New subcommanbd: fx2gff

[tseemann]

% cat FASTA
>seq1
AGTC
>seq2
AGTCAGTCAGTCAGTC
>seq3
AGTCAGTC

% seqkit fx2gff FASTA

#gff-version 3
##sequence-region seq1 1 4
##sequence-region seq1 1 16
##sequence-region seq3 1 8
##FASTA
>seq1
AGTC
>seq2
AGTCAGTCAGTCAGTC
>seq3
AGTCAGTC

# just the regions
# seqkit fx2tab --only-id --name --length FASTA | sed 's/\t/ 1 /' | sed 's/^/##sequence-region /'`

% seqkit fx2gff --only-regions FASTA

##sequence-region seq1 1 4
##sequence-region seq1 1 16
##sequence-region seq3 1 8

[shenwei356]

Can you tell the use case?

$ (echo '#gff-version 3'; \
    seqkit fx2tab --only-id --name --length FASTA \
        | sed 's/\t/ 1 /' | sed 's/^/##sequence-region /';\
    seqkit seq FASTA)
    
#gff-version 3
##sequence-region seq1 1 4
##sequence-region seq2 1 16
##sequence-region seq3 1 8
>seq1
AGTC
>seq2
AGTCAGTCAGTCAGTC
>seq3
AGTCAGTC

[tseemann]

Yes, that is how i am doing it currently :)

It's for tools creating GFF3 output files.
VCF also has a similar need (different format)

Would be good to have a robust/elegant way to to this easily. But would be nice to do this without the sed piping.

OPtionally output the 3 sections (header, seq-regions, then fasta, with ##FASTAindicator line, each can be turned off.

You currently don't support converting to GFF3 from FASTA, or from FASTA to GFF3.

But I understand your reluctance to add "obscure' features :-)