/usr/lib/python3/dist-packages/pymummer/snp.py is in python3-pymummer 0.10.3-1.
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 | class Error (Exception): pass
class Snp:
def __init__(self, line):
# Without the -C option to show-snps, looks like this:
#[P1] [SUB] [SUB] [P2] [BUFF] [DIST] [LEN R] [LEN Q] [FRM] [TAGS]
#187 A C 269 187 187 654 853 1 1 ref_name qry_name
# With the -C option to show-snps, looks like this:
#[P1] [SUB] [SUB] [P2] [BUFF] [DIST] [R] [Q] [LEN R] [LEN Q] [FRM] [TAGS]
#187 A C 269 187 187 0 0 654 853 1 1 ref_name qry_name
try:
l = line.rstrip().split('\t')
self.ref_pos = int(l[0]) - 1
self.ref_base = l[1]
self.qry_base = l[2]
self.qry_pos = int(l[3]) - 1
self.ref_length = int(l[-6])
self.qry_length = int(l[-5])
self.ref_name = l[-2]
self.qry_name = l[-1]
except:
raise Error('Error constructing pymummer.snp.Snp from mummer show-snps output at this line:\n' + line)
def __eq__(self, other):
return type(other) is type(self) and self.__dict__ == other.__dict__
def __str__(self):
return '\t'.join([str(x) for x in [
self.ref_pos + 1,
self.ref_base,
self.qry_base,
self.qry_pos + 1,
self.ref_length,
self.qry_length,
self.ref_name,
self.qry_name
]])
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