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
