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
|
import pysam
def test_idxstats_parse_split_lines():
bam_filename = "./pysam_data/ex2.bam"
lines = pysam.idxstats(bam_filename, split_lines=True) # Test pysam 0.8.X style output, which returns a list of lines
for line in lines:
_seqname, _seqlen, nmapped, _nunmapped = line.split()
def test_bedcov_split_lines():
bam_filename = "./pysam_data/ex1.bam"
bed_filename = "./pysam_data/ex1.bed"
lines = pysam.bedcov(bed_filename, bam_filename, split_lines=True) # Test pysam 0.8.X style output, which returns a list of lines
for line in lines:
fields = line.split('\t')
assert len(fields) in [4, 5], "bedcov should give tab delimited output with 4 or 5 fields. Split line (%s) gives %d fields." % (fields, len(fields))
def test_idxstats_parse():
bam_filename = "./pysam_data/ex2.bam"
idxstats_string = pysam.idxstats(bam_filename, split_lines=False) # Test pysam 0.9.X style output, which returns a string that needs to be split by \n
lines = idxstats_string.splitlines()
for line in lines:
splt = line.split("\t")
_seqname, _seqlen, nmapped, _nunmapped = splt
def test_bedcov():
bam_filename = "./pysam_data/ex1.bam"
bed_filename = "./pysam_data/ex1.bed"
bedcov_string = pysam.bedcov(bed_filename, bam_filename, split_lines=False) # Test pysam 0.9.X style output, which returns a string that needs to be split by \n
lines = bedcov_string.splitlines()
for line in lines:
fields = line.split('\t')
assert len(fields) in [4, 5], "bedcov should give tab delimited output with 4 or 5 fields. Split line (%s) gives %d fields." % (fields, len(fields))
|
