Error while reading GFF file

[mnshgl0110]

#50 (comment)

Thank you very much/ Actually there were an empty line (sorry for the inconveniences).

However, now I get a new error:
track - WARNING - Reading GFF file Dtol_annotation_genes_polished.gff. Overlapping transcripts would be plotted as such without any filtering.
Traceback (most recent call last):
File "/home/bogaerts/miniconda3/bin/plotsr", line 4, in
import('pkg_resources').run_script('plotsr==0.5.3', 'plotsr')
File "/home/bogaerts/miniconda3/lib/python3.9/site-packages/pkg_resources/init.py", line 662, in run_script
self.require(requires)[0].run_script(script_name, ns)
File "/home/bogaerts/miniconda3/lib/python3.9/site-packages/pkg_resources/init.py", line 1466, in run_script
exec(script_code, namespace, namespace)
File "/home/bogaerts/miniconda3/lib/python3.9/site-packages/plotsr-0.5.3-py3.9.egg/EGG-INFO/scripts/plotsr", line 6, in
File "/home/bogaerts/miniconda3/lib/python3.9/site-packages/plotsr-0.5.3-py3.9.egg/plotsr/main.py", line 55, in main
File "/home/bogaerts/miniconda3/lib/python3.9/site-packages/plotsr-0.5.3-py3.9.egg/plotsr/plotsr.py", line 257, in plotsr
File "/home/bogaerts/miniconda3/lib/python3.9/site-packages/plotsr-0.5.3-py3.9.egg/plotsr/func.py", line 729, in readtrack
File "/home/bogaerts/miniconda3/lib/python3.9/site-packages/plotsr-0.5.3-py3.9.egg/plotsr/func.py", line 699, in readdata
File "/home/bogaerts/miniconda3/lib/python3.9/site-packages/plotsr-0.5.3-py3.9.egg/plotsr/func.py", line 688, in _readgff
AttributeError: 'NoneType' object has no attribute 'keys'

Thank you in advance.

@m-bogaerts

[mnshgl0110]

It seems that there is some issue in the formatting of the GFF file. Could you please compare your input GFF with the example GFF. Also, ensure that the transcripts have 'mrna' and 'cds' elements.

[m-bogaerts]

Hello again,

Thank you for your response, however y still have the same issue. I checked the example GFF file and I think it is very similar so I am not sure which could be the issue. I leave here some lines of m GFF file:

chr1 Liftoff exon 15251069 15251169 . - . ID=exon-XR_006747185.1-1;Parent=rna-XR_006747185.1;Dbxref=GeneID:123678035,Genbank:XR_006747185.1;experiment=COORDINATES: polyA evidence [ECO:0006239];gbkey=misc_RNA;gene=LOC123678035;product=protein disulfide-isomerase-like%2C transcript variant X2;transcript_id=XR_006747185.1;extra_copy_number=0
chr1 Liftoff gene 15253501 15258586 . - . ID=gene-LOC123677994;Dbxref=GeneID:123677994;Name=LOC123677994;gbkey=Gene;gene=LOC123677994;gene_biotype=protein_coding;coverage=1.0;sequence_ID=1.0;valid_ORFs=1;extra_copy_number=0;copy_num_ID=gene-LOC123677994_0
chr1 Liftoff mRNA 15253501 15258586 . - . ID=rna-XM_045614755.1;Parent=gene-LOC123677994;Dbxref=GeneID:123677994,Genbank:XM_045614755.1;Name=XM_045614755.1;experiment=COORDINATES: polyA evidence [ECO:0006239];gbkey=mRNA;gene=LOC123677994;model_evidence=Supporting evidence includes similarity to: 14 Proteins%2C 4 long SRA reads%2C and 100%25 coverage of the annotated genomic feature by RNAseq alignments%2C including 51 samples with support for all annotated introns;product=protein disulfide-isomerase A5;transcript_id=XM_045614755.1;matches_ref_protein=True;valid_ORF=True;extra_copy_number=0

Thank you in advance.

[mnshgl0110]

Difficult to say what are the issues with the GFF. I assume you have ensured that genes have mrna and cds elements. Also, remove any empty lines from the GFF.

[asan-emirsaleh]

Hello! I faced the same issue too.

Overlapping transcripts would be plotted as such without any filtering.
Traceback (most recent call last):
  File "/home/asan/miniconda3/envs/syri-env/bin/plotsr", line 6, in <module>
    main(sys.argv[1:])
  File "/home/asan/miniconda3/envs/syri-env/lib/python3.8/site-packages/plotsr/scripts/plotsr.py", line 334, in main
    plotsr(args)
  File "/home/asan/miniconda3/envs/syri-env/lib/python3.8/site-packages/plotsr/scripts/plotsr.py", line 276, in plotsr
    tracks = readtrack(TRACKS, chrlengths)
  File "/home/asan/miniconda3/envs/syri-env/lib/python3.8/site-packages/plotsr/scripts/func.py", line 857, in readtrack
    t.readdata(chrlengths)
  File "/home/asan/miniconda3/envs/syri-env/lib/python3.8/site-packages/plotsr/scripts/func.py", line 827, in readdata
    self._readgff(chrlengths)
  File "/home/asan/miniconda3/envs/syri-env/lib/python3.8/site-packages/plotsr/scripts/func.py", line 816, in _readgff
    k = list(model.keys())[0]
AttributeError: 'NoneType' object has no attribute 'keys'

There is no empty line in the gff.

[novigit]

I also got the same error message @asan-emirsaleh but I was able to resolve it. In my case, the features I was trying to load were rRNA features. Simply replacing the rRNA with mrna resolved the issue for me.

@mnshgl0110 is it possible to allow more featuretypes in future releases?

[mnshgl0110]

@asan-emirsaleh Is your issue resolved?

@novigit Yes, theoretically that is possible. The tricky part is to find time to do that. Nevertheless, it would be great if you could list which feature types would be useful.

[novigit]

I'd say with rRNA, tRNA, exon, mRNA, CDS and gene you'd cover most common featuretypes