Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

attribute formats broken across several lines #68

Closed
LornaMGnify opened this issue Aug 23, 2021 · 2 comments
Closed

attribute formats broken across several lines #68

LornaMGnify opened this issue Aug 23, 2021 · 2 comments

Comments

@LornaMGnify
Copy link

Hello! Thanks for the great tool.
I am trying to include some tRNA annotations in my embl file. Here is how they are formatted in the gff (with the anticodon specification matching the format as described in the webfeatures of INSDC).

##gff-version 3
NODE_1_length_526174_cov_7.912666 tRNAScan-SE gene 489860 489943 73.2 - . ID=tRNA-Leu1_gene
NODE_1_length_526174_cov_7.912666 tRNAScan-SE tRNA 489860 489943 73.2 - . ID=tRNA-Leu1_tRNA;product=tRNA-Leu;anticodon=(pos:489860..489943,aa:Leu,seq:CAA);Parent=tRNA-Leu1_gene

However, after I run emblmygff3, the anticodon attributes get broken across several lines, (seemingly due to the commas?) and so fail the validation. Is there a way to maintain the format of the anticodon descriptions here?

134328 FT gene complement(489860..489943)
134329 FT /locus_tag="PBET_LOCUS64"
134330 FT /note="source:tRNAScan-SE"
134331 FT /note="ID:tRNA-Leu1_gene"
134332 FT tRNA complement(489860..489943)
134333 FT /locus_tag="PBET_LOCUS64"
134334 FT /note="source:tRNAScan-SE"
134335 FT /note="ID:tRNA-Leu1_tRNA"
134336 FT /anticodon="(pos:489860..489943"
134337 FT /anticodon="aa:Leu"
134338 FT /anticodon="seq:CAA)"
134339 FT /product="tRNA-Leu"

@Juke34
Copy link
Collaborator

Juke34 commented Aug 23, 2021

IN GFF3 an attribute can have several values separated by coma, so (pos:489860..489943,aa:Leu,seq:CAA)is seen as 3 values. You must quote it to be seen as one single value.

@LornaMGnify
Copy link
Author

I knew it would be something simple. Thank you so much for your help!

@Juke34 Juke34 closed this as completed Aug 24, 2021
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
None yet
Projects
None yet
Development

No branches or pull requests

2 participants