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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 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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