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Sequence length of fasta sequences with special characters removed

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!

sequence
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updated by cpad0112 cpad0112 • written by genomes_and_MGEs • genomes_and_MGEs

1 answer

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

or

sed '/^[^>]/s/X//g' in.fasta | awk...
• 0 views • link
written by Pierre Lindenbaum Pierre Lindenbaum

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?

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written by genomes_and_MGEs • genomes_and_MGEs 
$ 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
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written by cpad0112 cpad0112

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