Skip to content

Commit

Permalink
vidrl_upload: Use Human pool <year> as serum_id for human serum refs
Browse files Browse the repository at this point in the history
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.

¹ <https://github.com/nextstrain/seasonal-flu/blob/89f6cfd11481b2c51c50d68822c18d46ed56db51/workflow/snakemake_rules/download_from_fauna.smk#L93>
  • Loading branch information
joverlee521 committed Aug 27, 2024
1 parent 9b6cf56 commit 1720614
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,
Expand Down

0 comments on commit 1720614

Please sign in to comment.