def test_bam_pe(data_dir):
reads = load_reads(os.path.join(data_dir, 'test_reads_pe.bam'),
format='bam',
paired=True)
assert reads.chroms == ['chr1', 'chr9']
assert reads.size == 2
assert reads._data['chr1'] == [150]
assert reads._data['chr9'] == [2000]
def test_bedpe(data_dir):
reads = load_reads(os.path.join(data_dir, 'test_reads.bedpe'),
format='bedpe',
paired=True)
assert reads.chroms == ['chr1', 'chr9']
assert reads.size == 2
assert reads._data['chr1'] == [200]
assert reads._data['chr9'] == [2400]
def test_bed(data_dir):
reads = load_reads(os.path.join(data_dir, 'test_reads.bed'),
format='bed',
paired=False,
shift=100)
assert reads.chroms == ['chr1', 'chr2', 'chr9']
assert reads.size == 4
assert reads._data['chr1'] == [101, 400]
assert reads._data['chr2'] == [12445]
assert reads._data['chr9'] == [12245]
def load_input_data(args):
"""Load required input data."""
logger.info("Loading peaks of sample 1")
peaks1 = load_manorm_peaks(path=args.peak_file1,
format=args.peak_format,
name=args.name1)
logger.info("Loading peaks of sample 2")
peaks2 = load_manorm_peaks(path=args.peak_file2,
format=args.peak_format,
name=args.name2)
logger.info("Loading reads of sample 1")
reads1 = load_reads(path=args.read_file1,
format=args.read_format,
paired=args.paired,
shift=args.shift_size1,
name=args.name1)
logger.info("Loading reads of sample 2")
reads2 = load_reads(path=args.read_file2,
format=args.read_format,
paired=args.paired,
shift=args.shift_size2,
name=args.name2)
return peaks1, peaks2, reads1, reads2
def test_matched_bed(data_dir):
with pytest.raises(FormatModeConflictError):
load_reads(os.path.join(data_dir, 'test_reads.bed'), format='bed',
paired=True)
def test_invalid_format(data_dir):
with pytest.raises(FileFormatError):
load_reads(os.path.join(data_dir, 'test_reads.bed'), format='bedpe',
paired=True)
def test_unsupported_format(data_dir):
with pytest.raises(ValueError):
load_reads(os.path.join(data_dir, 'test_reads.bed'),
format='unknown_format')