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Update h3n2/titer-strain-map #309

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30 changes: 30 additions & 0 deletions config/h3n2/titer-strain-map.tsv
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Original file line number Diff line number Diff line change
@@ -1 +1,31 @@
TITER_STRAIN CURATED_STRAIN
A/Camb/925256/2020 A/Cambodia/925256/2020
A/Eng/538/2018 A/England/538/2018
A/Greecd/4/2017 A/Greece/4/2017
A/Hk/5738/2014 A/HongKong/5738/2014

@jameshadfield jameshadfield Apr 1, 2026

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If you use a pattern match (like #306) /Hk/ → HongKong you'd capture more occurrences of such misspelled titers!

$ grep '/Hk/' data/*/*_titers.tsv | wc -l
1888

You'd probably want some logging / checking to see what the actual changes were here & how many were found in the sequence data etc

Same for /Switz/ (n=444), /Switzerlandz/ (n=2184), /StEtienne/ (n=972), /Nor/ (n=628), Eng (n=2818), Greecd (n=32), Camb (n=68)

@joverlee521 joverlee521 Apr 2, 2026

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That's fair! I'm hesitant about something as general as /Hk/ but I'll look into the pattern replacements.

@jameshadfield jameshadfield Apr 2, 2026

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Yeah, and it's unclear how you ever really know (or how Tal originally knew for these specific strains).

The pattern matching is applied only after a few other approaches have failed, and the code (below) means it'll only be applied if it results in a sequence match. But still, that doesn't mean it's right

if case_corrected_strain != titer_strain and case_corrected_strain in metadata:

@joverlee521 joverlee521 Apr 2, 2026

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Yeah, and it's unclear how you ever really know (or how Tal originally knew for these specific strains).

Yeah, I should have paid closer attention to the logs after these changes...There were 14 titer strains removed from missing-titer-strains.tsv, but 11 titer strains were added! Will have to dig into each specific strain to check what the matching sequence strain would be after our latest ingest curations.

@jameshadfield jameshadfield Apr 2, 2026

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I wonder if we should add verbose logging for each (titer) strain name we change - it's encoded in the Match objects so should be easy. It's another TSV, but that seems worth it...

A/Hk/656/2018 A/HongKong/656/2018
A/Hk/675/2018 A/HongKong/675/2018
A/Lyon/CHU/R1811667/2018 A/Lyon/CHU-R1811667/2018
A/Lyon/CHU/R181282/2018 A/Lyon/CHU-R181282/2018
A/Lyon/CHU/R1813393/2018 A/Lyon/CHU-R1813393/2018
A/Lyon/CHU/R190259/2019 A/Lyon/CHU-R190259/2019
A/Lyon/CHU/R190377/2019 A/Lyon/CHU-R190377/2019
A/Lyon/CHU/R1914685/2019 A/Lyon/CHU-R1914685/2019
A/Lyon/CHU/R1915450/2019 A/Lyon/CHU-R1915450/2019
A/Lyon/EHPAD/108/2019 A/Lyon/EHPAD-108/2019
A/Nor/2516/2018 A/Norway/2516/2018
A/Nor/2620/2018 A/Norway/2620/2018
A/Nor/4436/2016 A/Norway/4436/2016
A/Norway/3806-egg A/Norway/3806/2016-egg
A/Singapore/INFIMH-16-001/2016 A/Singapore/INFIMH-16-0019/2016
A/Singapore/INFIMH-16-001/2016-egg A/Singapore/INFIMH-16-0019/2016-egg
A/Singapore/Infimh-16-0019/2016 A/Singapore/INFIMH-16-0019/2016
A/Singapore/Infimh-16-0019/2016-egg A/Singapore/INFIMH-16-0019/2016-egg
A/Singapore/Infimh-16-0019/2016-egg A/Singapore/INFIMH-16-0019/2016-egg
A/StEtienne/1912/2018 A/Saint-Etienne/1912/2018
A/StEtienne/1998/2018 A/Saint-Etienne/1998/2018
A/StEtienne/2539/2020 A/Saint-Etienne/2539/2020
A/Stock/6/2014 A/Stockholm/6/2014
A/Switz/8060/2017-egg A/Switzerland/8060/2017-egg
A/Switzerlandz/8060/2017-egg A/Switzerland/8060/2017-egg

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