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https://github.com/galaxyproject/galaxy.git
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Daniel Blankenberg
87eebd3206
These changes should only affect output when an input block has a species appearing more than once, with the exception being the MAF to multiple FASTA blocks converters: the FASTA headers have been revised to included the sequence index for a species in a block as well as the block index. A new tool "Split MAF Blocks by Species" has been added that will split MAF blocks into the complete combination of multiple blocks when a species appears more than once.
59 lines
2.1 KiB
Python
Executable File
59 lines
2.1 KiB
Python
Executable File
#!/usr/bin/env python
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"""
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Read a maf and output a multiple block fasta file.
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"""
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#Dan Blankenberg
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import sys
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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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try:
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maf_reader = maf.Reader( open( sys.argv[1] ) )
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except Exception, e:
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maf_utilities.tool_fail( "Error opening input MAF: %s" % e )
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try:
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file_out = open( sys.argv[2], 'w' )
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except Exception, e:
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maf_utilities.tool_fail( "Error opening file for output: %s" % e )
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try:
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species = maf_utilities.parse_species_option( sys.argv[3] )
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if species:
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num_species = len( species )
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else:
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num_species = 0
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except Exception, e:
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maf_utilities.tool_fail( "Error determining species value: %s" % e )
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try:
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partial = sys.argv[4]
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except Exception, e:
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maf_utilities.tool_fail( "Error determining keep partial value: %s" % e )
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if species:
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print "Restricted to species: %s" % ', '.join( species )
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else:
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print "Not restricted to species."
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for block_num, block in enumerate( maf_reader ):
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if species:
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block = block.limit_to_species( species )
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if len( maf_utilities.get_species_in_block( block ) ) < num_species and partial == "partial_disallowed": continue
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spec_counts = {}
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for component in block.components:
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spec, chrom = maf_utilities.src_split( component.src )
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if spec not in spec_counts:
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spec_counts[ spec ] = 0
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else:
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spec_counts[ spec ] += 1
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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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file_out.write( "%s\n" % component.text )
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file_out.write( "\n" )
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file_out.close()
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if __name__ == "__main__": __main__()
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