Shouldn't this code:

if (exists ($seq_id{$id})) {
        print ">";
        print $seq_id{$fasta_id};
        print "\n".$seq."\n";
    }

[download]

be

if (exists ($seq_id{$id})) {
        print ">";
        print $seq_id{$id};
        print "\n".$seq."\n";
    }

[download]
and

$seq_id{$fasta_id} => $_; be $seq_id{$fasta_id} = $_;

Update: Corrected print $seq_id{$id}; from print $id

In reply to Re^2: renaming 1000's of FASTA files by Cristoforo
in thread renaming 1000's of FASTA files by garyboyd

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