How to find the sum of all sequences in a multifasta file

Question

I have a multifasta file containing several genes from a genomic island. I want to know the total length of this island. How can I do this?

Answer 1

grep -v ">" multi.fasta | tr -d '\n' | wc -c

• grep -v ">" find all non header lines (i.e. without ">")
• tr -d '\n' delete all newlines
• wc -c count all characters

Answer 2

Here’s a function that I keep around for calculating the individual lengths of fasta sequences

falens(){
awk '/^>/ {if (seqlen){print seqlen}; print ;seqlen=0;next; } { seqlen += length($0)}END{print seqlen}' $1
}

And one I use for summing a column of numbers

sum(){
awk '{ sum += $1 } END { print sum}'
}

You can combine these by piping the output to do the sum for you:

falens myseqs.fa | grep -v “>” | awk '{ sum += $1 } END { print sum}'

(Can’t test this myself currently as I’m not at my laptop, but it’s based on 2 functions that work normally)