diff interpro/paso1.pl @ 0:c342ebb50f0b draft default tip

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/interpro/paso1.pl	Thu May 22 05:09:07 2014 -0400
@@ -0,0 +1,77 @@
+#Remote-blast "factory object" creation and blast-parameter initialization
+
+  use Bio::Tools::Run::RemoteBlast;
+  use strict;
+  my $prog = 'blastp';
+  my $db   = 'swissprot';
+  my $e_val= '1e-10';
+my ($input,$output)=@ARGV;
+  my @params = ( '-prog' => $prog,
+         '-data' => $db,
+         '-expect' => $e_val,
+         '-readmethod' => 'SearchIO' );
+
+  my $factory = Bio::Tools::Run::RemoteBlast->new(@params);
+
+  #change a paramter
+#  $Bio::Tools::Run::RemoteBlast::HEADER{'ENTREZ_QUERY'} = 'Homo sapiens [ORGN]';
+
+  #remove a parameter
+ # delete $Bio::Tools::Run::RemoteBlast::HEADER{'FILTER'};
+
+  my $v = 1;
+  #$v is just to turn on and off the messages
+
+  my $str = Bio::SeqIO->new(-file=>$input , '-format' => 'fasta' );
+
+  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.
+    my $r = $factory->submit_blast($input);
+    #my $r = $factory->submit_blast('amino.fa');
+
+    print STDERR "waiting..." if( $v > 0 );
+    while ( my @rids = $factory->each_rid ) {
+      foreach my $rid ( @rids ) {
+        my $rc = $factory->retrieve_blast($rid);
+        if( !ref($rc) ) {
+          if( $rc < 0 ) {
+            $factory->remove_rid($rid);
+          }
+          print STDERR "." if ( $v > 0 );
+          sleep 5;
+        } else {
+          my $result = $rc->next_result();
+          #save the output
+          # my $filename = $result->query_name()."\.out";
+	  my $filename="";
+          $factory->save_output($output);
+          $factory->remove_rid($rid);
+          #print "\nQuery Name: ", $result->query_name(), "\n";
+          #while ( my $hit = $result->next_hit ) {
+          #  next unless ( $v > 0);
+          #  print "\nhit name is ", $hit->name, "\n";
+          #  while( my $hsp = $hit->next_hsp ) {
+          #    print "HSP Len is ", $hsp->length('total'), " ",
+          # " E-value is ", $hsp->evalue, " Bit score ",
+          # $hsp->score, " \t",
+          # " Query loc: ",$hsp->query->start, " ",
+          # $hsp->query->end," ",
+          # " Sbject loc: ",$hsp->hit->start, " ",
+          # $hsp->hit->end,"\n";
+          #  }
+          #}
+        }
+      }
+    }
+  }
+
+  # This example shows how to change a CGI parameter:
+#  $Bio::Tools::Run::RemoteBlast::HEADER{'MATRIX_NAME'} = 'BLOSUM25';
+
+  # And this is how to delete a CGI parameter:
+ # delete $Bio::Tools::Run::RemoteBlast::HEADER{'FILTER'};