hotdogee / gff3-py Goto Github PK

Nice features, validation is good too.

Is there an option planned to be able to create correct CDS features
-where they go beyond exon features
-or if no CDS exist, create CDS features for every exon in the GFF3.

These would be useful.
Thanks, Colin

Phase was checked successfully in many of the features in a current GFF3, but are incorrect phases corrected?

Thanks.

Hi there,
I just discovered your nice gff3 tool during my search for a tool adding the phase to the CDS's in a gff file ( (phases are missing for all CDS, I have the corresponding genomic.fa from an insect). However, I have troubles with checking the phase of the CDS as it throws an error about unknown format code. Do you have any idea how to mitigate this? Any help would be greatly appreciated!

my command
python /opt/scripts/gff_fix.py --gff_file edit.1.0.annotations.formatted.gff --fasta_file Edil.fa --allowed_num_of_n 0 --check_n_feature_types CDS --report_file Edil.1.0.gff.validation_report.txt

output:
INFO Checking GFF3 file (edit.1.0.annotations.formatted.gff)...
INFO Checking syntax and formatting...
INFO Checking reference seqid, bounds and N count...
INFO Checking parent boundaries...
Traceback (most recent call last):
File "/opt/scripts/gff_fix.py", line 139, in
gff3.check_phase()
File "/usr/local/lib/python2.7/dist-packages/gff3/gff3.py", line 213, in check_phase
self.add_line_error(line, {'message': 'Wrong phase {0:d}, should be {1:d}'.format(line['phase'], phase), 'error_type': 'PHASE'})
ValueError: Unknown format code 'd' for object of type 'str'

when trying to use .parse on a normal gff file under Python 3.5 I get this:

gff.parse(gff_file)
---------------------------------------------------------------------------
TypeError                                 Traceback (most recent call last)
<ipython-input-6-3986eab23c03> in <module>()
----> 1 gff.parse(gff_file)

/home/ilya/miniconda2/envs/stdsci/lib/python3.5/site-packages/gff3/gff3.py in parse(self, gff_file, strict)
    441             if line_strip != line_raw[:len(line_strip)]:
    442                 self.add_line_error(line_data, {'message': 'White chars not allowed at the start of a line', 'error_type': 'FORMAT', 'location': ''})
--> 443             if current_line_num == 1 and not line_strip.startswith('##gff-version'):
    444                 self.add_line_error(line_data, {'message': '"##gff-version" missing from the first line', 'error_type': 'FORMAT', 'location': ''})
    445             if len(line_strip) == 0:

TypeError: startswith first arg must be bytes or a tuple of bytes, not str

On Ubuntu there's a problem with installation

$ sudo pip3 install gff3==1.0.0
Collecting gff3==1.0.0
ERROR: Could not find a version that satisfies the requirement gff3==1.0.0 (from versions: 1.0.0.macosx-10.14-x86_64, 0.1.0, 0.2.0, 0.3.0)