Skip to content

Commit

Permalink
change gene=* to gene_name=* in hku1/genemap.gff #2
Browse files Browse the repository at this point in the history
Initially, the workflow failed with the following error:

```
Error:
   0: When reading genome annotation
   1: When reading file: "config/hku1/genemap.gff"
   2: Attempted to parse the genome annotation as JSON and as GFF, but both attempts failed:
      JSON error: invalid type: string "NC_006577.2\tfeature\tsource\t1\t29926\t.\t+\t.\tgene=nuc NC_006577.2\tfeature\tgene\t206\t13600
\t.\t+\t.\tgene=ORF1a NC_006577.2\tfeature\tgene\t13600\t21753\t.\t+\t.\tgene=ORF1b NC_006577.2\tfeature\tgene\t21773\t22933\t.\t+\t.\tg
ene=HE NC_006577.2\tfeature\tgene\t22942\t27012\t.\t+\t.\tgene=Spike NC_006577.2\tfeature\tgene\t22978\t25221\t.\t+\t.\tgene=S1 NC_00657
7.2\tfeature\tgene\t27051\t27380\t.\t+\t.\tgene=S2 NC_006577.2\tfeature\tgene\t27051\t27380\t.\t+\t.\tgene=ORF4 NC_006577.2\tfeature\tge
ne\t27373\t27621\t.\t+\t.\tgene=E NC_006577.2\tfeature\tgene\t27633\t28304\t.\t+\t.\tgene=M NC_006577.2\tfeature\tgene\t28320\t29645\t.\
t+\t.\tgene=N NC_006577.2\tfeature\tgene\t28342\t28959\t.\t+\t.\tgene=N2", expected struct GeneMap at line 2 column 1

      GFF3 error: When processing gene, 'N': When processing feature group 'N' ('N') of type 'gene': genes must consist of exactly one f
eature: Expected exactly one element, but found: 2
   2:

Location:
   /workdir/packages/nextclade/src/gene/gene_map.rs:56
```

While looking at the referenced file, and comparing it to the other
`genemap.gff` files in the config, I noticed that all the others used
`gene_name` for everything after the first `gene` line. I changed this
file to match, and the workflow got past the point where it was
previously erroring out.

I have no idea why this worked; hopefully somebody will explain in the
code review.
  • Loading branch information
genehack committed May 14, 2024
1 parent e7fa734 commit 4eeffd8
Showing 1 changed file with 11 additions and 11 deletions.
22 changes: 11 additions & 11 deletions phylogenetic/config/hku1/genemap.gff
Original file line number Diff line number Diff line change
@@ -1,13 +1,13 @@
##sequence-region NC_006577.2 1 29926
NC_006577.2 feature source 1 29926 . + . gene=nuc
NC_006577.2 feature gene 206 13600 . + . gene=ORF1a
NC_006577.2 feature gene 13600 21753 . + . gene=ORF1b
NC_006577.2 feature gene 21773 22933 . + . gene=HE
NC_006577.2 feature gene 22942 27012 . + . gene=Spike
NC_006577.2 feature gene 22978 25221 . + . gene=S1
NC_006577.2 feature gene 27051 27380 . + . gene=S2
NC_006577.2 feature gene 27051 27380 . + . gene=ORF4
NC_006577.2 feature gene 27373 27621 . + . gene=E
NC_006577.2 feature gene 27633 28304 . + . gene=M
NC_006577.2 feature gene 28320 29645 . + . gene=N
NC_006577.2 feature gene 28342 28959 . + . gene=N2
NC_006577.2 feature gene 206 13600 . + . gene_name=ORF1a
NC_006577.2 feature gene 13600 21753 . + . gene_name=ORF1b
NC_006577.2 feature gene 21773 22933 . + . gene_name=HE
NC_006577.2 feature gene 22942 27012 . + . gene_name=Spike
NC_006577.2 feature gene 22978 25221 . + . gene_name=S1
NC_006577.2 feature gene 27051 27380 . + . gene_name=S2
NC_006577.2 feature gene 27051 27380 . + . gene_name=ORF4
NC_006577.2 feature gene 27373 27621 . + . gene_name=E
NC_006577.2 feature gene 27633 28304 . + . gene_name=M
NC_006577.2 feature gene 28320 29645 . + . gene_name=N
NC_006577.2 feature gene 28342 28959 . + . gene_name=N2

0 comments on commit 4eeffd8

Please sign in to comment.