[Bioperl-l] Need some help with : Error "Use of uninitialized value"

Bradyjoel joel.klein at wur.nl
Sun Apr 8 19:35:18 EDT 2012


Hi all,

I have little experiences in programming with Perl/Bioperl. I'm currently
working on a script that takes a whole genome from a bacteria as input,
converts it into a multiple fasta file containing all the open reading
frames and blast it against a multiple protein fasta file with know
proteins. When I get a hit I want to combine the header of the known protein
with the orf sequence, here it gives an error when I try to go through the
orf file and extract the right corresponding sequence. The error it gives is
: Use of uninitialized value $seq in print at blastscript.pl line .. 
Is there someone who has an idea what caused this error, and can help me
with solving it?

Regards, Joel (I put my script in the attachment) 
http://old.nabble.com/file/p33653318/blastscript.pl blastscript.pl 
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