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Manual Reference Pages  -  BIO::SEQIO::AGAVE (3)

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NAME

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

CONTENTS

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://github.com/bioperl/bioperl-live/issues



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 : Throws error message.  Calls SeqIOs 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::SeqIOs throw method.



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perl v5.20.3 BIO::SEQIO::AGAVE (3) 2016-04-05

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