[Bioperl-l] blastall problem

DeeGee gdorjee at hotmail.com
Wed Apr 4 17:44:27 EDT 2007


Thanks for your reply Dave. I don't think that there's anything wrong with
the open(OUTPUT,">result/fasta.faa"); line as I could get the 'fasta.faa'
file with the sequence in it. I see it. It looks like the blast is not being
able to read from the result/fasta.faa. 
^ ^* 




Dave Messina-2 wrote:
> 
> The code snippet worked fine for me. I believe the problem is that  
> 'result/fasta.faa' is not getting passed to your code properly. You  
> might try specifying a complete path to your input and output file --  
> relative paths, especially through a web app, can be tricky.
> 
>> 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'm not sure from what you wrote -- did you try running your script  
> on the command line (having created 'result/fasta.faa' manually  
> first)? If that is working for you, then the problem is with getting  
> the data from the webpage into the script, not with the blasting part.
> 
> Dave
> 
> This is what I did:
> 
>   % ls test.pl testp*
> test.pl       testp.fa
> 
> % formatdb -i testp.fa
> 
> % ls test.pl testp*
> test.pl       testp.fa      testp.fa.phr  testp.fa.pin  testp.fa.psq
> 
> % perl test.pl testp.fa
> %  head -10 out.blast
> BLASTP 2.2.10 [Oct-19-2004]
> 
> 
> Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A.  
> Schaffer,
> Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997),
> "Gapped BLAST and PSI-BLAST: a new generation of protein database search
> programs",  Nucleic Acids Res. 25:3389-3402.
> 
> Query= gi|64654269|gb|AAH96193.1| HOXB1 protein [Homo sapiens]
>           (235 letters)
> 
> 
> Your code: I changed only the input filename and the input database  
> name, and saved the script as test.pl
> -----------------------
> #!/usr/bin/perl
> 
> use strict;
> use warnings;
> use Bio::SeqIO;
> use Bio::Tools::Run::StandAloneBlast;
> 
> my $Seq_in = Bio::SeqIO->new (-file => $ARGV[0], '-format' =>
> 'Fasta');
> my $queryin = $Seq_in->next_seq();
> my $factory = Bio::Tools::Run::StandAloneBlast->new('program'  =>  
> 'blastp',
>                                                   'database' =>
> 'testp.fa',
>                                                   _READMETHOD => 'Blast'
>                                                    );
> $factory->outfile("out.blast");
> my $blastreport = $factory->blastall($queryin);
> ------------------------------------------------------------------------ 
> -----------
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> 
> 

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