#!/usr/bin/perl

use strict;
use warnings;

my %sequences;

# read the input files, passing in a filename and
# a reference to the sequences hash
read_file("file1", \%sequences);
read_file("file2", \%sequences);

# write the output file, passing in a filename and
# a reference to the sequences hash
write_file("file3", \%sequences);

sub read_file
{
    my $filename = shift;
    my $seqref = shift;

    open SEQFILE, "<$filename" or die "can't open $filename: $!";

    # use greater-than for record separator
    # see perldoc perlvar
    local $/ = ">";
    while(my $line = <SEQFILE>)
    {
        # the data will match a word, followed by a
        # newline, followed by another word
        # see perldoc perlretut and perlre
        if ($line =~ m/(\w+)\n(\w+)/s)
        {
            # the first word captured is the name
            my $name = $1;
            # the second word captured is the sequence
            my $sequence = $2;
            # add the sequence on to what ever is 
            # already there
            $seqref->{$name} .= $sequence;
        }
    }
    close SEQFILE;
}

sub write_file
{
    my $filename = shift;
    my $seqref = shift;

    open OUTPUT, ">$filename" or die "can't open $filename: $!";

    # write the sequences hash to the output file
    for my $key (sort keys %{$seqref})
    {
        print OUTPUT ">$key\n$seqref->{$key}\n" 
            or die "can't write: $!";
    }
    close OUTPUT or die "can't close $filename: $!";
}

__END__
[download]