def _open_results_file(self, result_file): file_handlers = FileHandlers() file_paths = file_handlers.search_directory() out_files = file_handlers.find_files(file_paths, 'out') for out_file in out_files: if result_file == file_handlers.get_file_name(out_file): Data = open(out_file, 'r') data = Data.readlines() Data.close() return data
def _get_fasta_file_paths(self): query_files = [] subject_files = [] for i in range(len(self.sequence_annotations)): organism_id = settings.ORGANISM_MAP[self.sequence_annotations[i][2].upper()] file_handlers = FileHandlers() file_paths = file_handlers.search_directory() fasta_files = file_handlers.find_files(file_paths, 'fasta') for fasta_file in fasta_files: if ( self.sequence_annotations[i][1] + '_' + organism_id ) == file_handlers.get_file_name(fasta_file).split('.fasta')[0]: query_files.append(fasta_file) elif ( self.sequence_annotations[i][1] + '_' + self.filename + '_chain-' + self.sequence_annotations[i][0] ) == file_handlers.get_file_name(fasta_file).split('.')[0]: subject_files.append(fasta_file) return query_files, subject_files