Hello,

i think this is not good :

push (@fasta, $seq);
push @fasta, "> COULDN'T FIND IT" unless defined $seq;
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It will push $seq even if it's not defined.
Use a full if/else statement :

if (defined $seq) { push @fasta, $seq }
else { push @fasta, "> COULDN'T FIND IT" }
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Or you can use the short A?B:C construct which does the same thing :

defined $seq ? push @fasta, $seq : push @fasta, "> COULDN'T FIND IT" ;
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As a note i think the declaration for $seq should be up there with the other my variables. And also $o is not a very good name :)

Hope this helps,
ZlR.