Provided by: libbio-perl-perl_1.6.901-2_all bug

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.