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Fix annotate metadata with numeric strains
Description of proposed changes
Fix annotate metadata with numeric strains by setting the dtype of the "strain" column in the sequence index to "string".
Related issue(s)
Fixes #948
Testing
- [x] Added functional test for issue, confirmed that test failed, and confirmed that fix in c49a5a6 makes the test pass
- [x] Tested by CI
CI fails on the "push" because this PR branches from the workflow with the old Nextalign/Nextclade commands, but the CI runs with the latest Docker image using new Nextalign/Nextclade:
python3 scripts/sanitize_sequences.py --sequences data/example_sequences.fasta.gz --strip-prefixes hCoV-19/ SARS-CoV-2/ --output /dev/stdout 2> logs/sanitize_sequences_gisaid.txt | nextalign --jobs=2 --reference defaults/reference_seq.fasta --genemap defaults/annotation.gff --genes ORF1a,ORF1b,S,ORF3a,E,M,ORF6,ORF7a,ORF7b,ORF8,N,ORF9b --sequences /dev/stdin --output-dir results/translations --output-basename seqs_gisaid --output-fasta results/aligned_gisaid.fasta --output-insertions results/insertions_gisaid.tsv > logs/align_gisaid.txt 2>&1;
xz -2 -T 2 results/aligned_gisaid.fasta;
xz -2 -T 2 results/translations/seqs_gisaid*.fasta
CI passes on the "pull" which runs the results we'd see after merging this PR into master
where the alignment commands match the Docker environment.
python3 scripts/sanitize_sequences.py --sequences data/example_sequences.fasta.gz --strip-prefixes hCoV-19/ SARS-CoV-2/ --output /dev/stdout 2> logs/sanitize_sequences_gisaid.txt | nextalign run --jobs=2 --reference defaults/reference_seq.fasta --genemap defaults/annotation.gff --output-translations results/translations/seqs_gisaid.gene.{gene}.fasta --output-fasta results/aligned_gisaid.fasta --output-insertions results/insertions_gisaid.tsv > logs/align_gisaid.txt 2>&1;
xz -2 -T 2 results/aligned_gisaid.fasta;
xz -2 -T 2 results/translations/seqs_gisaid.gene.*.fasta
Given that the latter passes and is the check that matters, we should be safe to merge.