Sequin table format

[lskatz]

Hi, I was wondering if there was any way to parse the NCBI Sequin tbl format? It is defined here: https://www.ncbi.nlm.nih.gov/projects/Sequin/table.html

I don't think I see any parser for it but I wanted be sure before writing my own. Thank you!

And the example starts like this.

>Feature Sc_16
1	7000	REFERENCE
			PubMed		8849441
<1	1050	gene
			gene		ATH1
<1	1009	CDS
			product		acid trehalase
			product		Ath1p
			codon_start	2
<1	1050	mRNA
			product		acid trehalase
[offset=2000]
1253	420	gene
			gene	YPR027C
1253	420	CDS
			product		Ypr027cp
			note		hypothetical protein
1253	420	mRNA
			product		Ypr027cp
2626	2535	gene
			gene	trnF
2626	2590	tRNA
2570	2535
			product		tRNA-Phe

[lskatz]

This format is used for Sequin for submitting sequences to genbank, but it has also turned up in the VADR package from NCBI most recently.

[cjfields]

I think there is a Bio::FeatureIO::table but I'm not sure whether that was developed for this particular NCBI format.

[cjfields]

Sorry, was mistaken. We do have a Bio::SeqIO::table but that doesn't mention anything about NCBI's table format. Saying that, it's possibly you could look at the structure for that one to build from.

[hyphaltip]

I would also look at the tools Jon Palmer has developed in @nextgenusfs https://github.com/nextgenusfs/funannotate which is python based but has some parsing of these tables to truncate and cleanup when we need to remove contigs or filter out contam overlapping regions.