Bio::SeqIO::agave(3pm)					User Contributed Perl Documentation				    Bio::SeqIO::agave(3pm)

NAME

       Bio::SeqIO::agave - AGAVE sequence output stream.

SYNOPSIS

       It is probably best not to use this object directly, but rather go through the SeqIO handler system. Go:

	 $in  = Bio::SeqIO->new('-file'   => "$file_in",
				'-format' => 'EMBL');

	 $out = Bio::SeqIO->new('-file'   => ">$file_out",
				'-format' => 'AGAVE');

	 while (my $seq = $in->next_seq){
	       $out->write_seq($seq);
	 }

DESCRIPTION

       This object can transform Bio::Seq objects to agave xml file and vice-versa.  I (Simon) coded up this module because I needed a parser to
       extract data from AGAVE xml to be utitlized by the GenQuire genome annotation system (See http://www.bioinformatics.org/Genquire).

       ***NOTE*** At the moment, not all of the tags are implemented.  In general, I followed the output format for the XEMBL project
       http://www.ebi.ac.uk/xembl/

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 - Simon K. Chan
       Email:

APPENDIX

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

   _process
	 Title	  : _process
	 Usage	  : $self->_process
	 Function : Parses the agave xml file.
	 Args	  : None.
	 Returns  : Nothing.
	 Note	  : Method(s) that call(s) this method : _initialize
		    Method(s) that this method calls   : _process_sciobj
		    FIRST/START sub.

   _process_sciobj
	 Title	  : _process_sciobj
	 Usage	  : $self->_process_sciobj
	 Function : Parses the data between the <sciobj></sciobj> tags.
	 Args	  : The string that holds the attributes for <sciobj>.
	 Returns  : Data structure holding the values parsed between
		    the <sciobj></sciobj> tags.
	 Note	  : Method(s) that call(s) this method : _process
		    Method(s) that this method calls   :
		    _helper_store_attribute_list , _process_contig

   _process_contig
	 Title	  : _process_contig
	 Usage	  : $self->_process_contig
	 Function : Parses the data between the <contig></contig> tags.
	 Args	  : 2 scalars:
		    - reference to a scalar holding the line to be parsed.
		    - scalar holding the attributes for the <contig> tag
		      to be parsed.
	 Returns  : Data structure holding the values parsed between
		    the <contig></contig> tags.
	 Note	  : Method(s) that call(s) this method : _process_sciobj
		    Method(s) that this method calls   :
		    _helper_store_attribute_list, _one_tag , _process_fragment_order

   _process_fragment_order
	 Title	  : _process_fragment_order
	 Usage	  : $self->_process_fragment_order
	 Function : Parses the data between the <fragment_order></fragment_order> tags.
	 Args	  : 2 scalars:
		    - reference to a scalar holding the value of the line to be parsed.
		    - reference to a data structure to store the <fragment_order> data.
	 Returns  : Nothing.
	 Note	  : Method(s) that call(s) this method : _process_contig
		    Method(s) that this method calls   :
		    _helper_store_attribute_list , _process_fragment_orientation

   _process_fragment_orientation
	 Title	  : _process_fragment_orientation
	 Usage	  : $self->_process_fragment_orientation
	 Function : Parses the data between the <fragment_orientation> and
		    </fragment_orientation> tags.
	 Args	  : 2 scalars:
		    - reference to a scalar holding the value of the line to be parsed.
		    - reference to a data structure to store the <fragment_orientation> data.
	 Returns  : Nothing.
	 Note	  : Method(s) that call(s) this method : _process_fragment_order

       Method(s) that this method calls : _helper_store_attribute_list , _process_bio_sequence

   _process_bio_sequence
	 Title	  : _process_bio_sequence
	 Usage	  : $self->_process_bio_sequence
	 Function : Parses the data between the <bio_sequence></bio_sequence> tags.
	 Args	  : 2 scalars:
		    - reference to a scalar holding the value of the line to be parsed.
		    - scalar holding the value of the attributes for <bio_sequence>
	 Returns  : data structure holding the values between <bio_sequence></bio_sequence>
	 Note	  : Method(s) that call(s) this method : _process_fragment_orientation

       Method(s) that this method calls : _helper_store_attribute_list , _one_tag , _question_mark_tag , _star_tag , _process_alt_ids ,
       _process_xrefs , _process_sequence_map

   _process_xrefs
	 Title	  : _process_xrefs
	 Usage	  : $self->_process_xrefs
	 Function : Parse the data between the <xrefs></xrefs> tags.
	 Args	  : reference to a scalar holding the value of the line to be parsed.
	 Return   : Nothing.
	 Note	  : Method(s) that call(s) this method: _process_bio_sequence
		    Method(s) that this method calls: _one_tag , _process_xref

   _process_xref
	 Title	  : _process_xref
	 Usage	  : $self->_process_xref
	 Function : Parses the data between the <xref></xref> tags.
	 Args	  : 2 scalars:
		    - reference to a scalar holding the value of the line to be parsed.
		    - reference to a data structure to store the <xref> data.
	 Returns  : Nothing.
	 Note	  : Method(s) that call(s) this method : _process_xrefs (note the 's' in 'xrefs')
		    Method(s) that this method calls   : _helper_store_attribute_list , _star_tag

   _process_sequence_map
	 Title	  : _process_sequence_map
	 Usage	  : $self->_process_sequence_map
	 Function : Parses the data between the <sequence_map></sequence_map> tags.
	 Args	  : Reference to scalar holding the line to be parsed.
	 Returns  : Data structure that holds the values that were parsed.
	 Note	  : Method(s) that call(s) this method : _process_bio_sequence
		    Method(s) that this method calls   : _helper_store_attribute_list ,
		       _question_mark_tag , _process_annotations

   _process_annotations
	 Title	  : _process_annotations
	 Usage	  : $self->_process_annotations
	 Function : Parse the data between the <annotations></annotations> tags.
	 Args	  : Reference to scalar holding the line to be parsed.
	 Returns  : Data structure that holds the values that were parsed.
	 Note	  : Method(s) that call(s) this method : _process_sequence_map
		    Method(s) that this method calls   : _process_seq_feature

   _process_seq_feature
	 Title	  : _process_seq_feature
	 Usage	  : $self->_process_seq_feature
	 Function : Parses the data between the <seq_feature></seq_feature> tag.
	 Args	  : 2 scalars:
		    - Reference to scalar holding the line to be parsed.
		    - Scalar holding the attributes for <seq_feature>.
	 Returns  : Data structure holding the values parsed.
	 Note	  : Method(s) that call(s) this method: _process_annotations

       Method(s) that this method calls: _helper_store_attribute_list , _process_classification , _question_mark_tag , _one_tag ,
       _process_evidence , _process_qualifier , _process_seq_feature , _process_related_annot

   _process_qualifier
	 Title	  : _process_qualifier
	 Usage	  : $self->_process_qualifier
	 Function : Parse the data between the <qualifier></qualifier> tags.
	 Args	  : 2 scalars:
		    - reference to a scalar holding the value of the line to be parsed.
		    - reference to a data structure to store the <qualifer> data.
	 Returns  : Nothing.
	 Note	  : Method(s) that call(s) this method : _process_seq_feature
		    Method(s) that this method calls   : _star_tag

   _process_classification
	 Title	 : _process_classification
	 Usage	 : $self->_process_classification
	 Function: Parse the data between the <classification></classification> tags.
	 Args	 :   2 scalars:
		   - reference to a scalar holding the value of the line to be parsed.
		   - reference to a data structure to store the <qualifer> data.
	 Returns : Nothing.
	 Note	 : Method(s) that call(s) this method: _process_seq_feature

	 Method(s) that this method calls: _helper_store_attribute_list ,
	 _question_mark_tag , _star_tag, _process_evidence

   _tag_processing_helper
	 Title	  : _tag_processing_helper
	 Usage	  : $self->_tag_processing_helper
	 Function : Stores the tag value within the data structure.
		    Also calls _helper_store_attribute_list to store the
		    attributes and their values in the data structure.
	 Args	  : 5 scalars:
		    - Scalar holding the value of the attributes
		    - Reference to a data structure to store the data for <$tag_name>
		    - Scalar holding the tag name.
		    - Scalar holding the value of the tag.
		    - Scalar holding the value of either 'star', 'plus',
		      or 'question mark' which specifies what type of method
		      called this method.
	 Returns  : Nothing.
	 Note	  : Method(s) that call(s) this method:
		    Method(s) that this method calls: _helper_store_attribute_list

   _one_tag
	 Title	  : _one_tag
	 Usage	  : $self->_one_tag
	 Function : A method to store data from tags that occurs just once.
	 Args	  : 2 scalars:
		    - reference to a scalar holding the value of the line to be parsed.
		    - reference to a data structure to store the data for <$tag_name>
	 Returns  : Nothing.
	 Note	  : Method(s) that call(s) this method : many
		    Method(s) that this method calls   : _tag_processing_helper

   _question_mark_tag
	 Title	  : _question_mark_tag
	 Usage	  : $self->_question_mark_tag
	 Function : Parses values from tags that occurs zero or one time. ie: tag_name?
	 Args	  : 3 scalars:
		    - reference to a scalar holding the value of the line to be parsed.
		    - reference to a data structure to store the data for <$tag_name>
		    - scalar holding the name of the tag.
	 Returns  : Nothing.
	 Note	  : Method(s) that call(s) this method : many.
		    Method(s) that this method calls   : _tag_processing_helper

   _star_tag
	 Title	  : _star_tag
	 Usage	  : $self->_star_tag
	 Function : Parses values from tags that occur zero or more times. ie: tag_name*
	 Args	  : 3 scalars:
		    - reference to a scalar holding the value of the line to be parsed.
		    - reference to a data structure to store the data for <$tag_name>
		    - scalar holding the name of the tag.
	 Returns  : Nothing.
	 Note	  : Method(s) that call(s) this method : many.
		    Method(s) that this method calls   : _tag_processing_helper

   _plus_tag
	 Title	  : _plus_tag
	 Usage	  : $self->_plus_tag
	 Function : Handles 'plus' tags (tags that occur one or more times).  tag_name+
	 Args	  : 3 scalars:
		    - reference to a scalar holding the value of the line to be parsed.
		    - reference to a data structure to store the data for <$tag_name>
		    - scalar holding the name of the tag.
	 Returns  : Nothing.
	 Note	  : Method(s) that call(s) this method : many.
		    Method(s) that this method calls   : _star_tag

   _helper_store_attribute_list
	 Title	  : _helper_store_attribute_list
	 Usage	  : $self->_helper_store_attribute_list
	 Function : A helper method used to store the attributes from
		    the tags into the data structure.
	 Args	  : 2 scalars:
		    - scalar holding the attribute values to be parsed.
		    - reference to a data structure to store the data between the 2 tags.
	 Returns  : Nothing.
	 Note	  : Method(s) that call(s) this method : Many.
		    Method(s) that this method call(s) : None.

   _store_seqs
	 Title	  : _store_seqs
	 Usage	  : $self->_store_seqs
	 Function : This method is called once in the life time of the script.
		    It stores the data parsed from the agave xml file into
		    the Bio::Seq object.
	 Args	  : None.
	 Returns  : Nothing.
	 Note	  : Method(s) that call(s) this method : next_seq
		    Method(s) that this method calls   : None.

   next_seq
	       Title	: next_seq
	       Usage	: $seq = $stream->next_seq()
	       Function : Returns the next sequence in the stream.
	       Args	: None.
	       Returns	: Bio::Seq object

       Method is called from the script.  Method(s) that this method calls: _store_seqs (only once throughout the life time of script execution).

   next_primary_seq
	 Title	 : next_primary_seq
	 Usage	 : $seq = $stream->next_primary_seq()
	 Function: returns the next primary sequence (ie no seq_features) in the stream
	 Returns : Bio::PrimarySeq object
	 Args	 : NONE

   write_seq
	 Title	 : write_seq
	 Usage	 : Not Yet Implemented! $stream->write_seq(@seq)
	 Function: writes the $seq object into the stream
	 Returns : 1 for success and 0 for error
	 Args	 : Bio::Seq object

   _write_each_record
	 Title	 : _write_each_record
	 Usage	 : $agave->_write_each_record( $seqI )
	 Function: change data into agave format
	 Returns : NONE
	 Args	 : Bio::SeqI object

   _write_seqfeature
	 Usage	 : $agave->_write_each_record( $seqfeature, $write )
	 Function: change seeqfeature data into agave format
	 Returns : NONE
	 Args	 : Bio::SeqFeature object and XML::writer object

   _filehandle
	 Title	 : _filehandle
	 Usage	 : $obj->_filehandle($newval)
	 Function:
	 Example :
	 Returns : value of _filehandle
	 Args	 : newvalue (optional)

   throw
	 Title	  : throw
	 Usage	  : $self->throw;
	 Function : Throw's error message.  Calls SeqIO's throw method.
	 Args	  : Array of string(s), holding error message(s).
	 Returns  : Nothing.
	 Note	  : Method(s) that call(s) this method: many.
		    Method(s) that this method calls: Bio::SeqIO's throw method.

perl v5.14.2							    2012-03-02						    Bio::SeqIO::agave(3pm)