Esempio n. 1
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 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!")
Esempio n. 2
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 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!")
Esempio n. 3
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 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])