/usr/lib/python3/dist-packages/pymummer/variant.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 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 | class Error (Exception): pass
SNP = 1
DEL = 2
INS = 3
var_types = {
1: 'SNP',
2: 'DEL',
3: 'INS',
}
class Variant:
def __init__(self, snp):
'''Create a Variant object from a pymummer.snp.Snp object'''
if snp.ref_base == '.':
self.var_type = INS
self.qry_base = snp.qry_base
self.ref_base = '.'
elif snp.qry_base == '.':
self.var_type = DEL
self.qry_base = '.'
self.ref_base = snp.ref_base
elif '.' not in [snp.ref_base, snp.qry_base]:
self.var_type = SNP
self.ref_base = snp.ref_base
self.qry_base = snp.qry_base
else:
raise Error('Error constructing Variant from pymummer.snp.Snp:' + str(snp))
self.ref_start = snp.ref_pos
self.ref_end = snp.ref_pos
self.ref_length = snp.ref_length
self.ref_name = snp.ref_name
self.qry_start = snp.qry_pos
self.qry_end = snp.qry_pos
self.qry_length = snp.qry_length
self.qry_name = snp.qry_name
def __eq__(self, other):
return type(other) is type(self) and self.__dict__ == other.__dict__
def __str__(self):
return '\t'.join([
str(self.ref_start + 1),
str(self.ref_end + 1),
str(self.ref_length),
str(self.ref_name),
self.ref_base,
str(self.qry_start + 1),
str(self.qry_end + 1),
str(self.qry_length),
str(self.qry_name),
self.qry_base
])
def update_indel(self, nucmer_snp):
'''Indels are reported over multiple lines, 1 base insertion or deletion per line. This method extends the current variant by 1 base if it's an indel and adjacent to the new SNP and returns True. If the current variant is a SNP, does nothing and returns False'''
new_variant = Variant(nucmer_snp)
if self.var_type not in [INS, DEL] \
or self.var_type != new_variant.var_type \
or self.qry_name != new_variant.qry_name \
or self.ref_name != new_variant.ref_name:
return False
if self.var_type == INS \
and self.ref_start == new_variant.ref_start \
and self.qry_end + 1 == new_variant.qry_start:
self.qry_base += new_variant.qry_base
self.qry_end += 1
return True
if self.var_type == DEL \
and self.qry_start == new_variant.qry_start \
and self.ref_end + 1 == new_variant.ref_start:
self.ref_base += new_variant.ref_base
self.ref_end += 1
return True
return False
|