Is there anything sensible I can do to speed this up?
Stop reading the same file over and over again. Maybe something like this can help you (untested):
#!/usr/bin/perl
use strict;
use warnings;
use Bio::SeqIO;
use Data::Dumper;
my %seq_id;
open HEADER , "<FASTA.headers" or die $!;
while (<HEADER>){
chomp $_;
my $fasta_id = $_;
$fasta_id =~ s/_.*//g ;
$seq_id{$fasta_id} => $_;
}
my $infile = $ARGV[0] || die ("Please give me an input fasta file\n");
my $inseq = new Bio::SeqIO(-format => 'fasta',
-file => $infile);
while (my $seq_obj = $inseq->next_seq ) {
my $id = $seq_obj->id ;
chomp $id;
my $seq = $seq_obj->seq ;
if (exists ($seq_id{$id})) {
print ">";
print $seq_id{$fasta_id};
print "\n".$seq."\n";
}
}