Often, one wants to calculate the sequence length from a FASTA file.

Example

Say you have a FASTA file called my_sequence.fasta:

>my_sequence
ATCGATCGATCG

Here, you’d like to compute “12” as the length of the ATCGATCGATCG sequence.

One-liner

To achieve this on a bigger FASTA file, run this code in your Shell:

awk '/^>/ {print; next; } { seqlen = length($0); print seqlen}' my_sequences.fasta

This will return results to the stdout (your screen):

12

You can execute this code on a multi-line FASTA file.

FASTQ to FASTA

If needed, first convert your FASTQ to FASTA with seqtk.

seqtk seq -a in.fq.gz > out.fa