def run_diamond(self, unique_AA_sequences_fasta_path, unique_AA_sequences_names_dict): diamond = Diamond(unique_AA_sequences_fasta_path, run=self.run, progress=self.progress, num_threads=self.num_threads, overwrite_output_destinations=self.overwrite_output_destinations) diamond.names_dict = unique_AA_sequences_names_dict diamond.search_output_path = self.get_output_file_path('diamond-search-results') diamond.tabular_output_path = self.get_output_file_path('diamond-search-results.txt') diamond.sensitive = self.sensitive return diamond.get_blast_results()
def search_with_diamond(self, aa_sequences_file_path): diamond = Diamond(aa_sequences_file_path, run=self.run, progress=self.progress, num_threads=self.num_threads) diamond.target_db_path = self.available_db_search_program_targets['diamond'] self.run.log_file_path = self.log_file_path or J(self.temp_dir_path, 'log.txt') diamond.search_output_path = J(self.temp_dir_path, 'diamond-search-results') diamond.tabular_output_path = J(self.temp_dir_path, 'diamond-search-results.txt') diamond.sensitive = self.sensitive diamond.max_target_seqs = 1 diamond.blastp() diamond.view() return diamond.tabular_output_path
def search_with_diamond(self, aa_sequences_file_path): diamond = Diamond(aa_sequences_file_path, run=self.run, progress=self.progress, num_threads=self.num_threads) diamond.target_fasta = self.available_db_search_program_targets['diamond'] self.run.log_file_path = self.log_file_path or J(self.temp_dir_path, 'log.txt') diamond.search_output_path = J(self.temp_dir_path, 'diamond-search-results') diamond.tabular_output_path = J(self.temp_dir_path, 'diamond-search-results.txt') diamond.sensitive = self.sensitive diamond.max_target_seqs = 1 diamond.blastp() diamond.view() return diamond.tabular_output_path