Fetch FASTA records by sequence

fetch_by_seq.pl

#!/usr/bin/env perl

use strict;
use warnings;
use File::Basename;

my $usage   = "perl ".basename($0)." seqsi.fas seqsj.fas > seqs_out.fas";
my $infilei = shift or die $usage;
my $infilej = shift or die $usage;

my %hash;
open my $ini, '<', $infilei or die $!;
while (my ($id, $seq) = fasta_it(\*$ini)) {
    $hash{$seq} = $id;
}
close $ini;

open my $inj, '<', $infilej or die $!;
while (my ($id, $seq) = fasta_it(\*$inj)) {
    if (exists $hash{$seq}) {
	print join "\n", ">".$hash{$seq}, "$seq\n";
    }
}
close $inj;

sub fasta_it {
    my ($fh) = @_;
    
    local $/ = "\n>";
    return unless my $entry = $fh->getline;
    chomp $entry;

    my ($id, $seq) = split /\n/, $entry, 2;
    defined $id && $id =~ s/>//g;
    return ($id, $seq);
}