Sequence filtration based on length

Question

[Sathish]

Hello Everyone,

I want to filter sequence based on length between 15 - 30 nt from large file of RNA sequences (fasta format).

How to do this?

I appreciate any help.

Thanks

Answer 1

[Alex Reynolds]

Assuming that your sequences are on one line:

​$ awk '{ \
    if ($0 ~ /^>/) { \
        header = $0; \
    } \
    else { \
        l = length($0); \
        if ((l >= 15) && (l <= 30)) { \
            printf("%s\n%s\n", header, $0); \
        } \
    } \
}' foo.fa

Look at this Biostars question if you need to preprocess your FASTA file to put its sequences on one line.

[Sathish]

Thanks for your response. How to get those sequences along their corresponding header?

Input file in .fasta format containing many sequences with different headers.

[Alex Reynolds]

I added some changes. Hope it helps.

[Sathish]

Its working. Thanks a lot.