Mercurial > repos > xuebing > sharplabtool
comparison tools/maf/maf_to_fasta_multiple_sets.py @ 0:9071e359b9a3
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| author | xuebing |
|---|---|
| date | Fri, 09 Mar 2012 19:37:19 -0500 |
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| children |
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| -1:000000000000 | 0:9071e359b9a3 |
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| 1 #!/usr/bin/env python | |
| 2 | |
| 3 """ | |
| 4 Read a maf and output a multiple block fasta file. | |
| 5 """ | |
| 6 #Dan Blankenberg | |
| 7 import sys | |
| 8 from galaxy import eggs | |
| 9 import pkg_resources; pkg_resources.require( "bx-python" ) | |
| 10 from bx.align import maf | |
| 11 from galaxy.tools.util import maf_utilities | |
| 12 | |
| 13 assert sys.version_info[:2] >= ( 2, 4 ) | |
| 14 | |
| 15 def __main__(): | |
| 16 try: | |
| 17 maf_reader = maf.Reader( open( sys.argv[1] ) ) | |
| 18 except Exception, e: | |
| 19 maf_utilities.tool_fail( "Error opening input MAF: %s" % e ) | |
| 20 try: | |
| 21 file_out = open( sys.argv[2], 'w' ) | |
| 22 except Exception, e: | |
| 23 maf_utilities.tool_fail( "Error opening file for output: %s" % e ) | |
| 24 try: | |
| 25 species = maf_utilities.parse_species_option( sys.argv[3] ) | |
| 26 if species: | |
| 27 num_species = len( species ) | |
| 28 else: | |
| 29 num_species = 0 | |
| 30 except Exception, e: | |
| 31 maf_utilities.tool_fail( "Error determining species value: %s" % e ) | |
| 32 try: | |
| 33 partial = sys.argv[4] | |
| 34 except Exception, e: | |
| 35 maf_utilities.tool_fail( "Error determining keep partial value: %s" % e ) | |
| 36 | |
| 37 if species: | |
| 38 print "Restricted to species: %s" % ', '.join( species ) | |
| 39 else: | |
| 40 print "Not restricted to species." | |
| 41 | |
| 42 for block_num, block in enumerate( maf_reader ): | |
| 43 if species: | |
| 44 block = block.limit_to_species( species ) | |
| 45 if len( maf_utilities.get_species_in_block( block ) ) < num_species and partial == "partial_disallowed": continue | |
| 46 spec_counts = {} | |
| 47 for component in block.components: | |
| 48 spec, chrom = maf_utilities.src_split( component.src ) | |
| 49 if spec not in spec_counts: | |
| 50 spec_counts[ spec ] = 0 | |
| 51 else: | |
| 52 spec_counts[ spec ] += 1 | |
| 53 file_out.write( "%s\n" % maf_utilities.get_fasta_header( component, { 'block_index' : block_num, 'species' : spec, 'sequence_index' : spec_counts[ spec ] }, suffix = "%s_%i_%i" % ( spec, block_num, spec_counts[ spec ] ) ) ) | |
| 54 file_out.write( "%s\n" % component.text ) | |
| 55 file_out.write( "\n" ) | |
| 56 file_out.close() | |
| 57 | |
| 58 if __name__ == "__main__": __main__() |