Add submission date to the INRB sequences

[j23414]

Description of proposed changes

This is an fixup and update of PR #242

Add submission date to the INRB sequences as 2024-04-12 (preprint date), so that they show up properly in the "submission_recency" coloring, etc.

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[$i++]";
    print "|2024-04-12";  # <= New
    print "|INRB";
    print "|Africa";
    print "|Democratic Republic of the Congo";
    print "|$header\n";
  }else{
    print;
  }
}

view commands

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

I ran a check of nextstrain build ingest to make sure the rule "curate" completed successfully before submitting the PR.

Related issue(s)

Checklist

• Checks pass

[j23414]

Tried submitting a test run at: https://github.com/nextstrain/mpox/actions/runs/8898724896

[corneliusroemer]

Excellent! I trust your testing, will merge and review - I'm working on mpox anyways so will test there in any case.