Comments (4)
It works fine for me on v0.3.2 and master, after copying the contents to a file. Could you upload the actual problematic file somewhere?
from genomicannotations.jl.
Thanks for such a quick response. Sorry, I updated my version of GenomicAnnotations and it reads the file now. However, there's still a problem when trying to access genes
. I think it's some issue with printing to stdout. For instance,
plasmid = readgbk("file.gb")[1]
plasmid.genes
will run indefinitely and not return anything, but
for gene in pAC03.genes
@show "$(plasmid.name)_$(gene.locus_tag)"
end
will return almost immediately. Similarly,
@genes(plasmid, ismissing(:gene))
will get stuck but
@genes(plasmid, ismissing(:gene)) |> length
works. Hopefully, you're able to replicate this behavior.
EDIT:
for gene in pAC03.genes
@show gene
end
gets stuck at
gene = primer 4277..4298
/label="oLAC18"
/note="sequence: AGGAcaagagacaggatactag"
/ApEinfo_revcolor="#faac61"
/ApEinfo_fwdcolor="#faac61"
Is there something wrong with the format of the .gb
file at or after this primer annotation?
from genomicannotations.jl.
/note="product: photostable monomeric orange derivative of DsRed fluorescent protein (Shaner et al., 2008) note: mammalian codon-optimized translation: MVSKGEENNMAIIKEFMRFKVRMEGSVNGHEFEIEGEGEGRPYEGFQTAKLKVTKGGPLPFAWDILSPHFTYGSKAYVKHPADIPDYFKLSFPEGFKWERVMNYEDGGVVTVTQDSSLQDGEFIYKVKLRGTNFPSDGPVMQKKTMGWEASSERMYPEDGALKGKIKMRLKLKDGGHYTSEVKTTYKAKKPVQLPGAYIVDIKLDITSHNEDYTIVEQYERAEGRHSTGGMDELYK"
This long line was causing problems with the printing. I've included a fix in v0.3.3 and registered it, until it is merged you can use the master branch. Thanks for the help!
from genomicannotations.jl.
Thanks for such quick responses. Really appreciate your work in this package
from genomicannotations.jl.
Related Issues (9)
- Error tagging new release
- Having location field in genes HOT 3
- [Feature Request] Support for GTF format! HOT 1
- Error tagging new release
- TagBot trigger issue HOT 14
- Error when loading genebank file from NCBI HOT 2
- GzipDecompressorStream not defined HOT 2
- Can GenomicAnnotations.jl deal with multi-exon genes? HOT 2
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from genomicannotations.jl.