- AUTHOR - Peili Zhang
Bio::SeqIO::chadoxml - chadoxml sequence output stream
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();
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.
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The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
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 describe the whole sequence record.
In the current implementation:
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.
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.
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)
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 :
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 :
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 :
Title : next_seq Usage : $obj->next_seq Function : Returns : Args : Status : Not implemented (write only adaptor)
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 :
Title : close_chadoxml Usage : $obj->close_chadoxml Function : Writes the closing xml tag Returns : None Args : None Status :
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 :
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 :
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 :
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 :
Title : handle_source Usage : $obj->handle_source Function : Returns : Args : Status :
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 :