def RunIgQUAST(params, log): log.info("\n======== IgQUAST starts") # run repertoire evaluator log.info("\n==== Computation of metrics") ReadRepertoires(params, log) CreateRepertoireSubdirs(params, log) if params.original_clusters != ["", ""]: params.evaluator.original_repertoire = reading_utils.read_repertoires( [params.original_clusters])[0][0] RunExactEvaluator(params, log) elif len(params.constructed_clusters) == 1 and not params.assembled_barcodes[0]: RunGeneralEvaluator(params, log) elif not params.assembled_barcodes[0]: RunInexactEvaluator(params, log) else: RunBarcodedDataEvaluator(params, log) # print histograms DrawHistograms(params, log) if params.deep_analysis: RunDeepAnalysis(params, log) ''' output clusters sizes CreateSizesOfClusters(params, log) ''' log.info("\n======== IgQUAST ends") if params.file_metrics: PrintMainOutput(params, log) log.info("\nThank you for using IgQUAST!")
def ReadRepertoires(params, log): repertoires, read_names = reading_utils.read_repertoires(params.constructed_clusters, params.assembled_barcodes) params.evaluator = RepertoireEvaluator(repertoires) log.info('\n==== Repertoires:') for rep in params.evaluator.repertoires: log.info(rep.clusters_filename + ' ==> ' + rep.name) log.info('')