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#!/usr/bin/python3
import argparse
import shasta
import sys
def main(useReadName, verbose):
a = shasta.Assembler()
print("Accessing data ...")
a.accessMarkers()
a.accessAlignmentCandidates()
if verbose:
a.accessAlignmentData()
a.accessReadGraph()
print("Writing to AlignmentCandidates.csv ...")
a.writeAlignmentCandidates(useReadName, verbose)
print("Done")
if __name__ == "__main__":
parser = argparse.ArgumentParser(prog='WriteAlignmentCandidates',
formatter_class=argparse.RawDescriptionHelpFormatter,
epilog="Program description:\n\tWrite all alignment candidates (pairs of ReadId) "
"to a file named AlignmentCandidates.csv")
parser.add_argument(
"--useReadName",
dest="useReadName",
action="store_true",
help="If this boolean flag is specified, the full read name"
" from the input sequence file will be written instead of the ID"
)
parser.add_argument(
"--verbose",
dest="verbose",
action="store_true",
help="If this boolean flag is specified, the result of filtering the"
" candidate will also be written to the csv"
)
args = parser.parse_args()
main(
useReadName=args.useReadName,
verbose=args.verbose
)
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