/tools/maf/maf_split_by_species.py
https://bitbucket.org/cistrome/cistrome-harvard/ · Python · 44 lines · 34 code · 6 blank · 4 comment · 12 complexity · 7401437a81702d5b8495e204415704fe MD5 · raw file
- #!/usr/bin/env python
- """
- Read a maf and split blocks by unique species combinations
- """
- import sys
- from galaxy import eggs
- import pkg_resources; pkg_resources.require( "bx-python" )
- from bx.align import maf
- from galaxy.tools.util import maf_utilities
- from galaxy.util import string_as_bool
- assert sys.version_info[:2] >= ( 2, 4 )
- def __main__():
- try:
- maf_reader = maf.Reader( open( sys.argv[1] ) )
- except Exception, e:
- maf_utilities.tool_fail( "Error opening MAF: %s" % e )
- try:
- out = maf.Writer( open( sys.argv[2], "w") )
- except Exception, e:
- maf_utilities.tool_fail( "Error opening file for output: %s" % e )
- try:
- collapse_columns = string_as_bool( sys.argv[3] )
- except Exception, e:
- maf_utilities.tool_fail( "Error determining collapse columns value: %s" % e )
-
- start_count = 0
- end_count = 0
- for start_count, start_block in enumerate( maf_reader ):
- for block in maf_utilities.iter_blocks_split_by_species( start_block ):
- if collapse_columns:
- block.remove_all_gap_columns()
- out.write( block )
- end_count += 1
- out.close()
-
- if end_count:
- print "%i alignment blocks created from %i original blocks." % ( end_count, start_count + 1 )
- else:
- print "No alignment blocks were created."
- if __name__ == "__main__": __main__()