[Bioperl-l] blastall problem

DeeGee gdorjee at hotmail.com
Wed Apr 4 14:17:57 EDT 2007


hi all,
can anyone plz help me out with this problem that i've been dealing with for
quite a while now. following is a part of my script that's not working for
some reason. it is suppose to get the sequence from 'result/fasta.faa' and
do the blast.

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

when i paste the protein sequence into the textarea of my html page and save
the same as 'result/fasta.faa', so that the above script would do the blast,
i get the following error: 

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
--------------------------------------
i would appreciate your help.
i would also like to add that the 'result/fasta.faa' has the sequence saved
in it.

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