Provided by: libbio-perl-perl_1.7.2-2_all bug


       Bio::Tools::Analysis::Protein::NetPhos - a wrapper around NetPhos server


         use Bio::Tools::Analysis::Protein::NetPhos;

         my $seq; # a Bio::PrimarySeqI object
         my $threshold  = "0.90";

         my $netphos = Bio::Tools::Analysis::Protein::NetPhos->new
            ( -seq => $seq,
              -threshold => $threshold );

         # run NetPhos prediction on a sequence
         my $netphos->run();

         # alternatively you can say

         die "Could not get a result" unless $netphos->status =~ /^COMPLETED/;

         print $netphos->result;     # print raw prediction to STDOUT

         foreach my $feat ( $netphos->result('Bio::SeqFeatureI') ) {

             # do something to SeqFeature
             # e.g. print as GFF
             print $feat->gff_string, "\n";
             # or store within the sequence - if it is a Bio::RichSeqI



       This class is wrapper around the NetPhos 2.0 server which produces neural network
       predictions for serine, threonine and tyrosine phosphorylation sites in eukaryotic

       See <>.

       This the first implementation of Bio::SimpleAnalysisI which hopefully will make it easier
       to write wrappers on various services. This class uses a web resource and therefore
       inherits from Bio::WebAgent.


       Bio::SimpleAnalysisI, Bio::WebAgent


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       Richard Adams,, Heikki Lehvaslaiho, heikki-at-bioperl-dot-org


       The rest of the documentation details each of the object methods. Internal methods are
       usually preceded with a _

        Name    : result
        Usage   : $job->result (...)
        Returns : a result created by running an analysis
        Args    : none (but an implementation may choose
                  to add arguments for instructions how to process
                  the raw result)

       The method returns a scalar representing a result of an executed job. If the job was
       terminated by an error the result may contain an error message instead of the real data
       (or both, depending on the implementation).

       This implementation returns differently processed data depending on argument:

          Returns the raw ASCII data stream but without HTML tags

          The argument string defined the type of bioperl objects returned in an array.  The
          objects are Bio::SeqFeature::Generic.

       anything else
          Array of array references of [ position, score, residue].

        Usage   : $job->threshold(...)
        Returns  : The significance threshold of a prediction
        Args     : None (retrieves value) or a value between 0 and 1.
        Purpose  : Get/setter of the threshold to be sumitted for analysis.