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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 split blocks by unique species combinations
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5 """
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6 import sys
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7 from galaxy import eggs
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8 import pkg_resources; pkg_resources.require( "bx-python" )
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9 from bx.align import maf
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10 from galaxy.tools.util import maf_utilities
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11 from galaxy.util import string_as_bool
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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 MAF: %s" % e )
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20 try:
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21 out = maf.Writer( 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 collapse_columns = string_as_bool( sys.argv[3] )
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26 except Exception, e:
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27 maf_utilities.tool_fail( "Error determining collapse columns value: %s" % e )
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28
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29 start_count = 0
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30 end_count = 0
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31 for start_count, start_block in enumerate( maf_reader ):
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32 for block in maf_utilities.iter_blocks_split_by_species( start_block ):
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33 if collapse_columns:
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34 block.remove_all_gap_columns()
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35 out.write( block )
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36 end_count += 1
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37 out.close()
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38
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39 if end_count:
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40 print "%i alignment blocks created from %i original blocks." % ( end_count, start_count + 1 )
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41 else:
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42 print "No alignment blocks were created."
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43
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44 if __name__ == "__main__": __main__()
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