NAME

       Bio::Tools::Analysis::Protein::Sopma - a wrapper around the Sopma protein secondary
       structure prediction server

SYNOPSIS

         use Bio::Tools::Analysis::Protein::Sopma;
         #get a Bio::Seq or Bio::PrimarySeq
         my $seq;

         my $sopma = Bio::Tools::Analysis::Protein::Sopma->new
             (-seq=>$seq, states=>4);
         $sopma->run;
         print $sopma->result;# #raw text to standard error

DESCRIPTION

       A module to remotely retrieve predictions of protein secondary structure.  Each residue in
       the protein receives a score representing the likelihood of existing in each of four
       different states (helix, coil, turn or sheet), e.g.,

         my $analysis_object = Bio::Tools::SimpleAnalysis::Protein::Sopma->new
             ( -seq          => $seq,
               -states       => 4,
               -window_width => 15,
             );

       creates a new object.  Compulsory argument -seq.  Optional arguments -states,
       -window_width,-similarity_threshold. These arguments can also be set by direct methods ,
       e.g.,

         $analysis_object->states(4);
         $analysis_object->run;

       submits the query to the server and obtains raw text output. Given an amino acid sequence
       the results can be obtained in 4 formats, determined by the argument to the result method:

       1.  The raw text of the program output.

             my $rawdata = $analysis_object->result;

       2.  A reference to an array of hashes of scores for each state and the assigned state.

             my $data_ref = $analysis_object->result('parsed');
             print "score for helix at residue 2 is $data_ref->[1]{'helix'}\n";
             print "predicted struc  at residue 2 is $data_ref->[1]{'struc}\n";

           Hash keys are 'helix', 'struc', 'sheet', 'coil', 'turn'.

       3.  An array of Bio::SeqFeature::Generic objects where each feature is a predicted unit of
           secondary structure. Only stretches of helix/sheet predictions for longer than 4
           residues are defined as helices/sheets.

             my @fts = $analysis_object->result(Bio::SeqFeatureI);
             for my $ft (@fts) {
                 print " From ",  $ft->start, " to  ",$ft->end, " struc: " ,
                        ($ft->each_tag_value('type'))[0]  ,"\n";
             }

       4.  A Bio::Seq::Meta::Array implementing sequence.

           This is a Bio::Seq object that can also hold data about each residue in the sequence.
           In this case, the sequence can be associated with a arrays of Sopma prediction scores.
           e.g.,

             my $meta_sequence = $analysis_object->result('meta');
             print "scores from residues 10 -20 are ",
                 $meta_sequence->named_submeta_text("Sopma_helix",10,20), "\n";

           Meta sequence names are : Sopma_helix, Sopma_sheet, Sopma_turn, Sopma_coil,
           Sopma_struc, representing the scores for each residue.

           Many methods common to all analyses are inherited from
           Bio::Tools::Analysis::SimpleAnalysisBase.

SEE ALSO

       Bio::SimpleAnalysisI, Bio::Tools::Analysis::SimpleAnalysisBase Bio::Seq::Meta::Array,
       Bio::WebAgent

FEEDBACK

   Mailing Lists
       User feedback is an integral part of the evolution of this and other Bioperl modules. Send
       your comments and suggestions preferably to one of the Bioperl mailing lists.  Your
       participation is much appreciated.

         bioperl-l@bioperl.org                  - General discussion
         http://bioperl.org/wiki/Mailing_lists  - About the mailing lists

   Support
       Please direct usage questions or support issues to the mailing list:

       bioperl-l@bioperl.org

       rather than to the module maintainer directly. Many experienced and reponsive experts will
       be able look at the problem and quickly address it. Please include a thorough description
       of the problem with code and data examples if at all possible.

   Reporting Bugs
       Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their
       resolution.  Bug reports can be submitted via the web:

         https://redmine.open-bio.org/projects/bioperl/

AUTHORS

       Richard Adams, Richard.Adams@ed.ac.uk,

APPENDIX

   similarity_threshold
         Useage  : $job->similarity_threshold(...)
         Returns : The  similarity threshold used in the analysis
         Args    : None (retrieves value) or  an integer (default = 8)
                   that sets the similarity threshold .

       This method gets/sets the  similarity threshold for the prediction.

   window_width
         Usage    : $job->window_width(...)
         Returns  : The window width used in the analysis
         Args     : None (retrieves value) or  an integer (default = 17)
                    that sets the window width.

       This method gets/sets the window width for the prediction, .  If attempted to set longer
       than the sequence, warns of error.

   states
         Usage    : $job->states(...)
         Returns  : The number of secondary structure prediction states
         Args     : None (retrieves value) or either '3' or '4' to set
                    prior to running analysis.

       This method gets/sets the number of states for the prediction, either 3 or 4 (includes
       turns).

   result
         Usage   : $job->result (...)
         Returns : a result created by running an analysis
         Args    : various

       The method returns 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.

       This implementation returns differently processed data depending on argument:

       undef
          Returns the raw ASCII data stream but without HTML tags

       'Bio::SeqFeatureI'
          The argument string defines the type of bioperl objects returned in an array.  The
          objects are Bio::SeqFeature::Generic.  Feature primary tag is "2ary".  Feature tags are
          "type" (which can be helix, sheet coil, or turn if 4 state prediction requested)
          "method" (Sopma)

       'parsed'
          Array of hash references of scores/structure assignations { helix => , sheet => , coil
          => , struc=>}.

       'all'
          A Bio::Seq::Meta::Array object. Scores can be accessed using methods from this class.
          Meta sequence names are Sopma_helix, Sopma_sheet, Sopma_coil, Sopma_turn (if defined),
          and Sopma_struc.