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Log median UMI count per TCR #57

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Merged
mvcowley merged 3 commits into from
May 18, 2026
Merged

Log median UMI count per TCR #57

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002803f
feat(collapse): log median UMI count per TCR
mvcowley May 18, 2026
cb53772
feat(collapse): type standardise median stat
mvcowley May 18, 2026
02c8e30
feat(collapse): update logging field names
mvcowley May 18, 2026
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8 changes: 6 additions & 2 deletions src/decombinator/collapse.py
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Original file line number Diff line number Diff line change
Expand Up @@ -59,6 +59,7 @@
import time
import typing
from importlib import metadata
from statistics import median

import networkx as nx
import polyleven
Expand Down Expand Up @@ -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")
Expand Down Expand Up @@ -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)
Expand Down
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