Provided by: libbio-perl-perl_1.6.901-2_all bug

NAME

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

SYNOPSIS

         use Bio::Tools::Analysis::Protein::Mitoprot;

         use Bio::PrimarySeq;
         my $seq = Bio::PrimarySeq->new
           (-seq=>'IKLCVHHJHJHJHJHJHJHNLAILAKAHLIELALAL',
            -primary_id=>'test'); # a Bio::PrimarySeqI object

         my $mitoprot = Bio::Tools::Analysis::Protein::Mitoprot->new
            ( -seq => $seq
            ); # sequence must be  >!5aa long and start with an M.

         # run Mitoprot prediction on a DNA sequence
         my $mitoprot->run();

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

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

         foreach my $feat ( $mitoprot->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
             $seq->add_SeqFeature($feat);

        }

DESCRIPTION

       This class is a wrapper around the Mitoprot web server which calculates the probability of
       a sequence containing a mitochondrial targetting peptide. See
       http://mips.gsf.de/cgi-bin/proj/medgen/mitofilter for more details.

       The results can be obtained in 3 formats:

       1. The raw text of the program output

            my $rawdata = $analysis_object->result;

       2. An reference to a hash of  scores :

            my $data_ref = $analysis_object->result('parsed'); print "predicted
            export prob is $data_ref->{'export_prob'}\n"; #

          key values of returned hash are input_length, basic_aas, acidic_aas, export_prob,
          charge, cleavage_site.

       3. A Bio::SeqFeature::Generic object

            my $ft = $analysis_object->result(Bio::SeqFeatureI);
            print "export prob is ", ($ft->each_tag_value('export_prob'))[0]  ,"\n";

          This the second implentation 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.

SEE ALSO

       Bio::SimpleAnalysisI, Bio::Tools::Analysis::SimpleAnalysisBase, 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

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

   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 "SigSeq".  Feature tags
          are input_length , basic_aas, acidic_aas, export_prob, charge, cleavage_site, method.

       'parsed'
          hash references of parsed results { input_length =>, basic_aas=>, acidic_aas=>,
          export_prob=>, charge=>, cleavage_site=>}.

perl v5.14.2                                2011-12-2Bio::Tools::Analysis::Protein::Mitoprot(3pm)