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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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