bio::tools::analysis::simpleanalysisbase(3pm) [debian man page]

Bio::Tools::Analysis::SimpleAnalysisBase(3pm)		User Contributed Perl Documentation	     Bio::Tools::Analysis::SimpleAnalysisBase(3pm)

NAME

       Bio::Tools::Analysis::SimpleAnalysisBase - abstract superclass for SimpleAnalysis implementations

SYNOPSIS

       # not to be run directly

DESCRIPTION

       This class is a generic implementation of SimpleAnalysisI and should be used as a base class for specific implementations.

       Modules implementing SimpleAnalysisBase only need to provide specific _init(), _run() and result() methods, plus any get/set methods for
       parameters to the analysis program.

SEE ALSO

       Bio::SimpleAnalysisI, 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, Heikki Lehvaslaiho, heikki-at-bioperl-dot-org

APPENDIX

       The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _

   new
	Usage	: $job->new(...)
	Returns : a new analysis object,
	Args	: none (but an implementation may choose
		  to add arguments representing parameters for the analysis
		  program. Each key value of must have a method implemented
		  for it in a subclass. A seq () method is provided here as
		  this will probably be needed by all sequence analysis programs

   seq
	Usage	: $job->seq()
	Returns : a Bio::PrimarySeqI implementing sequence object, or void
	Args	: None, or a Bio::PrimarySeqI implementing object

   analysis_name
	   Usage     : $analysis->analysis_name();
	   Returns   : The analysis name
	   Arguments : none

   analysis_spec
	   Usage    :  $analysis->analysis_spec();
	   Returns  :  a hash reference to  a hash of analysis parameters. See
		       Bio::SimpleAnalysisI for a list of recommended key values.
	   Arguments:  none

   clear
	   Usage     : $analysis->clear();
	   Returns   : true value on success
	   Arguments : none
	   Purpose   : to remove raw results from a previous analysis so that
		       an analysis can be repeated with different parameters.

   input_spec
	   Usage     : $analysis->input_spec();
	   Returns   : a  reference to	an array of  hashes of analysis parameters. See
		       Bio::SimpleAnalysisI for a list of recommended key values.
	   Arguments : none

   result_spec
	   Usage     : $analysis->result_spec();
	   Returns   : a  reference to	a   hashes of resultformats. See
		       Bio::SimpleAnalysisI for a list of recommended key values.
		       The key values can be used as parameters to the result()
		       method, the values provide descriptions.
	   Arguments : none

perl v5.14.2							    2012-03-02			     Bio::Tools::Analysis::SimpleAnalysisBase(3pm)

Bio::Tools::Analysis::Protein::NetPhos(3pm)		User Contributed Perl Documentation	       Bio::Tools::Analysis::Protein::NetPhos(3pm)

NAME

       Bio::Tools::Analysis::Protein::NetPhos - a wrapper around NetPhos server

SYNOPSIS

	 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('Bio::SeqFeatureI') ) {

	     # do something to SeqFeature
	     # e.g. print as GFF
	     print $feat->gff_string, "
";
	     # or store within the sequence - if it is a Bio::RichSeqI
	     $seq->add_SeqFeature($feat)

	}

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.

       See <http://www.cbs.dtu.dk/services/NetPhos/>.

       This the first 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::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, Heikki Lehvaslaiho, heikki-at-bioperl-dot-org

APPENDIX

       The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _

   result
	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)

       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).

       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 defined the type of bioperl objects returned in an array.  The objects are Bio::SeqFeature::Generic.

       anything else
	  Array of array references of [ position, score, residue].

   threshold
	Usage	: $job->threshold(...)
	Returns  : The significance threshold of a prediction
	Args	 : None (retrieves value) or a value beween 0 and 1.
	Purpose  : Get/setter of the threshold to be sumitted for analysis.

perl v5.14.2							    2012-03-02			       Bio::Tools::Analysis::Protein::NetPhos(3pm)