/usr/share/ray/scripts/getSeq.py is in ray-extra 2.3.1-5.
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 | #!/usr/bin/python
"""Get a sequence from a fasta file by specifying the sequence name
Usage:
getSeq.py fasta_file sequence_name
"""
# Importing modules
import sys
if len(sys.argv)!=3:
print __doc__
sys.exit(1)
file=sys.argv[1]
name=sys.argv[2]
dump=False
for line in open(file):
if line[0]=='>':
if line.find(name)>=0:
dump=True
elif dump:
break
if dump:
print line.strip()
|