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