def test_bamview_bam(bamfile):
from bam2bw.bampipes import bamview
from tempfile import NamedTemporaryFile
# Read BAM file, write to BAM file
f = bamview(open(bamfile), bam=True)
tmp = NamedTemporaryFile()
tmp.write(f.read())
tmp.flush()
f = bamview(open(tmp.name), bam=False)
assert 17 == len(f.readlines())
def test_bamview_sam_rmrepeat_rmdup(bamfile):
from bam2bw.bampipes import bamview
f = bamview(open(bamfile), bam=False, rmrepeat=True, rmdup=True)
assert 7 == len(f.readlines())
def test_bamview_bam_rmrepeat(bamfile):
from bam2bw.bampipes import bamview
f = bamview(open(bamfile), bam=True, rmrepeat=True)
assert f.read() != None
def test_bamview_sam_rmrepeat(bamfile):
from bam2bw.bampipes import bamview
f = bamview(open(bamfile), bam=False, rmrepeat=True)
lines = f.readlines()
assert 12 == len(lines)
def test_bamview_sam(bamfile):
from bam2bw.bampipes import bamview
f = bamview(open(bamfile), bam=False)
assert 17 == len(f.readlines())
def test_raise_error_if_not_file_object():
from bam2bw.bampipes import bamview
with pytest.raises(TypeError):
bamview("Im_a_string.bam")