[Bioperl-l] How to parse bl2seq report?

[szhan at uoguelph.ca]

Hello, Paulo:
Thank you very much for your help!
I modified the code as your instruction in the below but I got the message 
like this:

------------- EXCEPTION  -------------
MSG:  No hit object found for bl2seq report

STACK Bio::Tools::BPbl2seq::next_feature 
C:/Perl/site/lib/Bio/Tools/BPbl2seq.pm:
231
STACK toplevel pcompare3.pl:100

--------------------------------------

and the loop can't continue. However I put the error-prone code in the eval 
statement then the program can continue and finish looping over. But the some 
pairs of proteins were skipped. Could you fix it for me? I added the eval 
statement like this:
 eval{
	     my $blast_report=$factory->bl2seq($input1, $input2);
 
             # retrieve the outputs from blast_report output file: bl2seq.out
            $blast_report->sbjctName;  
            $blast_report->sbjctLength;
            print 
OUT "Score\tBits\tID_percent\tE_value\tMatch\tPositive\tLength\n";
	    #my $hsp = $blast_report->next_feature; # get one best alignment
	    while(my $hsp = $blast_report->next_feature) {# get all 
alignments         
               print    $hsp->score, "\t";
               print    $hsp->bits, "\t";
               print    $hsp->percent, "\t";         
               print    $hsp->P, "\t";
               print    $hsp->match, "\t";
               print    $hsp->positive, "\t";
               print    $hsp->length, "\n";
	    }
          
          };

          if( $@) {
	     print  "Caught exception\n";
          }
  
Thanks a lot!
Joshua   

Quoting Paulo Almeida <paulo.david at netvisao.pt>:

> Try enclosing the assignment of $blast_report in an 'if':
> 
> if (my $blast_report=$factory->bl2seq($input1, $input2)){
> 	while $blast_report->next_feature{
> 	print hsp->score;
> }
> 
> 
> -Paulo Almeida
> 
> szhan at uoguelph.ca wrote:
> 
> >Hello, Bioperl experts:
> >I want to parse an array of pairwise protein sequences alingments with BLAST
> 
> >bl2seq (standlone) in a loop. When there is no any "subject" (hit) in a
> bl2seq 
> >report, the program halted. Could you please help me catch the error and 
> >continue the loop?
> >Your help will be highly appreciated!
> >
> >The partial code like this:
> >@lucsarr is array of protein sequence objects
> >for(my $k=0; $k<=$#lucsarr; $k++){
> >   for(my $l=$k+1; $l<=$#lucsarr; $l++){
> >      if($k<$l && $l<=$#lucsarr){
> >              
> >            my $input1= $lucsarr[$k]; # take translated protein as an
> object
> >            my $input2= $lucsarr[$l];
> >                
> >            # create local factory object
> >            my $factory = Bio::Tools::Run::StandAloneBlast->new('outfile' 
> >=> 'bl2seq.out');
> >            my $prgm='blastp'; # set parameter p for blastp
> >            $factory->p($prgm);
> >             # call executale bl2seq 
> >             my $blast_report=$factory->bl2seq($input1, $input2);
> > 
> >             # retrieve the outputs from blast_report output file:
> bl2seq.out
> >             $blast_report->sbjctName;  
> >            $blast_report->sbjctLength;
> >            
> >print "Score\tBits\tID_percent\tE_value\tMatch\tPositive\tLength\n";
> >            
             if( $blast_report=$factory->bl2seq($input1, $input2)){
> >            while(my $hsp = $blast_report->next_feature) {# get all 
> >alignments         
> >               print   $hsp->score, "\t";
> >               print   $hsp->bits, "\t";
> >               print   $hsp->percent, "\t";         
> >               print   $hsp->P, "\t";
> >               print   $hsp->match, "\t";
> >               print   $hsp->positive, "\t";
> >               print   $hsp->length, "\n";
> >            }
              }
> >
> >      }
> >   }
> >}
> >
> >The output messages as follows:
> >Score   Bits    ID_percent      E_value Match   Positive        Length
> >Can't call method "nextHSP" on unblessed reference at 
> >C:/Perl/site/lib/Bio/Tools
> >/BPbl2seq.pm line 236, <GEN2> line 36.
> >
> >Again thank you in advance!
> >Joshua
> >
> 
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