[2] | 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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