/usr/lib/python2.7/dist-packages/cutadapt/align.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 | # coding: utf-8
"""
Alignment module.
"""
from __future__ import print_function, division, absolute_import
from cutadapt._align import Aligner, compare_prefixes, locate
# flags for global alignment
# The interpretation of the first flag is:
# An initial portion of seq1 may be skipped at no cost.
# This is equivalent to saying that in the alignment,
# gaps in the beginning of seq2 are free.
#
# The other flags have an equivalent meaning.
START_WITHIN_SEQ1 = 1
START_WITHIN_SEQ2 = 2
STOP_WITHIN_SEQ1 = 4
STOP_WITHIN_SEQ2 = 8
# Use this to get regular semiglobal alignment
# (all gaps in the beginning or end are free)
SEMIGLOBAL = START_WITHIN_SEQ1 | START_WITHIN_SEQ2 | STOP_WITHIN_SEQ1 | STOP_WITHIN_SEQ2
def compare_suffixes(s1, s2, wildcard_ref=False, wildcard_query=False):
"""
Find out whether one string is the suffix of the other one, allowing
mismatches. Used to find an anchored 3' adapter when no indels are allowed.
"""
s1 = s1[::-1]
s2 = s2[::-1]
_, length, _, _, matches, errors = compare_prefixes(s1, s2, wildcard_ref, wildcard_query)
return (len(s1) - length, len(s1), len(s2) - length, len(s2), matches, errors)
|