Is there a way to get the annotate outputs in a genbank format file?

[liliancaesarbio]

Hello,

Some tools require a gff or genbank file as input for synteny analysis, such as clinker. Is there a If there a way to obtain these file formats from the outputs of $ genomad annotate? If not, do you recommend any script or program to convert the outputs to these formats?

Thank you very much!

[apcamargo]

I wrote a script a while ago to convert the output of genomad annotate to a GFF. Let me know if it works for you.

[liliancaesarbio]

I had this error:

$ python convert_tabular_to_gff.py virus_genes.tsv genes.gff File "convert_tabular_togff.py", line 40 fout.write(f"{row.gene.rsplit('', 1)[0]}\t") ^ SyntaxError: invalid syntax

[apcamargo]

That's probably because the script expects you to execute it as ./convert_tabular_to_gff.py and not python convert_tabular_to_gff.py. Can you try again running ./convert_tabular_to_gff.py virus_genes.tsv genes.gff?

[liliancaesarbio]

I tried as you suggest, but still give me the same error.

[apcamargo]

That's strange. I just executed it here and it worked as expected. Maybe it is being caused by the copy-and-paste process? Try to download from the link below and run it again. convert_tabular_to_gff.py.zip

[apcamargo]

Another possibility: maybe python links to python2 in your system. Try to replace the first line with:

#!/usr/bin/env python3

This will guarantee that the script is executed with Python 3.

[liliancaesarbio]

It was exactly this, now I loaded the right python and it ran perfectly. Thank you very much!

[apcamargo]

No worries! Sorry that this was more complicated than it should be.

I'll leave this issue open and consider adding GFF outputs to a future release of geNomad.

[liliancaesarbio]

Thank you, this would be very useful, also an .gbk output would be great!