table of contents
Bio::SeqIO::game::seqHandler(3pm) | User Contributed Perl Documentation | Bio::SeqIO::game::seqHandler(3pm) |
NAME¶
Bio::SeqIO::game::seqHandler -- a class for handling game-XML sequencesSYNOPSIS¶
This modules is not used directlyDESCRIPTION¶
Bio::SeqIO::game::seqHandler processes all of the sequences associated with a game record and, via feature handlers, processes the associated annotationsFEEDBACK¶
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 of the bugs and their resolution. Bug reports can be submitted via the web:https://github.com/bioperl/bioperl-live/issues
AUTHOR - Sheldon McKay¶
Email mckays@cshl.eduAPPENDIX¶
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _new¶
Title : new Usage : my $seqHandler = Bio::SeqIO::game::seqHandler->new($seq, $ann, $comp, $map, $src ) Function: constructor method to create a sequence handler Returns : a sequence handler object Args : $seq -- an XML sequence element $ann -- a ref. to a list of <annotation> elements $comp -- a ref. to a list of <computational_analysis> elements (not used yet) $map -- a <map_position> element $src -- a flag to indicate that the sequence already has a source feature
convert¶
Title : convert Usage : @seqs = $seqHandler->convert Function: converts the main XML sequence element and associated annotations to Bio:: Returns : a ref. to a an array containing the sequence object and a ref. to a list of features Args : none Note : The features and sequence are kept apart to facilitate downstream filtering of features
_order_feats¶
Title : _order_feats Usage : $self->_order_feats( $self->{seq_h} ) Function: an internal method to ensure the source feature comes first and keep gene, mRNA and CDS features together Returns : a ref. to an array containing the sequence object and a ref. to a list of features Args : a ref. to a hash of sequences
_add_seq¶
Title : _add_seq Usage : $self->_add_seq($seq_element) Function: an internal method to process the sequence elements Returns : nothing Args : a sequence element
_map_position¶
Title : _map_position Usage : $self->_map_position($map_posn_element) Function: an internal method to process the <map_position> element Returns : nothing Args : a map_position element
_annotation¶
Title : _annotation Usage : $self->_annotation($annotation_element) Function: an internal method to process <annotation> elements Returns : nothing Args : an annotation element
_seq¶
Title : _seq Usage : my $seq = $self->_seq Function: an internal sequence getter/setter Returns : a Bio::RichSeq object Args : a sequence ID
_feat_handler¶
Title : _feat_handler Usage : my $featHandler = $self->_featHandler Function: an internal getter/setter for feature handling objects Returns : a Bio::SeqIO::game::featHandler object Args : none
2018-10-27 | perl v5.26.2 |