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1 #!/usr/bin/env python
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2 #Dan Blankenberg
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3 """
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4 Reads a list of block numbers and a maf. Produces a new maf containing the
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5 blocks specified by number.
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6 """
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7
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8 import sys
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9 from galaxy import eggs
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10 import pkg_resources; pkg_resources.require( "bx-python" )
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11 from galaxy.tools.util import maf_utilities
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12 import bx.align.maf
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13
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14 assert sys.version_info[:2] >= ( 2, 4 )
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15
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16 def __main__():
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17 input_block_filename = sys.argv[1].strip()
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18 input_maf_filename = sys.argv[2].strip()
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19 output_filename1 = sys.argv[3].strip()
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20 block_col = int( sys.argv[4].strip() ) - 1
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21 if block_col < 0:
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22 print >> sys.stderr, "Invalid column specified"
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23 sys.exit(0)
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24 species = maf_utilities.parse_species_option( sys.argv[5].strip() )
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25
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26 maf_writer = bx.align.maf.Writer( open( output_filename1, 'w' ) )
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27 #we want to maintain order of block file and write blocks as many times as they are listed
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28 failed_lines = []
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29 for ctr, line in enumerate( open( input_block_filename, 'r' ) ):
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30 try:
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31 block_wanted = int( line.split( "\t" )[block_col].strip() )
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32 except:
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33 failed_lines.append( str( ctr ) )
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34 continue
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35 try:
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36 for count, block in enumerate( bx.align.maf.Reader( open( input_maf_filename, 'r' ) ) ):
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37 if count == block_wanted:
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38 if species:
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39 block = block.limit_to_species( species )
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40 maf_writer.write( block )
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41 break
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42 except:
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43 print >>sys.stderr, "Your MAF file appears to be malformed."
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44 sys.exit()
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45 if len( failed_lines ) > 0: print "Failed to extract from %i lines (%s)." % ( len( failed_lines ), ",".join( failed_lines ) )
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46 if __name__ == "__main__": __main__()
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