Please read this documentation to help you learn:
perlfunc,
perlretut,
perlreftut,
perlre.
#!/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__