def _find_sequence_files(self):
if "amplicon_analysis.fastq" in os.listdir(self._data_dir):
return {"all": os.path.join(self._data_dir, "amplicon_analysis.fastq")}
elif "amplicon_analysis_fastq" in os.listdir(self._data_dir):
fastq_dir = os.path.join(self._data_dir, "amplicon_analysis_fastq")
filepaths = [os.path.join(fastq_dir, f) for f in os.listdir(fastq_dir)]
return {sample_from_file(f): f for f in filepaths}
else:
raise IOError("No valid sequence files found!")
def _find_sequence_files(self):
if 'amplicon_analysis.fastq' in os.listdir(self._data_dir):
return {
'all': os.path.join(self._data_dir, 'amplicon_analysis.fastq')
}
elif 'amplicon_analysis_fastq' in os.listdir(self._data_dir):
fastq_dir = os.path.join(self._data_dir, 'amplicon_analysis_fastq')
filepaths = [
os.path.join(fastq_dir, f) for f in os.listdir(fastq_dir)
]
return {sample_from_file(f): f for f in filepaths}
else:
raise IOError("No valid sequence files found!")
def __init__(self, filename):
self._filename = filename
self._barcodes = [sample_from_file(filename)]
self._records = self._parse_records()
self._types_by_name = {r.name: r.type for r in self._records}
self._loci = sorted_set([r.gtype.split('*')[0] for r in self._records])