Feature request: New switches for amplicon & stat?

[photocyte]

Prerequisites

• [x] make sure you're are using the latest version by seqkit version
• [x] read the usage

Describe your issue

• [x] describe the problem
• [x] provide a reproducible example

Hi there, thanks again for creating seqkit, I always find it really useful.

I have two feature requests:

(1) seqkit amplicon having a new switch, where it puts the string of -F and -R into the output FASTA record description

seqkit amplicon -NEWSWITCH -s -F GGCTTGCGCAACATGAAGAA -R GCACGTGAGAAGTGAGGACA example.fasta outputs:

>record_id GGCTTGCGCAACATGAAGAA_and_GCACGTGAGAAGTGAGGACA_amplicon
GGCTTGCGCA...

(2) seqkit stat having a setting, where it puts the seqkit stat results into the output FASTA record description.

seqkit stat -NEWSWITCH example.fasta outputs:

>record_id sum_len=460
GGCTTGCGCA...

[shenwei356]

(1) seqkit amplicon puts the string of -F and -R into the output FASTA record description

It's simple.

(2) seqkit stats puts the seqkit stat results into the output FASTA record description

It's not what stats should do. And it's simple to to:

$ echo -ne ">s\nactg\n"
>s
actg

$ echo -ne ">s\nactg\n" \
    | seqkit fx2tab -l -Q \
    | awk '{print $1" len="$3"\t"$2;}' \
    | seqkit tab2fx 
>s len=4
actg

[photocyte]

For (1), I found that isPcr (https://bioconda.github.io/recipes/ispcr/README.html) could do it. isPcr also reports all the amplicons, rather than just the longest like seqkit amplicon. For my application, I needed an in-silico PCR program that reports all the amplicons, so the (1) feature request is no longer needed.

For (2), I agree, it does seem to be a big change in the output style of seqkit stat . So, I think (2) is no longer needed either. Please close this issue if you agree.