Ingest INRB data with permission

[j23414]

Description of proposed changes

From slack, it was requested that the new INRB data on mpox clade I from https://www.medrxiv.org/content/10.1101/2024.04.12.24305195v2 be added to our Nextstrain analysis. INRB is working to add to NCBI, so this is a temporary solution similar to what has been done previously.

After obtaining permission to do so, this PR temporarily adds the records here to be included in the curated dataset.

• Mainly followed instructions from Adding new sequences not from GenBank
• Assigned records temporary IDs TMP0000 to TMP0046
• Set authors to "INRB"

Please feel free to push further commits to this branch or suggest changes.

Related issue(s)

Checklist

• [ ] Checks pass

[corneliusroemer]

Thanks @j23414! How did you populate the metadata? From the FASTA headers? We might need to s/find/replace some of the fields to conform with what ingest expects them to be called - unless you've already done so manually!

Have you done a test run of ingest to see whether the output looks right? Would be good to do that and link to the results! I'll see whether I can do that now.

This might work: https://github.com/nextstrain/mpox/actions/runs/8883875132 Will have to check once workflow is done.

[j23414]

How did you populate the metadata? From the FASTA headers?

Hi @corneliusroemer! I hacked a fix for the fasta file headers using the following perl script (add_ids.pl):

#! /usr/bin/env perl

use strict;
use warnings;

my @TMPIDS=();

for my $i ("TMP0000" .. "TMP0099") {
    push @TMPIDS, $i;
}

my $i=0;
while(<>){
  if(/>(.*)/){
    my $header=$1;
    print ">$TMPIDS[$i++]";
    print "|INRB";
    print "|Africa";
    print "|Democratic Republic of the Congo";
    print "|$header\n";
  }else{
    print;
  }
}

Then ran

perl add_ids.pl ingest/submission01_mpox47_2024.fasta > fixedheaders.fasta
./ingest/bin/fasta-to-ndjson \
 --fasta fixedheaders.fasta \
 --fields genbank_accession authors region country strain host ocountry division collected \
 --exclude ocountry \
 > ingest/data/inrb.ndjson

And then kept checking nextstrain build ingest runs, editing the field names as needed to get it to run successfully.

This might work: https://github.com/nextstrain/mpox/actions/runs/8883875132 Will have to check once workflow is done.

Ohh, thanks for submitted the github action check! 🙌 Should be able to grep "TMP" from the final sequences.fasta and metadata.tsv files.

[corneliusroemer]

Great, thanks for filling me in on the details! There might be a typo in one of your commands ocountry rather than country.

[j23414]

ocountry

Thanks for pointing this out! This was on purpose (-exclude ocountry) ;) It's so I could create a new country column and avoid

sed 's/DRC/Democratic Republic of the Congo/g'

While DRC shouldn't be in the nucleotides section of a fasta file, I've seen stranger things.

[corneliusroemer]

Test run seems to have worked!

wget data.nextstrain.org/files/workflows/mpox/branch/add-inrb-with-permission/metadata.tsv.gz
wget data.nextstrain.org/files/workflows/mpox/branch/add-inrb-with-permission/sequences.fasta.xz      

I'll merge then as it simplifies including the sequences in our builds. If there are outliers/issues, we can always simply exclude the accessions post-ingest, in the phylogenetic/nextclade workflows.

[joverlee521]

Nice work @j23414! I hope the old instructions were somewhat helpful? Please feel free to update it with any extra steps you had to take here.

---

Thanks for pointing this out! This was on purpose (-exclude ocountry) ;) It's so I could create a new country column and avoid

sed 's/DRC/Democratic Republic of the Congo/g'

While DRC shouldn't be in the nucleotides section of a fasta file, I've seen stranger things.

FYI, since all sources go through the ingest pipeline, you could have added this to the geolocation-rules.tsv as

Africa/DRC/*/*    Africa/Democratic Republic of the Congo/*/*