[Bioperl-l] blastall problem
cjfields at uiuc.edu
Thu Apr 5 19:32:55 EDT 2007
On Apr 5, 2007, at 4:09 PM, DeeGee wrote:
> Thanks again, Torsten. I tried (die "could not get seq" if not defined
> $queryin;) as you suggested, and now I get the following error
> 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
> your help.
This indicates there is likely some problem with your sequence file
(either it isn't fasta or something else is wrong), but w/o actually
seeing it we can't be sure. I can't be sure but I don't think it is
a next_seq() issue. Also, if there are problems accessing the file
the stream object should throw an error so I don't think it is that
> 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 =>
>> 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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