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")