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Counts in HI strain files need to be properly summed #62

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trvrb opened this issue Apr 14, 2017 · 0 comments
Closed

Counts in HI strain files need to be properly summed #62

trvrb opened this issue Apr 14, 2017 · 0 comments
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@barneypotter24

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trvrb commented Apr 14, 2017

The --all option in download_all.py is much appreciated. However, it needs to be smarter about how hi_strains.tsv files are combined. Here,

https://github.com/nextstrain/fauna/blob/master/download_all.py#L64

we need to combine the HI strain tsvs in a smarter fashion. Each individual tsv looks like:

A/Pakistan/431/2015	5
A/Mexico/4159/2016	6
A/Kazakhstan/646/2016	5
...
A/Pakistan/431/2015	6

The combined all_hi_strains.tsv needs to have

A/Pakistan/431/2015	11

The titers tsv files can be concatenated just as they are now.
@trvrb trvrb closed this as completed in 63672cb Apr 23, 2017
barneypotter24 added a commit that referenced this issue Jul 4, 2017
@barneypotter24
Merge branch 'master' of https://github.com/nextstrain/fauna
873266c 
* 'master' of https://github.com/nextstrain/fauna:
  Update Zika readme
  Update geo synonyms
  output H7N9 fauna date
  Update geo synonyms
  yellow fever
  h7n9 download instructions
  Update geo synonyms
  Revise download_all behavior. Fixes #62.
  Revert "Update download documentation."
  Revert "Make download filenames congruent with augur "DENV" serotypes."
  Make download filenames congruent with augur "DENV" serotypes.
  Update download documentation.
  Make download filenames congruent with augur "DENV" serotypes.
  Update download documentation.
  Fix region if geo_regions changes, even if doc location fields are same.
  Enable vdb/dengue updates in-place.
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