Example #1
0
 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)
Example #2
0
 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)
Example #3
0
 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)
Example #4
0
 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)