def __init__(self,
bedfile: str,
spacing: int = 20,
mindata: int = 50,
maxpool: int = None,
lines: list = None):
# spacing should be >= 0
if not type(spacing) == int or spacing < 0:
print("ROI: Invalid spacing: {0}; defaulting to 0".format(spacing))
spacing = 0
# mindata should be > 0
if not type(mindata) == int or mindata <= 0:
print("ROI: Invalid mindata: {0}; defaulting to 1".format(mindata))
mindata = 1
print("Loading .bed data.")
if maxpool:
print("ROI limited to max number of pools = {0}".format(maxpool))
self.source = bedfile
if lines is None:
bed_file = BedFileLoader(bedfile)
lines = bed_file.expand_columns()
self.amplicons = self.load_amplicons(lines, maxpool, -1)
if self.amplicons:
self.targets = self.define_targets(spacing, mindata)
else:
return
def test_search_map_for_general_bed():
bed_file = BedFileLoader(mock_dir_path + 'general.bed')
column_map = bed_file.get_map_with_column_indexes()
assert column_map[bed_file._BedFileLoader__region_id]['search'] is None
assert column_map[bed_file._BedFileLoader__attributes]['search'] is None
assert column_map[
bed_file._BedFileLoader__submitted_region]['search'] is None
def test_search_map_for_amplicon_cov():
bed_file = BedFileLoader(mock_dir_path + 'amplicon_cov.tsv')
column_map = bed_file.get_map_with_column_indexes()
assert column_map[bed_file._BedFileLoader__region_id]['search'] is not None
assert column_map[
bed_file._BedFileLoader__attributes]['search'] is not None
assert column_map[
bed_file._BedFileLoader__submitted_region]['search'] is None
def test_search_map_for_effective_regions():
bed_file = BedFileLoader(mock_dir_path + 'effective_regions.bed')
column_map = bed_file.get_map_with_column_indexes()
assert column_map[bed_file._BedFileLoader__region_id]['search'] is not None
assert column_map[
bed_file._BedFileLoader__attributes]['search'] is not None
assert column_map[
bed_file._BedFileLoader__submitted_region]['search'] is not None
def __init__(self, filename: str):
bed_file = BedFileLoader(filename)
print('Loading coverage data from {}'.format(filename))
# noinspection PyProtectedMember
if bed_file.file_type != bed_file._BedFileLoader__amplicon_cov:
print('{} is not a valid amplicon_coverage file'.format(filename))
sys.exit(1)
self.targets, self.counters = self.define_targets(
bed_file.expand_columns(), bed_file.columns)
def test_loader_strip_chr_works():
"""
test that when strip_chr is True, 'chr' is removed from first bed column
"""
bed_lines = BedFileLoader(mock_dir_path + 'general.bed',
strip_chr=True).bed_lines
assert bed_lines[0][0] == '7'
def test_loader_expanded_result_is_sorted_by_chrom_start_end():
"""
test that when bed_lines are expanded the resulting list is sorted by
chrom, chromStart, and chromEnd (ASC)
"""
expanded = BedFileLoader(mock_dir_path +
'mock_for_split.bed').expand_columns()
assert expanded[0] == ['chr1', '10000', '100000']
assert expanded[1] == ['1', '10001', '100000']
assert expanded[2] == ['12', '10000', '100000']
assert expanded[3] == ['chr12', '10001', '100000']
def test_loader_ignores_non_valid_data_lines():
"""
data lines are those that start with chrom\d* or \d*
"""
bed_file = BedFileLoader(mock_dir_path + 'mock_for_split.bed')
# check headers
assert len(bed_file.header_lines) == 3
assert bed_file.header_lines[0] == 'track'
assert bed_file.header_lines[1] == 'browser'
assert bed_file.header_lines[2] == 'chromosome\tbut\tignore\tit\tplease'
# check data
assert bed_file.bed_lines[0] == ['chr1', '10000', '100000']
assert bed_file.bed_lines[1] == ['chr12', '10001', '100000']
assert bed_file.bed_lines[2] == ['12', '10000', '100000']
assert bed_file.bed_lines[3] == ['1', '10001', '100000']
def test_len_columns_for_amplicon_cov():
bed_file = BedFileLoader(mock_dir_path + 'amplicon_cov.tsv')
expanded = bed_file.expand_columns()
assert len(bed_file.columns) == len(expanded[0])
def test_predict_file_type_for_amplicon_cov():
assert BedFileLoader(mock_dir_path +
'amplicon_cov.tsv').file_type == 'amplicon_cov'
def test_predict_file_type_for_ampliseq_exome():
assert BedFileLoader(mock_dir_path +
'ampliseq_exome.bed').file_type == 'ampliseq_exome'
def test_len_columns_for_effective_regions():
bed_file = BedFileLoader(mock_dir_path + 'effective_regions.bed')
expanded = bed_file.expand_columns()
assert len(bed_file.columns) == len(expanded[0])
def test_predict_file_type_for_effective_regions():
assert BedFileLoader(
mock_dir_path +
'effective_regions.bed').file_type == 'effective_regions'
def test_len_columns_for_general_bed():
bed_file = BedFileLoader(mock_dir_path + 'general.bed')
expanded = bed_file.expand_columns()
assert len(bed_file.columns) == len(expanded[0])
def test_predict_file_type_for_general_bed():
assert BedFileLoader(mock_dir_path +
'general.bed').file_type == 'general_tsv'
def test_len_columns_for_ampliseq_exome():
bed_file = BedFileLoader(mock_dir_path + 'ampliseq_exome.bed')
expanded = bed_file.expand_columns()
assert len(bed_file.columns) == len(expanded[0])