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tseemann / prokka

:zap: :aquarius: Rapid prokaryotic genome annotation
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no /pseudo gene in prokka-genbank_to_fasta_db #336

Open AlcaArctica opened 6 years ago

AlcaArctica commented 6 years ago

I am unable to build a database that contains /pseudo genes, although the prokka-genbank_to_fasta_db function has a pseudo gene option --pseudo! Include /pseudo

I am calling prokka-genbank_to_fasta_db --pseudo genome1.gbk genome1.gbk > proteins.faa

Both input genomes contain /pseudo genes. The resulting database works fine for annotating with prokka, however annotation does not include pseudo genes. Am I overlooking something obvious? Thanks for any hint!

tseemann commented 6 years ago

My script only works on CDS features.

I assume you are using a Genbank file from NCBI ?

Unfortunately NCBI do not generate CDS features for pseudo genes - it only produces a 'gene' feature and it is not guaranteed to be on a codon boundary etc

ie. every real gene has a gene AND a CDS. pseudogenes only have gene.

tseemann commented 6 years ago

I might be able to change the behaviour, i'll leave this issue open.

AlcaArctica commented 6 years ago

I see. Yes, I am using Genbank files from NCBI. Thanks for the quick response and explanation!