def select_consensus_files( consensus_file, output_file ): selected_files = [] with open( consensus_file ) as handle: for line in handle: sequence_file, reference_file, consensus_file = line.strip().split() if consensus_file.endswith('None'): pass elif fasta_count( consensus_file ) == 1: selected_files.append( consensus_file ) else: selected_files.append( reference_file ) output_selected_consensus( output_file, selected_files )
def select_consensus_files(consensus_file, output_file): selected_files = [] with open(consensus_file) as handle: for line in handle: sequence_file, reference_file, consensus_file = line.strip().split( ) if consensus_file.endswith('None'): pass elif fasta_count(consensus_file) == 1: selected_files.append(consensus_file) else: selected_files.append(reference_file) output_selected_consensus(output_file, selected_files)
def generate_consensus_files( cluster_list, consensus_tool, output_file ): consensus_files = [] with open( cluster_list ) as handle: for line in handle: sequence_file, reference_file, count = line.strip().split() print sequence_file, reference_file if reference_file.endswith('None'): consensus_files.append( (sequence_file, 'None', 'None') ) elif fasta_count( sequence_file ) == 1: consensus_files.append( (sequence_file, reference_file, 'None') ) else: consensus = consensus_tool( sequence_file, reference_file ) consensus_files.append( (sequence_file, reference_file, consensus) ) write_consensus_files( consensus_files, output_file )
def select_final_sequences( self, consensusFile ): outputFile = self.process_setup( consensusFile, 'SequenceSelector', suffix='consensus.selected' ) if self.output_files_exist( outputFile=outputFile ): return outputFile selectedFiles = [] with open( consensusFile ) as handle: for line in handle: referenceFile, consensusFile = line.strip().split() if consensusFile.endswith('None'): pass elif fasta_count( consensusFile ) == 1: selectedFiles.append( consensusFile ) else: selectedFiles.append( referenceFile ) with open( outputFile, 'w' ) as handle: for filename in selectedFiles: handle.write(filename + '\n') self.process_cleanup( outputFile=outputFile ) return outputFile
def select_final_sequences(self, consensusFile): outputFile = self.process_setup(consensusFile, 'SequenceSelector', suffix='consensus.selected') if self.output_files_exist(output_file=outputFile): return outputFile selectedFiles = [] with open(consensusFile) as handle: for line in handle: referenceFile, consensusFile = line.strip().split() if consensusFile.endswith('None'): pass elif fasta_count(consensusFile) == 1: selectedFiles.append(consensusFile) else: selectedFiles.append(referenceFile) with open(outputFile, 'w') as handle: for filename in selectedFiles: handle.write(filename + '\n') self.process_cleanup(output_file=outputFile) return outputFile