Sequence length of fasta sequences with special characters removed

Question

[genomes_and_MGEs]

Hi everyone,

When I want to calculate the sequence length of fasta nucleotide files, I use

awk '/^>/{if (l!="") print l; print; l=0; next}{l+=length($0)}END{print l}' file.fasta

However, my new fasta file has special characters in the nucleotide sequence. Besides the nucleotides A, C, G, and T, my file has the special character 'X'. So, I would like to adapt my code to only count the nucleotides A, C, G, and T, or to exclude the special character 'X' from the count. Can someone help me out?

Thanks!

Answer 1

[Pierre Lindenbaum]

insert {gsub(/[X]/,"");l+=length($0)....

or

sed '/^[^>]/s/X//g' in.fasta | awk...

[genomes_and_MGEs]

Thanks a lot! Both work. In case I have a multi-fasta nucleotide file, and want the sequence length for the whole fasta file, how can I do to prevent outputting the sequence lenght of each fasta sequence?

[cpad0112]

$ sed '/^[^>]/s/X//g' in.fasta | seqkit stats 
$ sed '/^[^>]/s/X//g' in.fasta | grep -v "^>" | tr -d '\n' | wc -c
$ bioawk -c fastx '{gsub("X","",$seq); sum+=length($seq)}END{print sum}' in.fasta