bio::liveseq::transcript(3pm) [debian man page]

Bio::LiveSeq::Transcript(3pm)				User Contributed Perl Documentation			     Bio::LiveSeq::Transcript(3pm)

NAME

       Bio::LiveSeq::Transcript - Transcript class for LiveSeq

SYNOPSIS

	 # documentation needed

DESCRIPTION

       This stores information about coding sequences (CDS).  The implementation is that a Transcript object accesses a collection of Exon
       objects, inferring from them the nucleotide structure and sequence.

AUTHOR - Joseph A.L. Insana
       Email:  Insana@ebi.ac.uk, jinsana@gmx.net

APPENDIX

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

   new
	 Title	 : new
	 Usage	 : $transcript = Bio::LiveSeq::Transcript->new(-exons => @obj_refs);

	 Function: generates a new Bio::LiveSeq::Transcript
	 Returns : reference to a new object of class Transcript
	 Errorcode -1
	 Args	 : reference to an array of Exon object references

   all_Exons
	Title	: all_Exons
	Usage	: $transcript_obj->all_Exons()
	Function: returns references to all Exon objects the Transcript is composed of
	Example : foreach $exon ($transcript->all_Exons()) { do_something }
	Returns : array of object references
	Args	: none

   downstream_seq
	Title	: downstream_seq
	Usage	: $transcript_obj->downstream_seq()
		: $transcript_obj->downstream_seq(64)
	Function: returns a string of nucleotides downstream of the end of the
		  CDS. If there is some information of the real mRNA, from features in
		  an attached Gene object, it will return up to those boundaries.
		  Otherwise it will return 1000 nucleotides.
		  If an argument is given it will override the default 1000 number
		  and return instead /that/ requested number of nucleotides.
		  But if a Gene object is attached, this argument will be ignored.
	Returns : string
	Args	: an optional integer number of nucleotides to be returned instead of
		  the default if no gene attached

   upstream_seq
	Title	: upstream_seq
	Usage	: $transcript_obj->upstream_seq()
		: $transcript_obj->upstream_seq(64)
	Function: just like downstream_seq but returns nucleotides before the ATG
	Note	: the default, if no Gene information present and no nucleotides
		  number given, is to return up to 400 nucleotides.

   get_Translation
	 Title	 : valid
	 Usage	 : $translation = $obj->get_Translation()
	 Function: retrieves the reference to the object of class Translation (if any)
		   attached to a LiveSeq object
	 Returns : object reference
	 Args	 : none

   translation_table
	Title	: translation_table
	Usage	: $name = $obj->translation_table;
		: $name = $obj->translation_table(11);
	Function: Returns or sets the translation_table used for translating the
		  transcript.
		  If it has never been set, it will return undef.
	Returns : an integer

   frame
	Title	: frame
	Usage	: $frame = $transcript->frame($label);
	Function: Returns the frame of a particular nucleotide.
		  Frame can be 0 1 or 2 and means the position in the codon triplet
		  of the particulat nucleotide. 0 is the first codon_position.
		  Codon_position (1 2 3) is simply frame+1.
		  If the label asked for is not inside the Transcript, -1 will be
		  returned.
	Args	: a label
	Returns : 0 1 or 2
	Errorcode -1

perl v5.14.2							    2012-03-02					     Bio::LiveSeq::Transcript(3pm)

Bio::Tools::Genscan(3pm)				User Contributed Perl Documentation				  Bio::Tools::Genscan(3pm)

NAME

       Bio::Tools::Genscan - Results of one Genscan run

SYNOPSIS

	  use Bio::Tools::Genscan;

	  $genscan = Bio::Tools::Genscan->new(-file => 'result.genscan');
	  # filehandle:
	  $genscan = Bio::Tools::Genscan->new( -fh  => *INPUT );

	  # parse the results
	  # note: this class is-a Bio::Tools::AnalysisResult which implements
	  # Bio::SeqAnalysisParserI, i.e., $genscan->next_feature() is the same
	  while($gene = $genscan->next_prediction()) {
	      # $gene is an instance of Bio::Tools::Prediction::Gene, which inherits
	      # off Bio::SeqFeature::Gene::Transcript.
	      #
	      # $gene->exons() returns an array of
	      # Bio::Tools::Prediction::Exon objects
	      # all exons:
	      @exon_arr = $gene->exons();

	      # initial exons only
	      @init_exons = $gene->exons('Initial');
	      # internal exons only
	      @intrl_exons = $gene->exons('Internal');
	      # terminal exons only
	      @term_exons = $gene->exons('Terminal');
	      # singleton exons:
	      ($single_exon) = $gene->exons();
	  }

	  # essential if you gave a filename at initialization (otherwise the file
	  # will stay open)
	  $genscan->close();

DESCRIPTION

       The Genscan module provides a parser for Genscan gene structure prediction output. It parses one gene prediction into a
       Bio::SeqFeature::Gene::Transcript- derived object.

       This module also implements the Bio::SeqAnalysisParserI interface, and thus can be used wherever such an object fits. See
       Bio::SeqAnalysisParserI.

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/

AUTHOR - Hilmar Lapp
       Email hlapp@gmx.net

APPENDIX

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

   analysis_method
	Usage	  : $genscan->analysis_method();
	Purpose   : Inherited method. Overridden to ensure that the name matches
		    /genscan/i.
	Returns   : String
	Argument  : n/a

   next_feature
	Title	: next_feature
	Usage	: while($gene = $genscan->next_feature()) {
			 # do something
		  }
	Function: Returns the next gene structure prediction of the Genscan result
		  file. Call this method repeatedly until FALSE is returned.

		  The returned object is actually a SeqFeatureI implementing object.
		  This method is required for classes implementing the
		  SeqAnalysisParserI interface, and is merely an alias for
		  next_prediction() at present.

	Example :
	Returns : A Bio::Tools::Prediction::Gene object.
	Args	:

   next_prediction
	Title	: next_prediction
	Usage	: while($gene = $genscan->next_prediction()) {
			 # do something
		  }
	Function: Returns the next gene structure prediction of the Genscan result
		  file. Call this method repeatedly until FALSE is returned.

	Example :
	Returns : A Bio::Tools::Prediction::Gene object.
	Args	:

   _parse_predictions
	Title	: _parse_predictions()
	Usage	: $obj->_parse_predictions()
	Function: Parses the prediction section. Automatically called by
		  next_prediction() if not yet done.
	Example :
	Returns :

   _prediction
	Title	: _prediction()
	Usage	: $gene = $obj->_prediction()
	Function: internal
	Example :
	Returns :

   _add_prediction
	Title	: _add_prediction()
	Usage	: $obj->_add_prediction($gene)
	Function: internal
	Example :
	Returns :

   _predictions_parsed
	Title	: _predictions_parsed
	Usage	: $obj->_predictions_parsed
	Function: internal
	Example :
	Returns : TRUE or FALSE

   _has_cds
	Title	: _has_cds()
	Usage	: $obj->_has_cds()
	Function: Whether or not the result contains the predicted CDSs, too.
	Example :
	Returns : TRUE or FALSE

   _read_fasta_seq
	Title	: _read_fasta_seq()
	Usage	: ($id,$seqstr) = $obj->_read_fasta_seq();
	Function: Simple but specialised FASTA format sequence reader. Uses
		  $self->_readline() to retrieve input, and is able to strip off
		  the traling description lines.
	Example :
	Returns : An array of two elements.

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