Should I use gffwriter?

[elenimijalis]

I'm sorry if I missed this in the docs, but what is the current accepted way to output a new gff file after you have created and manipulated the db from the old gff file? I see a script called "gffwriter.py", but I don't see anything in the docs. Please let me know if I am missing something.

[daler]

I really need to either update that or remove it! See this answer #37 (comment) for details. The "canonical" way to output a new file is to convert whatever features you want to string, and write them to a file:

with open('out.gff', 'w') as fout:
    for feature in db.all_features():
        fout.write(str(feature) + '\n'))

[elenimijalis]

Thanks so much for the quick reply-- However, what about the file header? For example, using the gff3writer from bcbio-gff, I also get something like this at the beginning of the file:

##gff-version 3
##sequence-region Miro 1 176055

[daler]

Good point, that's a reason to have a gffwriter class. Currently to get the directives in the output file, you need to write them out separately:

with open('out.gff', 'w') as fout:
    for d in db.directives:
        fout.write('## {0}\n'.format(d))
    for feature in db.all_features():
        fout.write(str(feature) + '\n')

[mictadlo]

Hi, I added Note=Gene description but I failed to write it to a new GFF3 file. This question I posted here.

How is it possible to fix it?

Thank you in advance,

Michal