flu-seqneut-2025to2026/results/final_titer_data/human_summary.txt at main · jbloomlab/flu-seqneut-2025to2026 · GitHub

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======================================================================
Processing final titer data for group: human
======================================================================

Loading input data...
  Loaded 27864 titer measurements from results/aggregated_titers/titers_human.csv
  Loaded 446 sera from results/sera_metadata/all_sera_metadata.csv
  Loaded 186 barcodes from data/viral_libraries/flu-seqneut-2025to2026-barcode-to-strain-actual.csv

Validating input data...
  All rows have correct group
  All serum-virus pairs are unique
  All sera found in metadata
  All viruses found in viral library

Processing titer data...
  Initial: 27864 rows, 307 sera, 91 viruses

Step 1: Dropping explicitly specified sera and viruses...
  No viruses specified in viruses_to_drop
  Dropped 455 rows for 5 sera in sera_to_drop

Step 2: Applying min_frac_viruses=0.9, min_frac_sera=0.8 (action=drop)...
  min_frac filters converged after 1 iterations

Processing complete:
  Final: 27409 rows, 302 sera, 91 viruses
  Dropped: 455 rows, 5 sera, 0 viruses

Generating output files...
  Written: results/final_titer_data/human_titers.csv (27409 rows)
  Written: results/final_titer_data/human_sera.csv (302 rows)
  Written: results/final_titer_data/human_sera_multicohort.csv (722 rows)
  Written: results/final_titer_data/human_viruses.csv (91 rows)
  Written: results/final_titer_data/human_titers_summarized_by_virus.csv (728 rows)

======================================================================
FINAL SUMMARY
======================================================================
Group: human
Sera: 302
Viruses: 91
Total titers: 27409

Cohorts in titers_summarized_by_virus.csv:
  All: 302 sera, 27409 titers
  CTS: 40 sera, 3637 titers
  HKU: 43 sera, 3904 titers
  NIID: 61 sera, 5530 titers
  PENN: 118 sera, 10721 titers
  SCH: 40 sera, 3617 titers
  PENN_0d-post-vax: 59 sera, 5356 titers
  PENN_28d-post-vax: 59 sera, 5365 titers

Viruses per subtype:
  H1N1: 34
  H3N2: 57