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
|
from .common import AlignmentRow, AlignmentColumn
from six.moves import map
#(c) 2013-2014 by Authors
#This file is a part of Ragout program.
#Released under the BSD license (see LICENSE file)
#Some helper functions to parse/process nucmer output
def parse_nucmer_coords(filename):
chr_alias = {}
chr_num = 1
alignment = []
for line in open(filename, "r"):
line = line.strip()
if not len(line) or not line[0].isdigit():
continue
vals = line.split(" | ")
s_ref, e_ref = list(map(int, vals[0].split()))
s_qry, e_qry = list(map(int, vals[1].split()))
len_ref, len_qry = list(map(int, vals[2].split()))
ref_id, qry_id = vals[4].split("\t")
if e_ref > s_ref:
ref_strand = 1
else:
ref_strand = -1
s_ref, e_ref = e_ref, s_ref
if e_qry > s_qry:
qry_strand = 1
else:
qry_strand = -1
s_qry, e_qry = e_qry, s_qry
if ref_id not in chr_alias:
chr_alias[ref_id] = "chr{0}".format(chr_num)
chr_num += 1
ref_row = AlignmentRow(s_ref, e_ref, ref_strand, None,
chr_alias[ref_id])
qry_row = AlignmentRow(s_qry, e_qry, qry_strand, None, qry_id)
alignment.append(AlignmentColumn(ref_row, qry_row))
return alignment
|
