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.\"
.IX Title "Bio::Tools::Analysis::Protein::Mitoprot 3pm"
.TH Bio::Tools::Analysis::Protein::Mitoprot 3pm "2012-03-02" "perl v5.14.2" "User Contributed Perl Documentation"
.\" For nroff, turn off justification.  Always turn off hyphenation; it makes
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.SH "NAME"
Bio::Tools::Analysis::Protein::Mitoprot \- a wrapper around Mitoprot
server
.SH "SYNOPSIS"
.IX Header "SYNOPSIS"
.Vb 1
\&  use Bio::Tools::Analysis::Protein::Mitoprot;
\&
\&  use Bio::PrimarySeq;
\&  my $seq = Bio::PrimarySeq\->new
\&    (\-seq=>\*(AqIKLCVHHJHJHJHJHJHJHNLAILAKAHLIELALAL\*(Aq,
\&     \-primary_id=>\*(Aqtest\*(Aq); # 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(\*(AqBio::SeqFeatureI\*(Aq) ) {
\&
\&      # do something to SeqFeature
\&      # e.g. print as GFF
\&      print $feat\->gff_string, "\en";
\&      # or store within the sequence \- if it is a Bio::RichSeqI
\&      $seq\->add_SeqFeature($feat);
\&
\& }
.Ve
.SH "DESCRIPTION"
.IX Header "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.
.PP
The results can be obtained in 3 formats:
.IP "1." 3
The raw text of the program output
.Sp
.Vb 1
\&  my $rawdata = $analysis_object\->result;
.Ve
.IP "2." 3
An reference to a hash of  scores :
.Sp
.Vb 2
\&  my $data_ref = $analysis_object\->result(\*(Aqparsed\*(Aq); print "predicted
\&  export prob is $data_ref\->{\*(Aqexport_prob\*(Aq}\en"; #
.Ve
.Sp
key values of returned hash are input_length, basic_aas, acidic_aas,
export_prob, charge, cleavage_site.
.IP "3." 3
A Bio::SeqFeature::Generic object
.Sp
.Vb 2
\&  my $ft = $analysis_object\->result(Bio::SeqFeatureI);
\&  print "export prob is ", ($ft\->each_tag_value(\*(Aqexport_prob\*(Aq))[0]  ,"\en";
.Ve
.Sp
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.
.SH "SEE ALSO"
.IX Header "SEE ALSO"
Bio::SimpleAnalysisI,
Bio::Tools::Analysis::SimpleAnalysisBase,
Bio::WebAgent
.SH "FEEDBACK"
.IX Header "FEEDBACK"
.SS "Mailing Lists"
.IX Subsection "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.
.PP
.Vb 2
\&  bioperl\-l@bioperl.org                  \- General discussion
\&  http://bioperl.org/wiki/Mailing_lists  \- About the mailing lists
.Ve
.SS "Support"
.IX Subsection "Support"
Please direct usage questions or support issues to the mailing list:
.PP
\&\fIbioperl\-l@bioperl.org\fR
.PP
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.
.SS "Reporting Bugs"
.IX Subsection "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:
.PP
.Vb 1
\&  https://redmine.open\-bio.org/projects/bioperl/
.Ve
.SH "AUTHORS"
.IX Header "AUTHORS"
Richard Adams, Richard.Adams@ed.ac.uk,
.SH "APPENDIX"
.IX Header "APPENDIX"
The rest of the documentation details each of the object
methods. Internal methods are usually preceded with a _
.SS "result"
.IX Subsection "result"
.Vb 3
\& Usage   : $job\->result (...)
\& Returns : a result created by running an analysis
\& Args    : various
.Ve
.PP
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.
.PP
This implementation returns differently processed data depending on
argument:
.IP "undef" 3
.IX Item "undef"
Returns the raw \s-1ASCII\s0 data stream but without \s-1HTML\s0 tags
.IP "'Bio::SeqFeatureI'" 3
.IX Item "'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 \*(L"SigSeq\*(R".  Feature tags are input_length , basic_aas,
acidic_aas, export_prob, charge, cleavage_site, method.
.IP "'parsed'" 3
.IX Item "'parsed'"
hash references of parsed results { input_length =>, basic_aas=>,
acidic_aas=>, export_prob=>, charge=>, cleavage_site=>}.