Update h3n2/titer-strain-map - #309
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| 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 |
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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
1888You'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)
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That's fair! I'm hesitant about something as general as /Hk/ but I'll look into the pattern replacements.
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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:There was a problem hiding this comment.
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.
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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...
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Description of proposed changes
Corrections from #60.
I left out the corrections that were just capitalization changes in the location name since these were updated in #306
Related issue(s)
Resolves #60
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