Beispiel #1
0
    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()
Beispiel #2
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    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
Beispiel #3
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    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