use strict;
use Bio::DB::Fasta;

my $db = new Bio::DB::Fasta( "Library.fa" )  # this should be the bigger file
    or die "Failed to create Fasta DB object on Library.fa\n";

open( IDLIST, "Name.fa" );  # this is the list of ID strings
open( IDDATA, ">", "Name-sequences.fa" )
    or die "Error opening Name-sequences.fa for output: $!";

while ( <IDLIST> ) {
    my ($id) = (/^>(\S+)/);  # capture the id string (without the initial ">")
    print IDDATA ">$id\n", $db->seq( $id ), "\n";
}

##</code><code>##

use strict;

my %falib;
my $idstr;

open( LIB, "Library.fa" );
while (<LIB>) {
    chomp;
    if ( /^>(\S+)/ ) {
        $idstr = $1;
    }
    elsif ( /^[acgt]+$/i ) {
        $falib{$idstr} .= uc();  # convert to upper-case
    }
}

open( IDLIST, "Name.fa" );  # this is the list of ID strings
open( IDDATA, ">", "Name-sequences.fa" )
    or die "Error opening Name-sequences.fa for output: $!";

while ( <IDLIST> ) {
    my ($id) = (/^>(\S+)/);  # capture the id string (without the initial ">")
    print IDDATA ">$id\n", $falib{$id}, "\n" if ( exists( $falib{$id} ));
}