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.\"
.IX Title "Bio::Tools::Analysis::Protein::Domcut 3pm"
.TH Bio::Tools::Analysis::Protein::Domcut 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::Domcut \-  a wrapper around Domcut server
.SH "SYNOPSIS"
.IX Header "SYNOPSIS"
.Vb 6
\&  use   Bio::Tools::Analysis::Protein::Domcut;
\&  #get a  Bio::PrimarySeq
\&  use Bio::PrimarySeq;
\&  my $seq = Bio::PrimarySeq\->new
\&     (\-seq=>\*(AqIKLCVNLAILAKAHLIELALAL\*(Aq,
\&     \-primary_id=>\*(Aqtest\*(Aq); # a Bio::PrimarySeqI object
\&
\&  my $domcut = Bio::Tools::Analysis::Protein::Domcut\->new (\-seq=>$seq);
\&  $domcut\->run;
\&  print $domcut\->result;# #raw text to standard out
.Ve
.SH "DESCRIPTION"
.IX Header "DESCRIPTION"
A module to remotely retrieve predictions of protein domain
boundaries.  Each residue in the protein receives a score, those
better than the significance threshold and at a local minimum receive
a rank \- i.e., the best minimum is rank 1, the second best minimum is
rank2 etc. These correspond to domain boundaries.  e.g.,
.PP
.Vb 2
\&  my $analysis_object = Bio::Tools::Analysis::Protein::Domcut\->new
\&     (\-seq => $seq);
.Ve
.PP
creates a new object. The sequence supplied must be a Bio::PrimarySeq and not
a Bio::Seq 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
A reference to an array of hashes of scores for each state and the
assigned state. Each element in the array is a residue (indexed from 0).
.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.
So, in order to add features to an existing Bio::Seq object;
.Sp
.Vb 5
\&  # get a Bio::Seq object
\&  my $seqobj;
\&  my $tool = Bio::Tools::Analysis::Protein::Domcut\->new
\&      ( \-seq => $seqobj\->primary_seq);
\&  $tool\->run;
\&
\&  my @fts = $tool\->result(Bio::SeqFeatureI);
\&
\&  $seqobj\->add_SeqFeature(@fts);
\&
\&  # if you want  meta sequences as well :
\&  my $meta = $tool\->result(\*(Aqmeta\*(Aq);
\&  $seqobj\->primary_seq($meta);
\&
\&  # can access meta data in a Bio::Seq object via a 
\&  # call to primary_seq:
\&
\&  print $seq4\->primary_seq\->named_submeta_text(\*(AqDomcut\*(Aq, 1,2), "\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 Domcut prediction scores.  e.g.,
.Sp
.Vb 3
\&  my $meta_sequence = $analysis_object\->result(\*(Aqmeta\*(Aq);
\&  print "scores from residues 10 \-20 are ",
\&      $meta_sequence\->submeta_text(10,20), "\en";
.Ve
.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 5
\& Name    : result
\& Purpose : To retrieve results of analysis in one of several formats.
\& Usage   : $job\->result (...)
\& Returns : a result created by running an analysis
\& Args    : various \- see keysin $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. Tagnames are 'score' 
and 'rank'.
.IP "'parsed'" 3
.IX Item "'parsed'"
Array of array references of [score, rank].
.IP "'all'" 3
.IX Item "'all'"
A Bio::Seq::Meta::Array object. Scores can be accessed using methods
from this class. Meta sequence name is Domcut.