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#!/usr/bin/python3
import argparse
import shasta
import sys
def main(useReadName):
a = shasta.Assembler()
print("Accessing data ...")
a.accessReadGraph()
print("Writing to ReadGraphEdges.csv ...")
a.writeReadGraphEdges(useReadName)
print("Done")
if __name__ == "__main__":
parser = argparse.ArgumentParser(prog='WriteReadGraphEdges',
formatter_class=argparse.RawDescriptionHelpFormatter,
epilog="Program description:\n\tWrite all read graph edges (pairs of ReadId) to a "
"file named ReadGraphEdges.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"
)
args = parser.parse_args()
main(
useReadName=args.useReadName
)
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