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  • #16
    Thank you andrews its getting now..if any problem persists i'll ask you stay in touch...thank you once again

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    • #17
      #!/usr/bin/perl -w

      use strict;
      use Bio::Tools::BPlite;
      use Bio::Tools::Run::StandAloneBlast;
      use Bio:B::SwissProt;

      my $blastfile = '/home/data/problemdata/problem8/ecoli1_ecoliaa.bls';

      my @params = ('database' => 'nr',
      'outfile' => 'blast1.out',
      '_READMETHOD' => 'BPlite',
      'program' => 'blastp');
      my $swissdb= new Bio:B::SwissProt();
      my $blastfactory = new Bio::Tools::Run::StandAloneBlast(@params);
      my $seq = $swissdb->get_Seq_by_acc('KPY1_ECOLI');
      my $report = $blastfactory->blastall($seq);


      #my $report = new Bio::Tools::BPlite(-file => $blastfile);


      print "report is ", $report->query, "\n";
      print "db is ", $report->database, "\n";;
      SUBJECT: while(my $sbjct = $report->nextSbjct) {
      print "subject name is ", $sbjct->name, "\n";

      HSP: while (my $hsp = $sbjct->nextHSP) {
      if( $hsp->P() > 1 ) { next SUBJECT;}
      print "\t score = ", $hsp->score;
      $hsp->bits;
      $hsp->percent;
      print " p value is ", $hsp->P, "\n";
      $hsp->match;
      $hsp->positive;
      $hsp->length;
      $hsp->querySeq;
      $hsp->sbjctSeq;
      $hsp->homologySeq;
      $hsp->query->start;
      $hsp->query->end;
      $hsp->subject->start;
      $hsp->subject->end;
      $hsp->subject->seqname;

      #$hsp->subject->overlaps($exon);
      }
      }


      while i am executing this perl program..in command prompt it is showing the following error...
      C:\Perl\bin>fasta.pl
      Can't locate Bio/Tools/BPlite.pm in @INC (@INC contains: C:/Perl/site/lib C:/Per
      l/lib .) at C:\Perl\bin\fasta.pl line 4.
      BEGIN failed--compilation aborted at C:\Perl\bin\fasta.pl line 4.


      please guide me....

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      • #18
        BPlite is deprecated in the latest BioPerl releases. You should use the SearchIO modules instead now.

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        • #19
          can u list out those modules..please..so that i can solve it...thank you

          Comment


          • #20
            I put a link in the last post. Go look at that and it talks you through how to do this with the SearchIO modules.

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