Bio::SeqIO::chadoxml.3pm

Langue: en

Version: 2010-04-29 (fedora - 01/12/10)

Section: 3 (Bibliothèques de fonctions)

NAME

Bio::SeqIO::chadoxml - chadoxml sequence output stream

SYNOPSIS

It is probably best not to use this object directly, but rather go through the SeqIO handler system:
     $writer = Bio::SeqIO->new(-file => ">chado.xml",
                               -format => 'chadoxml');
 
     # assume you already have Sequence or SeqFeature objects
     $writer->write_seq($seq_obj);
 
     #after writing all seqs
     $writer->close_chadoxml();
 
 

DESCRIPTION

This object can transform Bio::Seq objects to chadoxml flat file databases (for chadoxml DTD, see http://gmod.cvs.sourceforge.net/gmod/schema/chado/dat/chado.dtd).

This is currently a write-only module.

     $seqio = Bio::SeqIO->new(-file => '>outfile.xml',
                              -format => 'chadoxml'
                              -suppress_residues => 1,
                              -allow_residues => 'chromosome',
                              );
 
     # we have a Bio::Seq object $seq which is a gene located on
     # chromosome arm 'X', to be written out to chadoxml
     # before converting to chadoxml, $seq object B<must> be transformed
     # so that all the coordinates in $seq are against the source
     # feature to be passed into Bio::SeqIO::chadoxml->write_seq()
     # -- chromosome arm X in the example below.
 
     $seqio->write_seq(-seq=>$seq,
                       -genus   => 'Homo',
                       -species => 'sapiens',
                       -seq_so_type=>'gene',
                       -src_feature=>'X',
                       -src_feat_type=>'chromosome_arm',
                         -nounflatten=>1,
                       -is_analysis=>'true',
                       -data_source=>'GenBank');
 
 

The chadoxml output of Bio::SeqIO::chadoxml->write_seq() method can be passed to the loader utility in XORT package (http://gmod.cvs.sourceforge.net/gmod/schema/XMLTools/XORT/) to be loaded into chado.

This object is currently implemented to work with sequence and annotation data from whole genome projects deposited in GenBank. It may not be able to handle all different types of data from all different sources.

In converting a Bio::Seq object into chadoxml, a top-level feature is created to represent the object and all sequence features inside the Bio::Seq object are treated as subfeatures of the top-level feature. The Bio::SeqIO::chadoxml object calls Bio::SeqFeature::Tools::Unflattener to unflatten the flat feature list contained in the subject Bio::Seq object, to build gene model containment hierarchy conforming to chado central dogma model: gene --> mRNA --> exons and protein.

Destination of data in the subject Bio::Seq object $seq is as following:

     *$seq->display_id:  name of the top-level feature;
 
     *$seq->accession_number: if defined, uniquename and
                  feature_dbxref of the top-level
                  feature if not defined,
                  $seq->display_id is used as the
                  uniquename of the top-level feature;
 
     *$seq->molecule: transformed to SO type, used as the feature
             type of the top-level feature if -seq_so_type
             argument is supplied, use the supplied SO type
             as the feature type of the top-level feature;
 
     *$seq->species: organism of the top-level feature;
 
     *$seq->seq: residues of the top-level feature;
 
     *$seq->is_circular, $seq->division: feature_cvterm;
 
     *$seq->keywords, $seq->desc, comments: featureprop;
 
     *references: pub and feature_pub;
         medline/pubmed ids: pub_dbxref;
         comments: pubprop;
 
     *feature "source" span: featureloc for top-level feature;
 
     *feature "source" db_xref: feature_dbxref for top-level feature;
 
     *feature "source" other tags: featureprop for top-level feature;
 
     *subfeature 'symbol' or 'label' tag: feature uniquename, if
                      none of these is present, the chadoxml object
                      generates feature uniquenames as:
                      <gene>-<feature_type>-<span>
                      (e.g. foo-mRNA--1000..3000);
 
     *gene model: feature_relationship built based on the
                      containment hierarchy;
 
     *feature span: featureloc;
 
     *feature accession numbers: feature_dbxref;
 
     *feature tags (except db_xref, symbol and gene): featureprop;
 
 

Things to watch out for:

     *chado schema change: this version works with the chado
                                version tagged chado_1_01 in GMOD CVS.
 
     *feature uniquenames: especially important if using XORT
                               loader to do incremental load into
                               chado. may need pre-processing of the
                               source data to put the correct
                               uniquenames in place.
 
     *pub uniquenames: chadoxml->write_seq() has the FlyBase policy
                           on pub uniquenames hard-coded, it assigns
                           pub uniquenames in the following way: for
                           journals and books, use ISBN number; for
                           published papers, use MEDLINE ID; for
                           everything else, use FlyBase unique
                           identifier FBrf#. need to modify the code to
                           implement your policy. look for the comments
                           in the code.
 
     *for pubs possibly existing in chado but with no knowledge of
          its uniquename:put "op" as "match", then need to run the
                         output chadoxml through a special filter that
                         talks to chado database and tries to find the
                         pub by matching with the provided information
                         instead of looking up by the unique key. after
                         matching, the filter also resets the "match"
                         operation to either "force" (default), or
                         "lookup", or "insert", or "update". the
                         "match" operation is for a special FlyBase use
                         case. please modify to work according to your
                         rules.
 
     *chado initialization for loading:
 
         cv & cvterm: in the output chadoxml, all cv's and
                              cvterm's are lookup only. Therefore,
                              before using XORT loader to load the
                              output into chado, chado must be
                              pre-loaded with all necessary CVs and
                              CVterms, including "SO" , "property
                              type", "relationship type", "pub type",
                              "pubprop type", "pub relationship type",
                              "sequence topology", "GenBank feature
                              qualifier", "GenBank division". A pub by
                              the uniquename 'nullpub' of type 'null
                              pub' needs to be inserted.
 
 

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.bioperl.org
 
 

AUTHOR - Peili Zhang

Email peili@morgan.harvard.edu

APPENDIX

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

write_seq

  Title   : write_seq
  Usage   : $stream->write_seq(-seq=>$seq, -seq_so_type=>$seqSOtype,
                   -src_feature=>$srcfeature,
                   -src_feat_type=>$srcfeattype,
                   -nounflatten=>0 or 1,
                   -is_analysis=>'true' or 'false',
                   -data_source=>$datasource)
  Function: writes the $seq object (must be seq) into chadoxml.
  Returns : 1 for success and 0 for error
  Args     : A Bio::Seq object $seq, optional $seqSOtype, $srcfeature,
             $srcfeattype, $nounflatten, $is_analysis and $data_source.
 
 

When $srcfeature (a string, the uniquename of the source feature) is given, the location and strand information of the top-level feature against the source feature will be derived from the sequence feature called 'source' of the $seq object, a featureloc record is generated for the top -level feature on $srcfeature. when $srcfeature is given, $srcfeattype must also be present. All feature coordinates in $seq should be against $srcfeature. $seqSOtype is the optional SO term to use as the type of the top-level feature. For example, a GenBank data file for a Drosophila melanogaster genome scaffold has the molecule type of ``DNA'', when converting to chadoxml, a $seqSOtype argument of ``golden_path_region'' can be supplied to save the scaffold as a feature of type ``golden_path_region'' in chadoxml, instead of ``DNA''. a feature with primary tag of 'source' must be present in the sequence feature list of $seq, to decribe the whole sequence record.

In the current implementation:

*
non-mRNA records

A top-level feature of type $seq->alphabet is generated for the whole GenBank record, features listed are unflattened for DNA records to build gene model feature graph, and for the other types of records all features in $seq are treated as subfeatures of the top-level feature.

*
mRNA records

If a 'gene' feature is present, it must have a /symbol or /label tag to contain the uniquename of the gene. a top-level feature of type 'gene' is generated. the mRNA is written as a subfeature of the top-level gene feature, and the other sequence features listed in $seq are treated as subfeatures of the mRNA feature.

suppress_residues

  Title    : suppress_residues
  Usage    : $obj->suppress_residues()        #get existing value
             $obj->suppress_residues($newval) #set new value
  Function : Keep track of the flag to suppress printing of residues in the
             chadoxml file. The default it to allow all residues to go into the
             file.
  Returns  : value of suppress_residues (a scalar)
  Args     : new value of suppress_residues (to set)
 
 

allow_residues

  Title    : allow_residues
  Usage    : $obj->allow_residues()        #get existing value
             $obj->allow_residues($feature_type) #set new value
  Function : Track the allow_residues type.  This can be used in conjunction
             with the suppress_residues flag to only allow residues from a
             specific feature type to be printed in the xml file, for example,
             only printing chromosome residues. When suppress_residues is set to
             true, then only chromosome features would would go into the xml
             file. If suppress_residues is not set, this function has no effect
             (since the default is to put all residues in the xml file).
  Returns  : value of allow_residues (string that corresponds to a feature type)
  Args     : new value of allow_residues (to set)
  Status   :
 
 

return_ftype_hash

  Title    : return_ftype_hash
  Usage    : $obj->return_ftype_hash()
  Function : A simple hash where returning it has be factored out of the main
             code to allow subclasses to override it.
  Returns  : A hash that indicates what the name of the SO term is and what
             the name of the Sequence Ontology is in the cv table.
  Args     : The string that represents the SO term.
  Status   :
 
 

return_reltypename

  Title    : return_reltypename
  Usage    : $obj->return_reltypename
  Function : Return the appropriate relationship type name depending on the
             feature type (typically part_of, but derives_from for polypeptide).
  Returns  : A relationship type name.
  Args     : A SO type name.
  Status   :
 
 

next_seq

  Title    : next_seq
  Usage    : $obj->next_seq
  Function : 
  Returns  : 
  Args     : 
  Status   : Not implemented (write only adaptor)
 
 

_create_writer

  Title    : _create_writer
  Usage    : $obj->_create_writer
  Function : Creates XML::Writer object and writes start tag
  Returns  : Nothing, though the writer persists as part of the chadoxml object
  Args     : None
  Status   :
 
 

close_chadoxml

  Title    : close_chadoxml
  Usage    : $obj->close_chadoxml
  Function : Writes the closing xml tag
  Returns  : None
  Args     : None
  Status   :
 
 

handle_unreserved_tags

  Title    : handle_unreserved_tags
  Usage    : $obj->handle_unreserved_tags
  Function : Converts tag value pairs to xml-ready hashrefs
  Returns  : The array containing the hashrefs
  Args     : In order: the Seq or SeqFeature object, the key, and the hasharray
  Status   :
 
 

handle_Alias_tag

  Title    : handle_Alias_tag
  Usage    : $obj->handle_Alias_tag
  Function : Convert Alias values to synonym hash refs
  Returns  : An array of synonym hash tags
  Args     : The seq or seqFeature object and the synonym hash array
  Status   :
 
 

handle_Ontology_tag

  Title    : handle_Ontology_tag
  Usage    : $obj->handle_Ontology_tag
  Function : Convert Ontology_term values to ontology term hash refs
  Returns  : An array of ontology term hash refs
  Args     : The seq or seqFeature object and the ontology term array
  Status   :
 
 

handle_dbxref

  Title    : handle_dbxref
  Usage    : $obj->handle_dbxref
  Function : Convert Dbxref values to dbxref hashref
  Returns  : An array of dbxref hashrefs
  Args     : A seq or seqFeature object and the dbxref array 
  Status   :
 
 

handle_source

  Title    : handle_source
  Usage    : $obj->handle_source
  Function : 
  Returns  : 
  Args     : 
  Status   :
 
 

_srcf_hash

  Title    : _srcf_hash
  Usage    : $obj->_srcf_hash
  Function : Creates the srcfeature hash for use in featureloc hashes
  Returns  : The srcfeature hash
  Args     : The srcfeature name, the srcfeature type and a reference to the
             organism hash.
  Status   :