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?

  • 3
    $\begingroup$ What have you tried? How many sequences do you have? How are the position of each sequence stored in your multifasta or elsewhere? $\endgroup$
    – llrs
    Nov 15 '17 at 14:47
  • $\begingroup$ Most tools that calculate genome assembly summary stats will report total length. I use assembly-stats $\endgroup$ Nov 15 '17 at 15:06
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

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

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

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)


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