Extract FASTA sequences based on sequence length using Perl

Here are simple Perl scripts to filter out FASTA sequences from a multi-fasta file based on sequence length.

Let’s say our input file consisting of multiple FASTA sequences is ‘input.fasta’.
#!/usr/bin/perl
use strict;
use warnings;
my ($infile, $minlen) = @ARGV;
{
local $/=">";
while(<$infile>) {
chomp;
next unless /\w/;
my @keep = split /\n/;
my $header = shift @keep;
my $seqlen = length join "", @keep;
if($seqlen >= $minlen){
print ">$_";
}
}
local $/="\n";
}
exit;

Save this Perl script as ‘extractfasta.pl‘ and run in the terminal as

$ perl extractfasta.pl input.fasta <minlen> > output.fasta

For example,

$ perl extractfasta.pl input.fasta 100 > output.fasta

If you want to set a maximum length limit as well, then use the following script.
#!/usr/bin/perl
use strict;
use warnings;
my ($infile, $minlen, $maxlen) = @ARGV;
{
local $/=">";
while(<$infile>) {
chomp;
next unless /\w/;
my @keep = split /\n/;
my $header = shift @keep;
my $seqlen = length join "", @keep;
if($seqlen >= $minlen){
print ">$_";
}
}
local $/="\n";
}
exit;

Save this Perl script as ‘extractfasta.pl‘ and run in the terminal as

$ perl extractfasta.pl input.fasta <minlen> <maxlen> > output.fasta

For example,

$ perl extractfasta.pl input.fasta 100 350 > output.fasta