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import pysam
import os
from TestUtils import BAM_DATADIR
def test_idxstats_parse_split_lines():
bam_filename = os.path.join(BAM_DATADIR, "ex2.bam")
# Test pysam 0.8.X style output, which returns a list of lines
lines = pysam.idxstats(bam_filename, split_lines=True)
for line in lines:
_seqname, _seqlen, nmapped, _nunmapped = line.split()
def test_bedcov_split_lines():
bam_filename = os.path.join(BAM_DATADIR, "ex1.bam")
bed_filename = os.path.join(BAM_DATADIR, "ex1.bed")
# Test pysam 0.8.X style output, which returns a list of lines
lines = pysam.bedcov(bed_filename, bam_filename, split_lines=True)
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 = os.path.join(BAM_DATADIR, "ex2.bam")
# Test pysam 0.9.X style output, which returns a string that needs to be split by \n
idxstats_string = pysam.idxstats(bam_filename, split_lines=False)
lines = idxstats_string.splitlines()
for line in lines:
splt = line.split("\t")
_seqname, _seqlen, nmapped, _nunmapped = splt
def test_bedcov():
bam_filename = os.path.join(BAM_DATADIR, "ex1.bam")
bed_filename = os.path.join(BAM_DATADIR, "ex1.bed")
# Test pysam 0.9.X style output, which returns a string that needs to be split by \n
bedcov_string = pysam.bedcov(bed_filename, bam_filename, split_lines=False)
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)))
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