/usr/lib/python2.7/dist-packages/cutadapt/qualtrim.py is in python-cutadapt 1.9.1-1build1.
This file is owned by root:root, with mode 0o644.
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 29 30 31 32 33 34 35 36 37 38 39 40 41 | # coding: utf-8
"""
Quality trimming.
"""
from __future__ import print_function, division, absolute_import
import sys
if sys.version > '3':
xrange = range
def quality_trim_index(qualities, cutoff, base=33):
"""
Find the position at which to trim a low-quality end from a nucleotide sequence.
Qualities are assumed to be ASCII-encoded as chr(qual + base).
The algorithm is the same as the one used by BWA within the function
'bwa_trim_read':
- Subtract the cutoff value from all qualities.
- Compute partial sums from all indices to the end of the sequence.
- Trim sequence at the index at which the sum is minimal.
"""
s = 0
max_qual = 0
max_i = len(qualities)
for i in reversed(xrange(max_i)):
q = ord(qualities[i]) - base
s += cutoff - q
if s < 0:
break
if s > max_qual:
max_qual = s
max_i = i
return max_i
try:
from cutadapt._qualtrim import quality_trim_index
except:
pass
|