trusty (3) Bio::Tools::Analysis::Protein::Mitoprot.3pm.gz

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=>}.