[Bioperl-l] Parsing Blast Output

[AUnderwood@PHLS.org.uk]

Hi Mat and Brian,

Thank you for both your help. Together we're getting there. thanks.

The code that Mat wrote was

      while ( my @rids = $remote_blast_object->each_rid ) {
        foreach my $rid ( @rids ) {
          $rc = $remote_blast_object->retrieve_blast($rid);
          "retrieving results...\n";
          if( !ref($rc) ) {   # $rc not a reference => either error
                              # or job not yet finished
            if( $rc < 0 ) {
              $remote_blast_object->remove_rid($rid);
              print "Error return code for BlastID code $rid ... \n";
            }
            sleep 5;
          } else {
            $remote_blast_object->remove_rid($rid);
            while ( my $sbjct = $rc->nextSbjct ) {
              print "sbjct name is ", $sbjct->name, "\n";
              while ( my $hsp = $sbjct->nextHSP ) {
                print "score is ", $hsp->score, "\n";
              }




This method doesn't seem to work with the BioPerl 1.0 release since it comes
up with this message:


Can't locate object method "database" via package "Bio::SearchIO::blast"
(perhaps you forgot to load "Bio::SearchIO::blast"?) at blast_test4.pl line
34, <GEN14> line 228.

So I never got the problems with the $result and $rc variables and an error
that said
Can't locate object method "next_result" via package "Bio::Tools::BPlite" at
testremoteblast.pl line 32

However from your code I think that I can use methods in the
Bio::Search::HSP::HSPI module (which is the kind of object $hsp is) to
generate the same kind of output as in your script

$hsp->query_string
$hsp->hit_string
$hsp->homology_string.

SO the code I 'm using is
                 print "hit name is ", $hit->name, "\n";
                 while( my $hsp = $hit->next_hsp ) {
                 print "score is ", $hsp->score, "\n";
		 print "evalue is ", $hsp->evalue, "\n";
		 print $input->display_id,"\t\t", $hsp->query_string, "\n";
		 print "\t\t", $hsp->homology_string, "\n";
		 print $hit->description, "\t\t", $hsp->hit_string, "\n";
		 

Has this all changed again with Bioperl 1.01? I seem to understand that from
Brian's message about the next_result as opposed to next_Sbjct. Will this
all change again with 1.1??
My one remaining problem is that
$hsp->query_string/hit_string/homology-string generates very long strings if
there is a long region of homology. Is there a way of formatting these in
blocks of 50?

Thanks again for all your help,

Anthony




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