The script puts all the lines from the .txt file in a hash

It just keeps creating a new 1 element hash

%seq_id = ("$fasta_id" => "$_");

you would need to say instead
$seq_id{ $fasta_id } = $_;

However, moritz has shown the better solution (instead of reopening the file over and over).

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

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