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#!/usr/bin/python3
"""Update gene names in CNVkit .cnn/.cnr files.
"""
import argparse
import logging
import sys
from skgenome import tabio
from cnvlib.cmdutil import read_cna
logging.basicConfig(level=logging.INFO, format="%(message)s")
def main(args):
annot = tabio.read_auto(args.annotate)
cnarr = read_cna(args.cnv_file)
cnarr['gene'] = annot.into_ranges(cnarr, 'gene', '-')
tabio.write(cnarr, args.output or sys.stdout)
# ENH:
# --short-names
# --no-antitarget
# annotation: --merge, --flatten, --exons, ...
# cut antitargets & insert untargeted gene names
# some math for how to update probes, weight
if __name__ == '__main__':
AP = argparse.ArgumentParser(description=__doc__)
AP.add_argument('annotate', help="Genome annotations.")
AP.add_argument('cnv_file', help="CNVkit .cnn or .cnr file.")
AP.add_argument('-o', '--output', help="Output filename.")
main(AP.parse_args())
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