Concat sequences in the same file, and output BED file with concat regions

[fgvieira]

seqkit concat concatenates sequences with the same ID but, only between files. Also, after concatenating, it is not possible to know the coordinates of the original sequences. Would it be possible to also allow concatenation of sequences in the same file, and to get a (e.g.) BED file with the coordinates?

For example:

$ seqkit concat --all-seqs a.fa b.fa 
>A 1|x|2|x
a1-ax-a2-ax-

And with the the option:

$ seqkit concat --all-seqs --out-bed regions.bed a.fa b.fa 
>A 1|x|2|x
a1-ax-a2-ax-

would also output the file:

$ cat regions.bed
A    0    3   1
A    3    6   x
A    6    9   2
A    9    18   x

[shenwei356]

seqkit concat concatenates sequences with the same ID but, only between files.

Can split records into individual files.

left

It's quite tricky, highly custom operations. Sorry.