/usr/lib/python2.7/dist-packages/pbsuite/utils/fakeQuals.py is in python-pbsuite-utils 15.8.24+dfsg-2.
This file is owned by root:root, with mode 0o755.
The actual contents of the file can be viewed below.
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 28 | #!/usr/bin/python
import sys
from optparse import OptionParser
from FileHandlers import FastaFile
USAGE = """USAGE: %prog <input.fasta> <output.qual> [--options]
Creates fake quality information for fasta files that do not have associated \
quality information"""
if __name__ == '__main__':
parser = OptionParser(USAGE)
parser.add_option("-s", "--score", default="40", \
help=("Score to give every base in fasta file.\n" \
"DEFAULT = 40"))
opts, args = parser.parse_args()
if len(args) != 2:
parser.error("Error! Expected exactly 2 arguments.")
fastaName, outName = args
fasta = FastaFile(fastaName)
fout = open(outName,'w')
for entry in fasta:
fout.write(">" + entry + "\n" + \
((opts.score + " ") * len(fasta[entry])) + "\n")
fout.close()
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