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Missing features in GFF3 data
Hello,
I have a gff3 file with the following limits:
I am using the following to limit to the features of interest:
limit_info=dict(
gff_source_type=[
('ena', 'transcript'), ('ena', 'CDS'), ('ena', 'gene'), ('ena', 'exon'),
('ena', 'tRNA_gene'), ('ena', 'ncRNA_gene'), ('ena', 'rRNA_gene'),
('ena', 'pseudogene')
],
gff_source=['ena']
)
However, I am having trouble retrieving data about the transcripts and CDS when parsing and looking for feature.type == 'transcript'
or feature.type == 'CDS'
in rec.features
. It is as if these are not being captured.
What's interesting is that, when the limit_info
dict is reduced to ('ena', 'transcript')
or ('ena', 'CDS')
, I do retrieve this data.
What might be the issue here?