/usr/bin/gfapy-convert is in python3-gfapy 1.0.0+dfsg-2.
This file is owned by root:root, with mode 0o755.
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1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 | #!/usr/bin/python3
"""
Convert a GFA file to the other specification version
"""
import sys
import os
import gfapy
import argparse
op = argparse.ArgumentParser(description=__doc__)
op.add_argument("filename")
op.add_argument('--version', action='version', version='%(prog)s 1.0')
opts = op.parse_args()
gfa = gfapy.Gfa.from_file(opts.filename)
try:
for line in gfa.lines:
if gfa.version == "gfa1":
print(line.to_gfa2_s())
else:
converted_line = line.to_gfa1_s()
if (converted_line):
print(converted_line)
except gfapy.Error as err:
sys.stderr.write(str(err))
sys.exit(1)
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