Joshua Orvis

Not sure how I missed this! OK, I see documented header pattern CSV file, but could you give an example of using this? Some example input headers, a csv file,...

Interesting. This section of code first checks to see if the gff3 has a polypeptide line and uses the annotation there, else falls back to the RNA feature, which yours...

Hmm, in the documentation of the convert_augustus_to_gff3.py script it has an example gene block from Augustus. Can you see how yours compares with that structure? Maybe it has been updated....

Thanks for the report - do you think you can attach at least a partial test input file?

Not sure how I missed this, but if you're still interested in doing it could you comment on how yours differs from the existing tool to do this? I think...

I don't use conda but will happily accept a pull request with this added to the README if you're interested in doing it. My only suggestions to change would be...

Good catch. Would you like to submit a pull request for attribution?

Well isn't this ugly. According to the [Genbank flat file spec](https://www.ncbi.nlm.nih.gov/genbank/genomesubmit_annotation/#RNA) for these features: ``` RNA features (rRNA, tRNA, ncRNA) must include a corresponding gene feature with a locus_tag qualifier....

When you ran Augustus, did you tell it to output GFF? By default its output is GTF. The important option is: ``` --gff3=on/off output in gff3 format ``` [Source](http://augustus.gobics.de/binaries/README.TXT) This...

Leaving this open so the script can be modified to support either format from Augustus On Jan 11, 2018 1:48 PM, "Olukayode Daramola" wrote: > thanks Jorvis > > I...