>sequence_5849 CCTGCGGAAGATCGGCACTAGAATAGCCAGAACCGTTTCTCTGAGGCTTCCGGCCTTCCC TCCCACTAATAATTCTGAGG >sequence_5959 CCATCGGTAGCGCATCCTTAGTCCAATTAAGTCCCTATCCAGGCGCTCCGCCGAAGGTCT ATATCCATTTGTCAGCAGACACGC >sequence_0808 CCACCCTCGTGGTATGGCTAGGCATTCAGGAACCGGAGAACGCTTCAGACCAGCCCGGAC TGGGAACCTGCGGGCAGTAGGTGGAAT #### #! /usr/bin/perl use strict; use warnings; use Data::Dumper; use feature qw(say); my $file = 'file.txt'; open (my $fh, '<', $file) or die "Could not open file '$file' $!"; my (%sequence_hash, $header, $seq, $count); while ( my $line = <$fh> ) { chomp($line); if ( $line =~ m/^>(.*)/ ) { if ( $seq ) { say $seq; $sequence_hash{$header} = $seq; } $header = $1; $seq = ''; } else { $seq .= $line; } } close $fh; print Dumper(\%sequence_hash);