Augustus conversion failing

[jorvis]

Augustus conversion failing

[kayDaramola]

Regarding the version of Augustus, the file was generated using braker, the AUGUSTUS version should be augustus-3.2.3, although I have augustus.2.5.5 in my environment.

[jorvis]

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

This is also documented in the conversion script:

https://github.com/jorvis/biocode/blob/master/gff/convert_augustus_to_gff3.py#L9

[kayDaramola]

thanks Jorvis

I would repeat the augustus analysis.

[jorvis]

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 would repeat the augustus analysis. — You are receiving this because you were assigned. Reply to this email directly, view it on GitHub <#51 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AAUMk9-tN6Tz65eXDlFcqqORlS6Nszp0ks5tJmWCgaJpZM4RZrJ6> .

[Kapeel]

Hi, I used the example gtf in the script convert_augustus_to_gff3.py. I get the below error:

convert_augustus_to_gff3.py -i test.gtf -o test.gff3
Traceback (most recent call last):
  File "/Users/kchougul/development/anaconda3/bin/convert_augustus_to_gff3.py", line 189, in <module>
    main()
  File "/Users/kchougul/development/anaconda3/bin/convert_augustus_to_gff3.py", line 91, in main
    gene.print_as(fh=fout, source='AUGUSTUS', format='gff3')
AttributeError: 'NoneType' object has no attribute 'print_as'