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.\" ========================================================================
.\"
.IX Title "Bio::Tools::Analysis::Protein::GOR4 3pm"
.TH Bio::Tools::Analysis::Protein::GOR4 3pm "2018-10-27" "perl v5.26.2" "User Contributed Perl Documentation"
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.SH "NAME"
Bio::Tools::Analysis::Protein::GOR4 \- a wrapper around GOR4 protein
secondary structure prediction server
.SH "SYNOPSIS"
.IX Header "SYNOPSIS"
.Vb 6
\&  use Bio::Tools::Analysis::Protein::GOR4;
\&  #get a Bio::Seq or Bio::PrimarySeq
\&  use Bio::PrimarySeq;
\&  $seq = Bio::PrimarySeq\->new
\&    (\-seq=>\*(AqIKLCVHHJHJHJHJHJHJHNLAILAKAHLIELALAL\*(Aq,
\&     \-primary_id=>\*(Aqtest\*(Aq); # a Bio::PrimarySeqI object
\&
\&  my $gor4 = Bio::Tools::Analysis::Protein::GOR4\->new (\-seq=>$seq);
\&  $gor4\->run;
\&  print $gor4\->result;# #raw text to standard error
.Ve
.SH "DESCRIPTION"
.IX Header "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 three different states (helix,
coil or sheet), e.g.,
.PP
.Vb 2
\&  my $analysis_object = Bio::Tools::SimpleAnalysis::Protein::GOR4\->
\&      new(\-seq => $seq);
.Ve
.PP
creates a new object
.PP
.Vb 1
\&  $analysis_object\->run;
.Ve
.PP
submits the query to the server and obtains raw text output
.PP
Given an amino acid sequence the results can be obtained in 4 formats,
determined by the argument to the result method
.IP "1." 4
The raw text of the program output
.Sp
.Vb 1
\&  my $rawdata = $analysis_object\->result;
.Ve
.IP "2." 4
An reference to an array of hashes of scores for each state and the
assigned state.
.Sp
.Vb 3
\&  my $data_ref = $analysis_object\->result(\*(Aqparsed\*(Aq);
\&  print "score for helix at residue 2 is $data_ref\->[1]{\*(Aqhelix\*(Aq}\en";
\&  print "predicted struc  at residue 2 is $data_ref\->[1]{\*(Aqstruc}\en";
.Ve
.IP "3." 4
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. See 
Bio::Tools::Analysis::Domcut.pm for examples of how to add sequence
features.
.Sp
.Vb 5
\&  my @fts = $analysis_object\->result(Bio::SeqFeatureI);
\&  for my $ft (@fts) {
\&      print " From ",  $ft\->start, " to  ",$ft\->end, " struc: " ,
\&             ($ft\->each_tag_value(\*(Aqtype\*(Aq))[0]  ,"\en";
\&  }
.Ve
.IP "4." 4
A Bio::Seq::Meta::Array implementing sequence.
.Sp
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
single array of \s-1GOR4\s0 prediction scores.  e.g.,
.Sp
.Vb 3
\&  my $meta_sequence = $analysis_object\->result(\*(Aqall\*(Aq);
\&  print "helix scores from residues 10\-20 are ",
\&      $meta_sequence\->named_submeta_text("GOR4_helix",10,20), "\en";
.Ve
.Sp
Meta sequence names are : GOR4_helix, GOR4_sheet, GOR4_coil,
GOR4_struc, representing the scores for each residue.
.Sp
Many methods common to all analyses are inherited from
Bio::Tools::Analysis::SimpleAnalysisBase.
.SH "SEE ALSO"
.IX Header "SEE ALSO"
Bio::SimpleAnalysisI, 
Bio::Tools::Analysis::SimpleAnalysisBase, 
Bio::Seq::Meta::Array, 
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,
.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 4
\& Name    : result
\& Usage   : $job\->result (...)
\& Returns : a result created by running an analysis
\& Args    : see keys of $RESULT_SPEC
.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"2ary\*(R".  Feature tags are \*(L"type\*(R" (which can be helix, sheet or
coil) \*(L"method\*(R" (\s-1GOR4\s0).
.IP "'parsed'" 3
.IX Item "'parsed'"
Array of hash references of { helix =>, sheet => , coil => , struc=>}.
.IP "'meta'" 3
.IX Item "'meta'"
A Bio::Seq::Meta::Array object. Scores can be accessed using methods
from this class. Meta sequence names are GOR4_helix, GOR4_sheet,
GOR4_coil, GOR4_struc.