Bug: Update dropped strains file to list accession instead of strain

[j23414]

Current Behavior

Currently, strains listed in phylogenetic/config/dropped_strains.txt are not being dropped since 8ab810f

Expected behavior

Strains listed in dropped_strains.txt are not in the final phylogenetic tree.

How to reproduce

Possible solution

Perhaps cherry pick a commit like:

• 67016d1

Your environment: if browsing Nextstrain online

• Operating system:
• Browser:

Your environment: if running Nextstrain locally

• Operating system:
• Browser:
• Version (e.g. auspice 2.7.0):

Additional context

Add any other context about the problem here.

[victorlin]

Good catch! If I understand correctly, phylogenetic/config/dropped_strains.txt is used for augur filter --exclude so it should be updated alongside 8ab810f. Looking more carefully at #12, the --sequences input should also be updated to match the new ID values but I don't see that it was changed. Does it still work?

[j23414]

Correct, and yes the --sequences input still works :D

git clone https://github.com/nextstrain/dengue.git
cd dengue/phylogenetic
nextstrain build . data/sequences_all.fasta
grep  ">" data/sequences_all.fasta | head -n5

Which shows the sequences are ID'd by accession, not strain name:

>NC_075403
>NC_075435
>OQ919688
>ON123563
>ON123564

[victorlin]

Good to know! But how did it work before #12 if the sequences were ID'd by accession and augur filter was using strain as the ID column?

[j23414]

augur filter was using strain as the ID column?

This worked when we were still pulling strains from fauna (which also took advantage of the deduplication of strain names of fauna).

However, we shifted to using the ingest folder and pulling data using ncbi datasets. After ingest was merged, the data.nextstrain.org/files were updated so we could have a smooth transition.

[victorlin]

Closed by #26