[Bioperl-l] blastall problem

DeeGee gdorjee at hotmail.com
Thu Apr 5 17:09:14 EDT 2007


Thanks again, Torsten. I tried (die "could not get seq" if not defined
$queryin;) as you suggested, and now I get the following error message:

Software error:
could not get seq at /usr/local/apache2/htdocs/remote_ncbi.pl line 50.

Does this mean that next_seq() method in 'my $queryin =
$Seq_in->next_seq();' has some problem? How can I fix it? I would appreciate
your help.
Cheers!





Torsten Seemann wrote:
> 
> DeeGee,
> 
> Please add the following lines to help deduce the problem:
> 
>> my $Seq_in = Bio::SeqIO->new (-file => 'result/fasta.faa', '-format' =>
>> 'Fasta');
> 
> die "could not open fasta" if not defined $Seq_in;
> 
>> my $queryin = $Seq_in->next_seq();
> 
> die "could not get seq" if not defined $queryin;
> 
> Does anything happen now?
> 
> ...
> 
> Some other comments:
> 
>> my $factory = Bio::Tools::Run::StandAloneBlast->new('program'  =>
>> 'blastp',
>> STACK Bio::Tools::Run::StandAloneBlast::blastpgp
> 
> I'm not sure why it is in the blastpgp() method when you chose
> $factory->blastall() ?
> 
>>                                                  _READMETHOD => 'Blast'
> 
> I don't think this is required anymore in modern Bioperl. Are you
> using 1.5.x or bioperl-live ?
> 
>> when i paste the protein sequence into the textarea of my html page and
>> STACK toplevel /usr/local/apache2/htdocs/remote_ncbi.pl:50
> 
> So this is a CGI script?
> Does the script run as user 'apache' or 'httpd', or as yourself via
> SuEXEC?
> Does 'apache' have permissions to READ/WRITE the result/ directory?
> 
> --Torsten
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
> 
> 

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