def _assign_dna_reads_to_database(self, query_fasta_fp, database_fasta_fp, raw_output_fp, temp_dir, params, HALT_EXEC): _params = {} _params.update(params) bwa_assign_dna_reads_to_dna_database( query_fasta_fp=query_fasta_fp, database_fasta_fp=database_fasta_fp, out_fp=raw_output_fp, params=_params)
def _assign_dna_reads_to_database(self, query_fasta_fp, database_fasta_fp, raw_output_fp, temp_dir, params, HALT_EXEC): _aln_params = {'-f': splitext(raw_output_fp)[0] + '.sai'} if 'aln_params' in params: _aln_params.update(params['aln_params']) params['algorithm'] = 'bwa-short' params['aln_params'] = _aln_params bwa_assign_dna_reads_to_dna_database( query_fasta_fp=query_fasta_fp, database_fasta_fp=database_fasta_fp, out_fp=raw_output_fp, params=params)