add some function to extract cdna and/or protein sequences.

[xiekunwhy]

Hi,

Hope that seqkit can extract transrcipt/cdna/gene/protein sequences from references fasta and gff/gtf file. gffread can do this but it can not handle large chromosomes correctly.

Best,
Kun

[shenwei356]

Is this what you want ? https://bioinf.shenwei.me/seqkit/usage/#subseq

How about other tools such as bedtools, bedops?

[xiekunwhy]

No exactly, bedtools and bedops also not have function meet gffread (https://github.com/gpertea/gffread, gpertea/gffread#125) exactly. gffio (https://github.com/lh3/gffio) works but output empty file when extract protein sequence using gff and reference sequence.

[shenwei356]

can extract transrcipt/cdna/gene/protein sequences from references fasta and gff/gtf file

Can seqkit subseq do that? It supports GTF files if I remember correctly.