NAME
FAST::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:
$in = FAST::Bio::SeqIO->new('-file' => "$file_in",
'-format' => 'EMBL');
$out = FAST::Bio::SeqIO->new('-file' => ">$file_out",
'-format' => 'AGAVE');
while (my $seq = $in->next_seq){
$out->write_seq($seq);
}DESCRIPTION
This object can transform FAST::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 listsSupport
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_orderMethod(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_orientationMethod(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_annotationsMethod(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 FAST::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 : FAST::Bio::Seq objectMethod 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 : FAST::Bio::PrimarySeq object
Args : NONEwrite_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 : FAST::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 : FAST::Bio::SeqI object_write_seqfeature
Usage : $agave->_write_each_record( $seqfeature, $write )
Function: change seeqfeature data into agave format
Returns : NONE
Args : FAST::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: FAST::Bio::SeqIO's throw method.