Bio::SeqIO::agave.3pm

Langue: en

Version: 2010-05-19 (ubuntu - 24/10/10)

Section: 3 (Bibliothèques de fonctions)

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:
   http://bugzilla.open-bio.org/
 
 

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.