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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"; } }

In reply to Re: renaming 1000's of FASTA files by moritz
in thread renaming 1000's of FASTA files by garyboyd

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