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.\"
.IX Title "Bio::Tools::Analysis::Protein::NetPhos 3pm"
.TH Bio::Tools::Analysis::Protein::NetPhos 3pm "2018-10-27" "perl v5.26.2" "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::NetPhos \- a wrapper around NetPhos server
.SH "SYNOPSIS"
.IX Header "SYNOPSIS"
.Vb 1
\&  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
\&  $netphos\->seq($seq)\->threshold($threshold)\->run;
\&
\&  die "Could not get a result" unless $netphos\->status =~ /^COMPLETED/;
\&
\&  print $netphos\->result;     # print raw prediction to STDOUT
\&
\&  foreach my $feat ( $netphos\->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 wrapper around the NetPhos 2.0 server which produces
neural network predictions for serine, threonine and tyrosine
phosphorylation sites in eukaryotic proteins.
.PP
See <http://www.cbs.dtu.dk/services/NetPhos/>.
.PP
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.
.SH "SEE ALSO"
.IX Header "SEE ALSO"
Bio::SimpleAnalysisI, 
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://github.com/bioperl/bioperl\-live/issues
.Ve
.SH "AUTHORS"
.IX Header "AUTHORS"
Richard Adams, Richard.Adams@ed.ac.uk, 
Heikki Lehvaslaiho, heikki-at-bioperl-dot-org
.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 6
\& 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)
.Ve
.PP
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).
.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 defined the type of bioperl objects returned in an
array.  The objects are Bio::SeqFeature::Generic.
.IP "anything else" 3
.IX Item "anything else"
Array of array references of [ position, score, residue].
.SS "threshold"
.IX Subsection "threshold"
.Vb 4
\& 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.
.Ve