diff --git a/src/decombinator/collapse.py b/src/decombinator/collapse.py index d81d336..fa684cb 100644 --- a/src/decombinator/collapse.py +++ b/src/decombinator/collapse.py @@ -59,6 +59,7 @@ import time import typing from importlib import metadata +from statistics import median import networkx as nx import polyleven @@ -942,6 +943,7 @@ def collapsinate( counts["number_output_unique_dcrs"] = len(collapsed) counts["number_output_total_dcrs"] = sum(collapsed.values()) + counts["median_barcodes_per_tcr"] = float(median(collapsed.values())) t1 = time.time() print(" ", round(t1 - t0, 2), "seconds") @@ -1170,10 +1172,12 @@ def collapsinator(inputargs: dict, data: list = None) -> list: + str(counts["readdata_fail_no_bclocs"]) + "\nBarcodeFail_LowQuality," + str(counts["readdata_fail_low_barcode_quality"]) - + "\nMultiTCRBarcodes," + + "\nNumberMultiTCRBarcodes," + str(counts["multi_tcr_barcodes"]) - + "\nMultiTCRBarcodeReads," + + "\nNumberMultiTCRBarcodeReads," + str(counts["multi_tcr_barcode_reads"]) + + "\nMedianUMIsPerTCR," + + str(counts["median_barcodes_per_tcr"]) ) print(summstr, file=summaryfile)