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_narrowpeak_parser(data_dir):
peaks = load_manorm_peaks(os.path.join(data_dir, 'test_peaks.narrowPeak'),
format='narrowpeak')
assert sorted(peaks.chroms) == ['chr1', 'chr2', 'chr22']
assert peaks.size == 10
assert peaks.fetch('chr1')[0].start == 569795
assert peaks.fetch('chr1')[0].end == 570052
assert peaks.fetch('chr1')[0].summit == 569927
assert peaks.fetch('chr1')[1].start == 713873
assert peaks.fetch('chr1')[1].end == 714348
assert peaks.fetch('chr1')[1].summit == 714069
assert peaks.fetch('chr2')[0].start == 778179
assert peaks.fetch('chr2')[0].end == 778484
assert peaks.fetch('chr2')[0].summit == 778368
assert peaks.fetch('chr22')[0].start == 834127
assert peaks.fetch('chr22')[0].end == 834359
assert peaks.fetch('chr22')[0].summit == 834280
def test_bed_parser(data_dir):
peaks = load_manorm_peaks(os.path.join(data_dir, 'test_peaks.bed'),
format='bed')
assert peaks.chroms == ['chr1', 'chr2', 'chr9']
assert peaks.size == 4
assert peaks.fetch('chr1')[0].start == 1
assert peaks.fetch('chr1')[0].end == 100
assert peaks.fetch('chr1')[0].summit == 50
assert peaks.fetch('chr1')[1].start == 2
assert peaks.fetch('chr1')[1].end == 200
assert peaks.fetch('chr1')[1].summit == 101
assert peaks.fetch('chr2')[0].start == 1
assert peaks.fetch('chr2')[0].end == 150
assert peaks.fetch('chr2')[0].summit == 75
assert peaks.fetch('chr9')[0].start == 5
assert peaks.fetch('chr9')[0].end == 123
assert peaks.fetch('chr9')[0].summit == 64
def test_macs_parser(data_dir):
peaks = load_manorm_peaks(os.path.join(data_dir, 'test_peaks_macs.xls'),
format='macs')
assert sorted(peaks.chroms) == ['chr1', 'chr2', 'chr22']
assert peaks.size == 9
assert peaks.fetch('chr1')[0].start == 16192292
assert peaks.fetch('chr1')[0].end == 16193176
assert peaks.fetch('chr1')[0].summit == 16192491
assert peaks.fetch('chr1')[1].start == 17081409
assert peaks.fetch('chr1')[1].end == 17082059
assert peaks.fetch('chr1')[1].summit == 17081819
assert peaks.fetch('chr2')[0].start == 17082916
assert peaks.fetch('chr2')[0].end == 17084523
assert peaks.fetch('chr2')[0].summit == 17084177
assert peaks.fetch('chr22')[0].start == 17565233
assert peaks.fetch('chr22')[0].end == 17567384
assert peaks.fetch('chr22')[0].summit == 17565935
def test_unsupported_format(data_dir):
with pytest.raises(ValueError):
load_manorm_peaks(os.path.join(data_dir, 'test_peaks.bed'),
format='unknown_format')
def test_invalid_format(data_dir):
with pytest.raises(FileFormatError):
load_manorm_peaks(os.path.join(data_dir, 'test_peaks.bed'),
format='bed3-summit')