SYNOPSIS

# Do not use this module directly. Use it via the Bio::SeqIO class.
use Bio::SeqIO;

# read a SeqXML file
my $seqio = Bio::SeqIO->new(-format => 'seqxml',
-file => 'my_seqs.xml');
while (my $seq_object = $seqio->next_seq) {
print join("\t",
$seq_object->display_id,
$seq_object->description,
$seq_object->seq,
), "\n";
}

# write a SeqXML file
#
# Note that you can (optionally) specify the source
# (usually a database) and source version.
my $seqwriter = Bio::SeqIO->new(-format => 'seqxml',
-file => ">outfile.xml",
-source => 'Ensembl',
-sourceVersion => '56');
$seqwriter->write_seq($seq_object);
# once you've written all of your seqs, you may want to do
# an explicit close to get the closing </seqXML> tag
$seqwriter->close;

DESCRIPTION

This object can transform Bio::Seq objects to and from SeqXML format. For more information on the SeqXML standard, visit <http://www.seqxml.org>.

In short, SeqXML is a lightweight sequence format that takes advantage of the validation capabilities of XML while not overburdening you with a strict and complicated schema.

This module is based in part (particularly the XML-parsing part) on Bio::TreeIO::phyloxml by Mira Han.

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.

  [email protected]                  - General discussion
  http://bioperl.org/wiki/Mailing_lists  - About the mailing lists

Support

Please direct usage questions or support issues to the mailing list:

[email protected]

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

AUTHORS - Dave Messina

Email: [email protected]

CONTRIBUTORS

APPENDIX

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

_initialize

 Title   : _initialize
 Usage   : $self->_initialize(@args) 
 Function: constructor (for internal use only).
 
           Besides the usual SeqIO arguments (-file, -fh, etc.),
           Bio::SeqIO::seqxml accepts three arguments which are used
           when writing out a seqxml file. They are all optional.
 Returns : none
 Args    : -source         => source string (usually a database name)
           -sourceVersion  => source version. The version number of the source
           -seqXMLversion  => the version of seqXML that will be used
 Throws  : Exception if XML::LibXML::Reader or XML::Writer
           is not initialized

next_seq

 Title   : next_seq
 Usage   : $seq = $stream->next_seq()
 Function: returns the next sequence in the stream
 Returns : L<Bio::Seq> object, or nothing if no more available
 Args    : none

write_seq

 Title   : write_seq
 Usage   : $stream->write_seq(@seq)
 Function: Writes the $seq object into the stream
 Returns : 1 for success and 0 for error
 Args    : Array of 1 or more L<Bio::PrimarySeqI> objects

_initialize_seqxml_node_methods

 Title   : _initialize_seqxml_node_methods
 Usage   : $self->_initialize_xml_node_methods
 Function: sets up code ref mapping of each seqXML node type
           to a method for processing that node type 
 Returns : none
 Args    : none

schemaLocation

 Title   : schemaLocation
 Usage   : $self->schemaLocation
 Function: gets/sets the schema location in the <seqXML> header
 Returns : the schema location string
 Args    : To set the schemaLocation, call with a schemaLocation as the argument.

source

 Title   : source
 Usage   : $self->source
 Function: gets/sets the data source in the <seqXML> header
 Returns : the data source string
 Args    : To set the source, call with a source string as the argument.

sourceVersion

 Title   : sourceVersion
 Usage   : $self->sourceVersion
 Function: gets/sets the data source version in the <seqXML> header
 Returns : the data source version string
 Args    : To set the source version, call with a source version string
           as the argument.

seqXMLversion

 Title   : seqXMLversion
 Usage   : $self->seqXMLversion
 Function: gets/sets the seqXML version in the <seqXML> header
 Returns : the seqXML version string.
 Args    : To set the seqXML version, call with a seqXML version string
           as the argument.

Methods for parsing the XML document

processXMLNode

 Title   : processXMLNode
 Usage   : $seqio->processXMLNode
 Function: reads the XML node and processes according to the node type
 Returns : none
 Args    : none
 Throws  : Exception on unexpected XML node type, warnings on unexpected
           XML element names.

processAttribute

 Title   : processAttribute
 Usage   : $seqio->processAttribute(\%hash_for_attribute);
 Function: reads the attributes of the current element into a hash
 Returns : none
 Args    : hash reference where the attributes will be stored.

parseHeader

 Title   : parseHeader
 Usage   : $self->parseHeader();
 Function: reads the opening <seqXML> block and grabs the metadata from it,
           namely the source, sourceVersion, and seqXMLversion.
 Returns : none
 Args    : none
 Throws  : Exception if it hits an <entry> tag, because that means it's
           missed the <seqXML> tag and read too far into the file.

element_seqXML

 Title   : element_seqXML
 Usage   : $self->element_seqXML
 Function: processes the opening <seqXML> node
 Returns : none
 Args    : none

element_entry

 Title   : element_entry
 Usage   : $self->element_entry
 Function: processes a sequence <entry> node
 Returns : none
 Args    : none
 Throws  : Exception if sequence ID is not present in <entry> element

element_species

 Title   : element_entry
 Usage   : $self->element_entry
 Function: processes a <species> node, creating a Bio::Species object
 Returns : none
 Args    : none
 Throws  : Exception if <species> tag exists but is empty,
           or if the attributes 'name' or 'ncbiTaxID' are undefined

element_description

 Title   : element_description
 Usage   : $self->element_description
 Function: processes a sequence <description> node;
           a no-op -- description text is read by
           processXMLnode
 Returns : none
 Args    : none

element_RNAseq

 Title   : element_RNAseq
 Usage   : $self->element_RNAseq
 Function: processes a sequence <RNAseq> node
 Returns : none
 Args    : none

element_DNAseq

 Title   : element_DNAseq
 Usage   : $self->element_DNAseq
 Function: processes a sequence <DNAseq> node
 Returns : none
 Args    : none

element_AAseq

 Title   : element_AAseq
 Usage   : $self->element_AAseq
 Function: processes a sequence <AAseq> node
 Returns : none
 Args    : none

element_DBRef

 Title   : element_DBRef
 Usage   : $self->element_DBRef
 Function: processes a sequence <DBRef> node,
           creating a Bio::Annotation::DBLink object
 Returns : none
 Args    : none

element_property

 Title   : element_property
 Usage   : $self->element_property
 Function: processes a sequence <property> node, creating a
           Bio::Annotation::SimpleValue object
 Returns : none
 Args    : none

end_element_RNAseq

 Title   : end_element_RNAseq
 Usage   : $self->end_element_RNAseq
 Function: processes a sequence <RNAseq> node
 Returns : none
 Args    : none

end_element_DNAseq

 Title   : end_element_DNAseq
 Usage   : $self->end_element_DNAseq
 Function: processes a sequence <DNAseq> node
 Returns : none
 Args    : none

end_element_AAseq

 Title   : end_element_AAseq
 Usage   : $self->end_element_AAseq
 Function: processes a sequence <AAseq> node
 Returns : none
 Args    : none

end_element_entry

 Title   : end_element_entry
 Usage   : $self->end_element_entry
 Function: processes the closing </entry> node, creating the Seq object
 Returns : a Bio::Seq object
 Args    : none
 Throws  : Exception if sequence, sequence ID, or alphabet are missing

end_element_default

 Title   : end_element_default
 Usage   : $self->end_element_default
 Function: processes all other closing tags;
           a no-op.
 Returns : none
 Args    : none

DESTROY

 Title   : DESTROY
 Usage   : called automatically by Perl just before object
           goes out of scope
 Function: performs a write flush
 Returns : none
 Args    : none

close

 Title   : close
 Usage   : $seqio_obj->close(). 
 Function: writes closing </seqXML> tag.
 
           close() will be called automatically by Perl when your
           program exits, but if you want to use the seqXML file
           you've written before then, you'll need to do an explicit
           close first to get the final </seqXML> tag.
 Returns : none
 Args    : none