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
|
#!/usr/bin/python3
### positional comparison script useful for tagging alignments with their true position
# length.bp unaligned.bp known.nodes known.bp novel.nodes novel.bp
import sys
threshold = int(sys.argv[1])
for line in sys.stdin:
fields = line.split(' ')
# every input has a true position, and if it has less than the expected number of fields we assume alignment failed
aln_name = fields[0]
if len(fields) != 13:
print(aln_name, 0, 0, 0, 0, 0, 0, 0, 0, 0)
continue
aln_chr = fields[1]
aln_pos = int(fields[2])
aln_mapq = int(fields[3])
aln_score = 0
try: aln_score = int(fields[4])
except: pass
true_chr = fields[5]
true_pos = int(fields[6])
length = int(fields[7])
unaligned = int(fields[8])
known_nodes = int(fields[9])
known_bp = int(fields[10])
novel_nodes = int(fields[11])
novel_bp = int(fields[12])
aln_correct = 1 if aln_chr == true_chr and abs(true_pos - aln_pos) < threshold else 0
print(aln_name, aln_correct, aln_mapq, aln_score, length, unaligned, known_nodes, known_bp, novel_nodes, novel_bp)
|
