[Bioperl-l] problem with Bio::SeqIO->write_seq

[Jason Stajich]

Well it can't find that seq with the id "$r"  There was a whole discussion
on thie list about this last month.  Pls try out the suggestions related
there.
http://bioperl.org/pipermail/bioperl-l/2003-April/012031.html

On Fri, 2 May 2003, Prachi Shah wrote:

> Hi,
>
> I was playing around with the Bio::Index::Fasta
> module, but got the following error. I index a Fasta
> formatted sequence file and then try to search for
> sequences with the fetch function.
> I copied the code from the documentation of
> Bio::Index::Fasta. The only difference is that the
> example code in the documentation prints to STDIO and
> I wanted it to write to a file. I have a very silly
> mistake. I will really appreciate any help.
>
> thanks,
> Prachi.
>
> ------------- EXCEPTION  -------------
> MSG: Did not provide a valid Bio::PrimarySeqI object
> STACK Bio::SeqIO::fasta::write_seq
> C:/Perl/site/lib/Bio\SeqIO\fasta.pm:166
> STACK toplevel intersectionsequence-cmd.pl:367
>
> --------------------------------------
>
>
> ### snippet of code ###
> my $inx1 = Bio::Index::Fasta->new(
> '-filename' => $Index_File_Name1,
> '-write_flag' => 1);
> my $out = Bio::SeqIO->new('-format' => 'Fasta','-file'
> => ">$clusterfile");
> my $seq = $inx1->fetch($r);
> $out->write_seq($seq);
> ################
>
>
>
>
>
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--
Jason Stajich
Duke University
jason at cgt.mc.duke.edu