[Bioperl-l] blastall problem

DeeGee gdorjee at hotmail.com
Wed Apr 4 20:59:08 EDT 2007


hi Torsten,
Yes, it still gives me the same error even if I give the full path to the
fasta file. Following is how I did: 

####### part of my script #######
my $Seq_in = Bio::SeqIO->new (-file =>
'/export/home/local/apache2/htdocs/result/fasta.faa', -format => 'Fasta');
my $queryin = $Seq_in->next_seq();
my $factory = Bio::Tools::Run::StandAloneBlast->new('program'  => 'blastp',
                                                 'database' =>
'/export/home/dorjee/database/nrpart',
                                                 _READMETHOD => 'Blast'
                                                   );
$factory->outfile("/export/home/local/apache2/htdocs/result/out.blast");
my $blastreport = $factory->blastall($queryin);
....

thanks man.



Torsten Seemann wrote:
> 
>> Software error:
>> ------------- EXCEPTION  -------------
>> MSG:    not Bio::Seq object or array of Bio::Seq objects or file name!
>> STACK Bio::Tools::Run::StandAloneBlast::blastpgp
>> /usr/perl5/5.6.1/lib/Bio/Tools/Run/StandAloneBlast.pm:611
>> STACK toplevel /usr/local/apache2/htdocs/remote_ncbi.pl:50
> 
>> my $Seq_in = Bio::SeqIO->new (-file => 'result/fasta.faa', '-format' =>
>> 'Fasta');
> 
> Does this still happen if you give the full path to the FASTA file?
> eg. -file => /usr/local/apache2/htdocs/result/fasta.faa
> (I'm guessing what the full path is here)
> 
> --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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