Filter Fasta using regexp on header

Question

[sacha]

I would like to filter my fasta file using a regexp on header. For exemple, keep only sequence where size != 0

>A1;size=43
ACGTATATATATATATATAT
>A1;size=21
ACGTATATATATATATATAT
>A1;size=4
ACGTATATATATATATATAT
>A1;size=0
ACGTATATATATATATATAT
>A1;size=14
ACGTATATATATATATATAT

Answer 1

[sacha]

Just found an incredible tools !

https://github.com/bcthomas/pullseq

I do my task with the following command :

pullseq -i test.fasta -g size=[^0]

Answer 2

[Sej Modha]

If the file is not too big and the sequences are saved in a single line stead of folded to a length then you can use the following solution.

grep -A1 --no-group-separator -vFf - file.fa < <(grep  -A1 'size=0' file.fa )

Answer 3

[Matt Shirley]

You can use pyfaidx for this:

$ pip install pyfaidx
$ faidx -g size=[^0] test.fasta

Answer 4

[shenwei356]

Here's the solution of SeqKit, using subcommand grep.

seqkit grep -r -p size=0$ seq.fa

It's ultra fast, explorer more functions of SeqKit