Bio::SeqIO::chadoxml - chadoxml sequence input/output stream It is probably best not to use this object directly, but rather go through the SeqIO handler system. Go: $stream = Bio::SeqIO->new(-file => $filename, -format => 'chadoxml'); while ( my $seq = $stream->next_seq() ) { # do something with $seq } This object can transform Bio::Seq objects to and from chadoxml flat file databases (for chadoxml DTD, see http://cvs.sourceforge.net/cgi-bin/viewcvs.cgi/gmod/schema/chado/dat/chado.dtd). CURRENTLY ONLY TO $seqio = Bio::SeqIO->new(-file => '>outfile.xml', -format => 'chadoxml'); #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, -seq_so_type=>'gene', -src_feature=>'X', -src_feat_type=>'chromosome_arm'); The chadoxml output of Bio::SeqIO::chadoxml->write_seq() method can be passed to the loader utility in XORT package (http://cvs.sourceforge.net/cgi-bin/viewcvs.cgi/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 id's: 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.

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://www.bioperl.org/MailList.shtml - About the mailing lists

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://bio.perl.org/bioperl-bugs/ Email peili@morgan.harvard.edu 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) Function: writes the $seq object (must be seq) into chadoxml. Current implementation: 1. for 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. 2. for mRNA records, if a 'gene' feature is present, it B<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. Returns : 1 for success and 0 for error Args : A Bio::Seq object $seq, optional $seqSOtype, $srcfeature, $srcfeattype. 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.