[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 multiple block fasta file. |
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| 5 | """ |
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| 6 | #Dan Blankenberg |
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| 7 | import sys |
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| 8 | from galaxy import eggs |
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| 9 | import pkg_resources; pkg_resources.require( "bx-python" ) |
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| 10 | from bx.align import maf |
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| 11 | from galaxy.tools.util import maf_utilities |
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| 12 | |
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| 13 | assert sys.version_info[:2] >= ( 2, 4 ) |
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| 14 | |
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| 15 | def __main__(): |
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| 16 | try: |
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| 17 | maf_reader = maf.Reader( open( sys.argv[1] ) ) |
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| 18 | except Exception, e: |
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| 19 | maf_utilities.tool_fail( "Error opening input MAF: %s" % e ) |
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| 20 | try: |
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| 21 | file_out = open( sys.argv[2], 'w' ) |
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| 22 | except Exception, e: |
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| 23 | maf_utilities.tool_fail( "Error opening file for output: %s" % e ) |
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| 24 | try: |
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| 25 | species = maf_utilities.parse_species_option( sys.argv[3] ) |
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| 26 | if species: |
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| 27 | num_species = len( species ) |
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| 28 | else: |
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| 29 | num_species = 0 |
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| 30 | except Exception, e: |
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| 31 | maf_utilities.tool_fail( "Error determining species value: %s" % e ) |
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| 32 | try: |
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| 33 | partial = sys.argv[4] |
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| 34 | except Exception, e: |
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| 35 | maf_utilities.tool_fail( "Error determining keep partial value: %s" % e ) |
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| 36 | |
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| 37 | if species: |
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| 38 | print "Restricted to species: %s" % ', '.join( species ) |
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| 39 | else: |
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| 40 | print "Not restricted to species." |
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| 41 | |
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| 42 | for block_num, block in enumerate( maf_reader ): |
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| 43 | if species: |
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| 44 | block = block.limit_to_species( species ) |
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| 45 | if len( maf_utilities.get_species_in_block( block ) ) < num_species and partial == "partial_disallowed": continue |
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| 46 | spec_counts = {} |
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| 47 | for component in block.components: |
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| 48 | spec, chrom = maf_utilities.src_split( component.src ) |
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| 49 | if spec not in spec_counts: |
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| 50 | spec_counts[ spec ] = 0 |
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| 51 | else: |
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| 52 | spec_counts[ spec ] += 1 |
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| 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 ] ) ) ) |
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| 54 | file_out.write( "%s\n" % component.text ) |
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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 | if __name__ == "__main__": __main__() |
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