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#!/usr/bin/python
import argparse, sys
from pbsuite.utils.setupLogging import *
from pbsuite.honey import bampie, TGraf, HSpots, Force, ComplexResolver, \
massivePhrap
STAGES = {"pie": bampie.run, \
"tails": TGraf.run, \
"spots": HSpots.run, \
"force": Force.run , \
"asm": massivePhrap.run, \
"cpxres": ComplexResolver.run}
USAGE = """\
Honey - genomic variant calling with long sequencing reads
STAGE is one of
pie Extract and map soft-clipped Tails from a bam.
tails Cluster mapped tails to make break-points of larger events.
spots Find genomic variants within reads' spans.
force Given a BedFile of predicted variants, force search for matching
asm Assemble reads around a variant and remap contigs to a reference
cpxres Complex multi-break-point resolution (beta)
See HoneyReadme.txt for documentation or --help for details\
"""
def parseArgs():
parser = argparse.ArgumentParser(prog="Honey.py", description=USAGE, \
formatter_class=argparse.RawDescriptionHelpFormatter)
#parser.add_argument("-h", "--help", action="store_true")
parser.add_argument("stage", metavar="STAGE", choices=STAGES.keys(), type=str, \
help="Stage to execute")
parser.add_argument("options", metavar="OPTIONS", nargs=argparse.REMAINDER,\
help="Options to pass to the stage")
args = parser.parse_args()
sys.stderr.write("""
Please Cite: English, Adam C., William J. Salerno, Jeffery G.
Reid. "PBHoney: identyfying genomic variants via
long-read discordance and interrupted mapping."
BMC Bioinformatics 2014, 15:180 (June 10, 2014).
doi:10.1186/1471-2105-15-180\n\n""")
STAGES[args.stage](args.options)
if __name__ == '__main__':
parseArgs()
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