = sys.argv.pop( 1 )
23 species = sys.argv.pop( 1 ).split( ',' )
24
25 try:
26 maf_reader = bx.align.maf.Reader( open( input_file ) )
27 except:
28 print >> sys.stderr, "Unable to open source MAF file"
29 sys.exit()
30 try:
31 maf_writer = FusingAlignmentWriter( bx.align.maf.Writer( open( output_file, 'w' ) ) )
32 except:
33 print >> sys.stderr, "Unable to open output file"
34 sys.exit()
35 try:
36 for m in maf_reader:
37 new_components = m.components
38 if species != ['None']:
39 new_components = get_components_for_species( m, species )
40 if new_components:
41 remove_all_gap_columns( new_components )
42 m.components = new_components
43 m.score = 0.0
44 maf_writer.write( m )
45 except Exception, e:
46 print >> sys.stderr, "Error steping through MAF File: %s" % e
47 sys.exit()
48 maf_reader.close()
49 maf_writer.close()
50
51 print "Restricted to species: %s." % ", ".join( species )
52
53 if __name__ == "__main__": main()