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47 lines
1.3 KiB
Python
47 lines
1.3 KiB
Python
#!/usr/bin/env python
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"""
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Read a maf and split blocks by unique species combinations
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"""
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from __future__ import print_function
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import sys
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from bx.align import maf
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from galaxy.tools.util import maf_utilities
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from galaxy.util import string_as_bool
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def __main__():
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try:
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maf_reader = maf.Reader(open(sys.argv[1]))
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except Exception as e:
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maf_utilities.tool_fail("Error opening MAF: %s" % e)
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try:
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out = maf.Writer(open(sys.argv[2], "w"))
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except Exception as e:
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maf_utilities.tool_fail("Error opening file for output: %s" % e)
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try:
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collapse_columns = string_as_bool(sys.argv[3])
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except Exception as e:
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maf_utilities.tool_fail("Error determining collapse columns value: %s" % e)
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start_count = 0
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end_count = 0
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for start_count, start_block in enumerate(maf_reader): # noqa: B007
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for block in maf_utilities.iter_blocks_split_by_species(start_block):
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if collapse_columns:
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block.remove_all_gap_columns()
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out.write(block)
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end_count += 1
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out.close()
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if end_count:
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print("%i alignment blocks created from %i original blocks." % (end_count, start_count + 1))
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else:
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print("No alignment blocks were created.")
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if __name__ == "__main__":
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__main__()
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