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https://github.com/galaxyproject/galaxy.git
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Dannon Baker
45 lines
1.1 KiB
Python
45 lines
1.1 KiB
Python
#!/usr/bin/env python
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"""
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Reads a MAF file. Produces a MAF file containing
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the reverse complement for each block in the source file.
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usage: %prog input_maf_file output_maf_file
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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 galaxy.tools.util import maf_utilities
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def __main__():
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# Parse Command Line
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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 = maf_utilities.parse_species_option(sys.argv.pop(1))
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try:
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maf_writer = bx.align.maf.Writer(open(output_file, "w"))
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except Exception:
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print(sys.stderr, "Unable to open output file")
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sys.exit()
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try:
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count = 0
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for count, maf in enumerate(bx.align.maf.Reader(open(input_file))): # noqa: B007
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maf = maf.reverse_complement()
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if species:
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maf = maf.limit_to_species(species)
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maf_writer.write(maf)
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except Exception:
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print("Your MAF file appears to be malformed.", file=sys.stderr)
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sys.exit()
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print("%i regions were reverse complemented." % count)
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maf_writer.close()
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if __name__ == "__main__":
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__main__()
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