[Bioperl-l] blastall problem
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:
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
Torsten Seemann wrote:
> Please add the following lines to help deduce the problem:
>> my $Seq_in = Bio::SeqIO->new (-file => 'result/fasta.faa', '-format' =>
> 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' =>
>> 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
> Does 'apache' have permissions to READ/WRITE the result/ directory?
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
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