Mercurial > repos > xuebing > sharplabtool

comparison tools/maf/maf_by_block_number.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 #Dan Blankenberg
3 """
4 Reads a list of block numbers and a maf. Produces a new maf containing the
5 blocks specified by number.
6 """
7
8 import sys
9 from galaxy import eggs
10 import pkg_resources; pkg_resources.require( "bx-python" )
11 from galaxy.tools.util import maf_utilities
12 import bx.align.maf
13
14 assert sys.version_info[:2] >= ( 2, 4 )
15
16 def __main__():
17 input_block_filename = sys.argv[1].strip()
18 input_maf_filename = sys.argv[2].strip()
19 output_filename1 = sys.argv[3].strip()
20 block_col = int( sys.argv[4].strip() ) - 1
21 if block_col < 0:
22 print >> sys.stderr, "Invalid column specified"
23 sys.exit(0)
24 species = maf_utilities.parse_species_option( sys.argv[5].strip() )
25
26 maf_writer = bx.align.maf.Writer( open( output_filename1, 'w' ) )
27 #we want to maintain order of block file and write blocks as many times as they are listed
28 failed_lines = []
29 for ctr, line in enumerate( open( input_block_filename, 'r' ) ):
30 try:
31 block_wanted = int( line.split( "\t" )[block_col].strip() )
32 except:
33 failed_lines.append( str( ctr ) )
34 continue
35 try:
36 for count, block in enumerate( bx.align.maf.Reader( open( input_maf_filename, 'r' ) ) ):
37 if count == block_wanted:
38 if species:
39 block = block.limit_to_species( species )
40 maf_writer.write( block )
41 break
42 except:
43 print >>sys.stderr, "Your MAF file appears to be malformed."
44 sys.exit()
45 if len( failed_lines ) > 0: print "Failed to extract from %i lines (%s)." % ( len( failed_lines ), ",".join( failed_lines ) )
46 if __name__ == "__main__": __main__()