Mercurial > repos > xuebing > sharplabtool
comparison tools/maf/maf_to_fasta_concat.py @ 0:9071e359b9a3
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| author | xuebing |
|---|---|
| date | Fri, 09 Mar 2012 19:37:19 -0500 |
| parents | |
| 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 single block fasta file, concatenating blocks | |
| 5 | |
| 6 usage %prog species1,species2 maf_file out_file | |
| 7 """ | |
| 8 #Dan Blankenberg | |
| 9 import sys | |
| 10 from galaxy import eggs | |
| 11 import pkg_resources; pkg_resources.require( "bx-python" ) | |
| 12 from bx.align import maf | |
| 13 from galaxy.tools.util import maf_utilities | |
| 14 | |
| 15 assert sys.version_info[:2] >= ( 2, 4 ) | |
| 16 | |
| 17 def __main__(): | |
| 18 try: | |
| 19 species = maf_utilities.parse_species_option( sys.argv[1] ) | |
| 20 except Exception, e: | |
| 21 maf_utilities.tool_fail( "Error determining species value: %s" % e ) | |
| 22 try: | |
| 23 input_filename = sys.argv[2] | |
| 24 except Exception, e: | |
| 25 maf_utilities.tool_fail( "Error reading MAF filename: %s" % e ) | |
| 26 try: | |
| 27 file_out = open( sys.argv[3], 'w' ) | |
| 28 except Exception, e: | |
| 29 maf_utilities.tool_fail( "Error opening file for output: %s" % e ) | |
| 30 | |
| 31 if species: | |
| 32 print "Restricted to species: %s" % ', '.join( species ) | |
| 33 else: | |
| 34 print "Not restricted to species." | |
| 35 | |
| 36 if not species: | |
| 37 try: | |
| 38 species = maf_utilities.get_species_in_maf( input_filename ) | |
| 39 except Exception, e: | |
| 40 maf_utilities.tool_fail( "Error determining species in input MAF: %s" % e ) | |
| 41 | |
| 42 for spec in species: | |
| 43 file_out.write( ">" + spec + "\n" ) | |
| 44 try: | |
| 45 for start_block in maf.Reader( open( input_filename, 'r' ) ): | |
| 46 for block in maf_utilities.iter_blocks_split_by_species( start_block ): | |
| 47 block.remove_all_gap_columns() #remove extra gaps | |
| 48 component = block.get_component_by_src_start( spec ) #blocks only have one occurrence of a particular species, so this is safe | |
| 49 if component: | |
| 50 file_out.write( component.text ) | |
| 51 else: | |
| 52 file_out.write( "-" * block.text_size ) | |
| 53 except Exception, e: | |
| 54 maf_utilities.tool_fail( "Your MAF file appears to be malformed: %s" % e ) | |
| 55 file_out.write( "\n" ) | |
| 56 file_out.close() | |
| 57 | |
| 58 | |
| 59 if __name__ == "__main__": __main__() |