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vidrl_upload: Use Human pool <year> as serum_id for human serum refs
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Because the `serum_host` field is unreliable in fauna, seasonal-flu
uses substring matches on the `serum_id` field to separate ferret,
human, and mouse sera.¹

Updating the `serum_id` to be `Human pool <year>` so that it can be
matched in seasonal-flu. This also has the side-effect of setting the
`serum_host` field to "human" within fauna because of the `serum_id`
matching in tdb/upload.py.²

¹ <https://github.com/nextstrain/seasonal-flu/blob/89f6cfd11481b2c51c50d68822c18d46ed56db51/workflow/snakemake_rules/download_from_fauna.smk#L93>
² <https://github.com/nextstrain/fauna/blob/88a607db53d36fc91482cae2009eefddf9477f97/tdb/upload.py#L382-L383>
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joverlee521 committed Aug 27, 2024
1 parent 5b053e8 commit b36f7cc
Showing 1 changed file with 4 additions and 2 deletions.
6 changes: 4 additions & 2 deletions tdb/vidrl_upload.py
Original file line number Diff line number Diff line change
Expand Up @@ -71,8 +71,10 @@ def parse_human_serum_references(human_serum_data, subtype):
# Use the first match of the potential fields
if matches is not None:
year = matches.group(2)
# Follow a standard pattern where serum_id is `SH {year}`
new_serum_id = f"SH {year}"
# Follow a standard pattern where serum_id is `Human pool <year>`
# Need "human" in serum_id because this is how we match for human sera in seasonal flu
# <https://github.com/nextstrain/seasonal-flu/blob/89f6cfd11481b2c51c50d68822c18d46ed56db51/workflow/snakemake_rules/download_from_fauna.smk#L93>
new_serum_id = f"Human pool {year}"
break

# year is required to know which vaccine reference strain to use,
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