/usr/bin/rsem-refseq-extract-primary-assembly is in rsem 1.2.31+dfsg-1.
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 | #!/usr/bin/env python
from sys import argv, exit
if len(argv) != 3:
print("Usage: rsem-refseq-extract-primary-assembly input_top_level_assembly.fna output_primary_assembly.fna")
exit(-1)
writeOut = True
with open(argv[1]) as fin:
with open(argv[2], "w") as fout:
for line in fin:
line = line.strip()
if line[0] == '>':
writeOut = line.rfind("Primary Assembly") >= 0
if writeOut:
fout.write(line + "\n")
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