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:

  https://github.com/bioperl/bioperl-live/issues

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 describe 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   :