[Bioperl-l] remote blast bioperl

[Chris Fields]

Roopa,

We have received all 4+ of your posts.  There is absolutely no need for you to keep repeatedly posting the same thing to the list.  Be patient, we'll try to get to you as soon as we can!

chris

On Jan 25, 2010, at 7:44 AM, Roopa Raghuveer wrote:

> Hello all,
> 
> I have a small problem again. I am working on Remote blast. The program works well. But the problem is this.  The program accesses the server and gets the output correctly. I am trying to send the result sequences into an array and I found that always the first sequence among the Result sequences is missing. The code is
> 
>  my $str = Bio::SeqIO->new('-file' => $nuc , '-format' => 'fasta' , '-organism' => "$organ\[ORGN]");
> - Show quoted text -
> 
> 
> while (my $input = $str->next_seq())
> {
>    #Blast a sequence against a database:
>     #Alternatively, you could  pass in a file with many
>     #sequences rather than loop through sequence one at a time
>     #Remove the loop starting 'while (my $input = $str->next_seq())'
>     #and swap the two lines below for an example of that.
> 
>              open(OUTFILE,'>',$debugfile);
>                print OUTFILE $input;
>               close(OUTFILE);
> 
> 
>    my $r = $factory->submit_blast($input);
> 
>                 open(OUTFILE,'>',$debugfile);
>              #   print OUTFILE $r;
>                 close(OUTFILE);
> 
> 
>    print STDERR "waiting...." if($v>0);
> 
>   while ( my @rids = $factory->each_rid ) {
>       open(OUTFILE,'>',$debugfile);
>             #   print OUTFILE "while entered";
>               close(OUTFILE);
>      foreach my $rid ( @rids ) {
> 
>                open(OUTFILE,'>',$debugfile);
>  #  print OUTFILE "foreach entered";
>               close(OUTFILE);
> 
>         my $rc = $factory->retrieve_blast($rid);
> 
>         if( !ref($rc) )
>         {
>         if( $rc < 0 )
>         {
>         $factory->remove_rid($rid);
>         }
>          open(OUTFILE,'>',$debugfile);
>               # print OUTFILE "if entered";
>               close(OUTFILE);
>          print STDERR "." if ( $v > 0 );
>          sleep 5;
>         }
>        else {
>               open(OUTFILE,'>',$debugfile);
>               # print OUTFILE "else entered";
>               close(OUTFILE);
> 
>           my $result = $rc->next_result();
>          #save the output
>         $blastdebugfile = $serverpath."/blastdebug_".time().".txt";
> 
>           open(BLASTDEBUGFILE,'>',$blastdebugfile);
>           print BLASTDEBUGFILE $result->next_hit();
>           close(BLASTDEBUGFILE);
> 
>         my $filename = $serverpath."/blastdata_".
> time()."\.out";
> 
> 
>          # open(DEBUGFILE,'>',$debugfile);
>          # open(new,'>',$filename);
>          # @arra=<new>;
>          # print DEBUGFILE @arra;
>          # close(DEBUGFILE);
>          # close(new);
> 
>          $factory->save_output($filename);
> 
>        # open(BLASTDEBUGFILE,'>',$debugfile);
>        # print BLASTDEBUGFILE  "Hello $rid";
>        # close(BLASTDEBUGFILE);
> 
>        $factory->remove_rid($rid);
> 
>        open(BLASTDEBUGFILE,'>',$blastdebugfile);
>        print BLASTDEBUGFILE  $organism;
>         close(BLASTDEBUGFILE);
> 
>     # open(OUTFILE,'>',$outfile);
>     # print OUTFILE "Test2 $result->database_name()";
>     # close(OUTFILE);
> 
> #$hit = $result->next_hit;
> #open(new,'>',$debugfile);
> #print $hit;
> #close(new);
> $dummy=0;
> 
>    while ( my $hit = $result->next_hit ) {
> 
>             next unless ( $v >= 0);
> 
>           #     open(OUTFILE,'>',$debugfile);
>            #    print OUTFILE "$hit in while hits";
>             #  close(OUTFILE);
>  my $sequ = $gb->get_Seq_by_version($hit->name);
>            my $dna = $sequ->seq(); # get the sequence as a string
>         $dummy++;
>              open(OUTFILE,'>',$debugfile);
>           #     print OUTFILE $dummy;
>               close(OUTFILE);
>           push(@seqs,$dna);
>          }
>         }
>       }
>     }
>   }
> 
> $warum=@seqs;
>  open(OUTFILE,'>',$debugfile);
>              #  print OUTFILE $warum;
>                print OUTFILE @seqs;
> 
>               close(OUTFILE);
> return(@seqs);
> }
> 
> open(OUTFILE, '>',$outfile) || die ;
> 
> print OUTFILE "<HTML>\n
> <head><title>RNAi Result</title>
> <meta http-equiv=\"expires\" content=\"0\"></head>\n
> <body>\n
> <p><font face=\"Courier, monospace font set\">
> Inputsequence: <br>";
> 
> 
> Here in the above code, I was trying to debug the code and trying to get the count of the array and even the sequence. But when the output data was giving 1 sequence, the count of the array was 0 and when I tried to print the output sequence I could not get any. It was the same when the no of output sequences was  3, I tried to print the sequences but was getting the count of the array as 2 and was printing only two sequences.
> 
> Please help me in sorting out this problem.
> 
> Regards,
> Roopa.