def _samples_from_input_files(src_re, filter_suffix="", **kwargs):
"""Generate sample names from input files.
src_re (IOTarget): IOTarget object corresponding to the source
regular expression
filter_suffix (str): only use given suffix to filter for input
file names. Useful if many result files exist
for a sample
Returns:
samples (list): list of dictionaries, where the keys of each
dictionary correspond to read group identifiers
"""
smllogger.debug("Getting sample information from input files")
inputs = find_files(regexp=src_re.pattern + filter_suffix, use_full_path=True, **kwargs)
return [src_re.search(f, return_instance=True).concat_groupdict for f in inputs]
def test_find_files_search(self, walk, mocker):
"""Find files using search"""
mock_walk = mocker.patch('os.walk')
mock_walk.return_value = walk
f = find_files(regexp=".fastq", search=True)
assert f == ['./1_121023_FLOWCELL_FOO.fastq.gz', './foo/1_121023_FLOWCELL_BAR.fastq.gz']
def test_find_fastq_files(self, walk, mocker):
"""Find fastq files using match"""
mock_walk = mocker.patch('os.walk')
mock_walk.return_value = walk
f = find_files(regexp="\w+.fastq.gz")
assert f == ['./1_121023_FLOWCELL_FOO.fastq.gz', './foo/1_121023_FLOWCELL_BAR.fastq.gz']