Revise truncated pseudo attributes #333
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Bakta and various standard output formats (Genbank, EMBL, GFF3) use slightly different terms and approaches how to declare truncated genes and pseudogenes.
In Bakta, a feature is declared as truncated if there is information from a downstream analysis tool, e.g. Pyrodigal, Infernal, etc.
Besides these, Bakta accepts true pseudogenes from tRNAscan-SE and from its own internal CDS workflow.
To strictly follow INSDC specs, for Genbank, EMBL and GFF3 output files (#330), Bakta now declares all truncated features as
pseudoreflecting technical issues like sequencing and assembly errors on the one side, and truepseudogeneson the other side emerging from biological pseudogenization events like InDels and mutations.Internally, Bakta uses
truncatedandpseudogeneattributes to reflect the different states. In the human readableTSVoutput file (meant for a quick glimpse), Bakta adds feature product prefixes(pseudo),(truncated),(5' truncated)and (3' truncated)`.