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69 lines
2.7 KiB
Python
69 lines
2.7 KiB
Python
#!/usr/bin/env python
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"""
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Read a maf and output intervals for specified list of species.
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"""
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import sys, os
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from galaxy import eggs
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import pkg_resources; pkg_resources.require( "bx-python" )
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from bx.align import maf
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from galaxy.tools.util import maf_utilities
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assert sys.version_info[:2] >= ( 2, 4 )
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def __main__():
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input_filename = sys.argv[1]
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output_filename = sys.argv[2]
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output_id = sys.argv[3]
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#where to store files that become additional output
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database_tmp_dir = sys.argv[4]
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primary_spec = sys.argv[5]
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species = sys.argv[6].split( ',' )
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all_species = sys.argv[7].split( ',' )
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partial = sys.argv[8]
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keep_gaps = sys.argv[9]
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out_files = {}
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if "None" in species:
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species = []
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if primary_spec not in species:
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species.append( primary_spec )
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if primary_spec not in all_species:
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all_species.append( primary_spec )
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all_species.sort()
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for spec in species:
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if spec == primary_spec:
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out_files[ spec ] = open( output_filename, 'wb+' )
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else:
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out_files[ spec ] = open( os.path.join( database_tmp_dir, 'primary_%s_%s_visible_interval_%s' % ( output_id, spec, spec ) ), 'wb+' )
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out_files[ spec ].write( '#chrom\tstart\tend\tstrand\tscore\tname\t%s\n' % ( '\t'.join( all_species ) ) )
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num_species = len( all_species )
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file_in = open( input_filename, 'r' )
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maf_reader = maf.Reader( file_in )
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for i, m in enumerate( maf_reader ):
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for j, block in enumerate( maf_utilities.iter_blocks_split_by_species( m ) ):
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if len( block.components ) < num_species and partial == "partial_disallowed": continue
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sequences = {}
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for c in block.components:
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spec, chrom = maf_utilities.src_split( c.src )
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if keep_gaps == 'remove_gaps':
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sequences[ spec ] = c.text.replace( '-', '' )
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else:
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sequences[ spec ] = c.text
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sequences = '\t'.join( [ sequences.get( spec, '' ) for spec in all_species ] )
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for spec in species:
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c = block.get_component_by_src_start( spec )
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if c is not None:
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spec2, chrom = maf_utilities.src_split( c.src )
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assert spec2 == spec, Exception( 'Species name inconsistancy found in component: %s != %s' % ( spec, spec2 ) )
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out_files[ spec ].write( "%s\t%s\t%s\t%s\t%s\t%s\t%s\n" % ( chrom, c.forward_strand_start, c.forward_strand_end, c.strand, m.score, "%s_%s_%s" % (spec, i, j), sequences ) )
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file_in.close()
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for file_out in out_files.values():
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file_out.close()
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if __name__ == "__main__": __main__()
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