Migrate to Nextclade v3 #7
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joverlee521
approved these changes
Oct 25, 2024
phylogenetic/defaults/genemap.gff
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| NC_002728.1 RefSeq gene 8943 10751 . + 0 ID=cds-NP_112027.1;Parent=gene-Nvgp5;Dbxref=GenBank:NP_112027.1,GeneID:920955;Name=NP_112027.1;gbkey=CDS;gene=G;locus_tag=Nvgp5;product=attachment glycoprotein;protein_id=NP_112027.1 | ||
| NC_002728.1 RefSeq gene 11412 18146 . + 0 ID=cds-NP_112028.1;Parent=gene-Nvgp6;Dbxref=GenBank:NP_112028.1,GeneID:920950;Name=NP_112028.1;gbkey=CDS;gene=L;locus_tag=Nvgp6;product=polymerase;protein_id=NP_112028.1 | ||
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| NC_002728.1 RefSeq CDS 113 1711 . + 0 ID=cds-NP_112021.1;Dbxref=GenBank:NP_112021.1,GeneID:920951;Name=N;gbkey=CDS;gene=N;locus_tag=Nvgp1;product=nucleocapsid protein;protein_id=NP_112021.1 |
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non-blocking
I was confused by the changes here until I noticed you had updated the issue. Small suggestion to put the reason for changes into the commit message as well.
- use CDS instead of gene
- update Name=... annotations to produce the exact translation files needed by augur ancestral
- drop Parent=gene-Nvgp\d; annotations due to errors about not finding the parent, and since this annotation is not relevant for the output files
Separately, based on Nextclade docs, I might just remove the Name annotation.
Note: For historical reasons, Nextclade uses gene name when it really means CDS name. The “gene name” is taken from the CDS’s first attribute found in the following list: Gene, gene, gene_name, locus_tag, Name, name, Alias, alias, standard_name, old-name, product, gene_synonym, gb-synonym, acronym, gb-acronym, protein_id, ID.
It is recommended that the gene attribute is used to specify the gene/CDS name.
- use CDS instead of gene - drop Name=... annotations to preferentially use gene=... annotations to produce the exact translation files needed by augur ancestral - drop Parent=gene-Nvgp\d; annotations due to errors about not finding the parent, and since this annotation is not relevant for the output files
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Description of proposed changes
This PR directly addresses issue and items listed in #4
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