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To retrieve gene name & function thorugh Genbank id (gi|9910297)
08-11-2009
To retrieve gene name & function thorugh Genbank id (gi|9910297)
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Bio::SeqIO::game::featHandler(3pm) User Contributed Perl Documentation Bio::SeqIO::game::featHandler(3pm) NAME
Bio::SeqIO::game::featHandler -- a class for handling feature elements SYNOPSIS
This module is not used directly DESCRIPTION
Bio::SeqIO::game::featHandler converts game XML <annotation> elements into flattened Bio::SeqFeature::Generic objects to be added to the sequence 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 of the bugs and their resolution. Bug reports can be submitted via the web: https://redmine.open-bio.org/projects/bioperl/ AUTHOR - Sheldon McKay Email mckays@cshl.edu APPENDIX
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ new Title : new Usage : my $featHandler = Bio::SeqIO::game::featHandler->new($seq, $seq_h, $ann_l) Function: creates an object to deal with sequence features Returns : a handler object Args : $seq -- a Bio::SeqI compliant object $seq_h -- ref. to a hash of other sequences associated with the main sequence (proteins, etc) $ann_l -- ref. to a list of annotations add_source Title : add_source Usage : $featHandler->add_source($seq->length, \%tags); Function: creates a source feature Returns : a Bio::SeqFeature::Generic object Args : sequence length and a ref. to a hash of tag/value attributes has_gene Title : has_gene Usage : my $gene = $self->_has_gene($gene, $gname, $id) Function: method to get/set the current gene feature Returns : a Bio::SeqFeature::Generic object (if there is a gene) Args : (optional) $gene -- an XML element for the annotation $gname -- gene name $id -- gene ID (not always the same as the name) _has_CDS Title : _has_CDS Usage : my $cds = $self->_has_CDS Function: internal getter/setter for CDS features Returns : a Bio::SeqFeature::Generic transcript object (or nothing) Args : a Bio::SeqFeature::Generic transcript feature add_annotation Title : add_annotation Usage : $featHandler->add_annotation($seq, $type, $id, $tags, $feats) Function: converts a containment hierarchy into an ordered list of flat features Returns : nothing Args : $seq -- a Bio::SeqI compliant object $type -- the annotation type $id -- the anotation ID $tags -- ref. to a hash of tag/value attributes $feats -- ref to an array of Bio::SeqFeature::Generic objects _add_generic_annotation Title : _add_generic_annotation Usage : $self->_add_generic_annotation($seq, $type, $id, $tags, $feats) Function: an internal method to handle non-gene annotations Returns : nothing Args : $seq -- a Bio::SeqI compliant object $type -- the annotation type $id -- the anotation ID $tags -- ref. to a hash of tag/value attributes $feats -- ref to an array of Bio::SeqFeature::Generic objects feature_set Title : feature_set Usage : push @feats, $featHandler->feature_set($id, $gname, $set, $anntype); Function: handles <feature_span> hierarchies (usually a transcript) Returns : a list of Bio::SeqFeature::Generic objects Args : $id -- ID of the feature set $gname -- name of the gene $set -- the <feature_set> object $anntype -- type of the parent annotation _build_feature_set Title : _build_feature_set Usage : $self->_build_feature_set($set, 1) # 1 flag means retain the exon as a subfeat Function: an internal method to process attributes and subfeats of a feature set Returns : nothing Args : $set -- a <feature_set> element 1 -- optional flag to retain exons as subfeats. Otherwise, they will be converted to sublocations of a parent CDS feature _add_feature_span Title : _add_feature_span Usage : $self->_add_feature_span($el, 1) Function: an internal method to process <feature_span> elements Returns : nothing Args : $el -- a <feature_span> element 1 -- an optional flag to retain exons as subfeatures _add_CDS Title : _add_CDS Usage : my $cds = $self->_add_CDS($transcript, $tags) Function: an internal method to create a CDS feature from a transcript feature Returns : a Bio::SeqFeature::Generic object Args : $transcript -- a Bio::SeqFeature::Generic object for a transcript $tags -- ref. to a hash of tag/value attributes perl v5.14.2 2012-03-02 Bio::SeqIO::game::featHandler(3pm)