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56 lines
1.7 KiB
Python
56 lines
1.7 KiB
Python
#!/usr/bin/env python
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"""
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Read a maf file and write out a new maf with only blocks having all of
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the passed in species, after dropping any other species and removing columns
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containing only gaps. This will attempt to fuse together any blocks
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which are adjacent after the unwanted species have been dropped.
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usage: %prog input_maf output_maf species1,species2
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"""
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# Dan Blankenberg
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from __future__ import print_function
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import sys
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import bx.align.maf
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from bx.align.tools.fuse import FusingAlignmentWriter
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from bx.align.tools.thread import get_components_for_species, remove_all_gap_columns
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def main():
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input_file = sys.argv.pop(1)
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output_file = sys.argv.pop(1)
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species = sys.argv.pop(1).split(',')
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try:
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maf_reader = bx.align.maf.Reader(open(input_file))
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except Exception:
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print("Unable to open source MAF file", file=sys.stderr)
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sys.exit()
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try:
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maf_writer = FusingAlignmentWriter(bx.align.maf.Writer(open(output_file, 'w')))
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except Exception:
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print("Unable to open output file", file=sys.stderr)
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sys.exit()
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try:
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for m in maf_reader:
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new_components = m.components
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if species != ['None']:
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new_components = get_components_for_species(m, species)
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if new_components:
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remove_all_gap_columns(new_components)
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m.components = new_components
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m.score = 0.0
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maf_writer.write(m)
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except Exception as e:
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print("Error steping through MAF File: %s" % e, file=sys.stderr)
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sys.exit()
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maf_reader.close()
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maf_writer.close()
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print("Restricted to species: %s." % ", ".join(species))
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if __name__ == "__main__":
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main()
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