bio::seqfeature::collectioni(3pm) [debian man page]
Bio::SeqFeature::CollectionI(3pm) User Contributed Perl Documentation Bio::SeqFeature::CollectionI(3pm) NAME
Bio::SeqFeature::CollectionI - An interface for a collection of SeqFeatureI objects. SYNOPSIS
# get a Bio::SeqFeature::CollectionI somehow # perhaps a Bio::SeqFeature::Collection use Bio::SeqFeature::Collection; my $collection = Bio::SeqFeature::Collection->new(); $collection->add_features(@featurelist); $collection->features(-attributes => [ { 'location' => Bio::Location::Simple->new (-start=> 1, -end => 300) , 'overlaps' }]); DESCRIPTION
This interface describes the basic methods needed for a collection of Sequence Features. 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 the Bioperl mailing list. 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 - Jason Stajich Email jason@bioperl.org APPENDIX
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ add_features Title : add_features Usage : $collection->add_features(@features); Function: Returns : number of features added Args : arrayref of Bio::SeqFeatureI objects to index features Title : features Usage : my @f = $collection->features(@args); Returns : a list of Bio::SeqFeatureI objects Args : see below Status : public This routine will retrieve features associated with this collection object. It can be used to return all features, or a subset based on their type, location, or attributes. -types List of feature types to return. Argument is an array of Bio::Das::FeatureTypeI objects or a set of strings that can be converted into FeatureTypeI objects. -callback A callback to invoke on each feature. The subroutine will be passed to each Bio::SeqFeatureI object in turn. -attributes A hash reference containing attributes to match. The -attributes argument is a hashref containing one or more attributes to match against: -attributes => { Gene => 'abc-1', Note => 'confirmed' } Attribute matching is simple exact string matching, and multiple attributes are ANDed together. See Bio::DB::ConstraintsI for a more sophisticated take on this. If one provides a callback, it will be invoked on each feature in turn. If the callback returns a false value, iteration will be interrupted. When a callback is provided, the method returns undef. perl v5.14.2 2012-03-02 Bio::SeqFeature::CollectionI(3pm)
Check Out this Related Man Page
Bio::SeqFeature::Gene::TranscriptI(3pm) User Contributed Perl Documentation Bio::SeqFeature::Gene::TranscriptI(3pm) NAME
Bio::SeqFeature::Gene::TranscriptI - Interface for a feature representing a transcript of exons, promoter(s), UTR, and a poly-adenylation site. SYNOPSIS
#documentation needed DESCRIPTION
A feature representing a transcript. 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 the bugs and their resolution. Bug reports can be submitted via the web: https://redmine.open-bio.org/projects/bioperl/ AUTHOR - Hilmar Lapp Email hlapp@gmx.net APPENDIX
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ promoters Title : promoters() Usage : @proms = $transcript->promoters(); Function: Get the promoter features of this transcript. Note that OO-modeling of regulatory elements is not stable yet. This means that this method might change or even disappear in a future release. Be aware of this if you use it. Returns : An array of Bio::SeqFeatureI implementing objects representing the promoter regions or sites. Args : exons Title : exons() Usage : @exons = $transcript->exons(); @inital = $transcript->exons('Initial'); Function: Get the individual exons this transcript comprises of, or all exons of a specified type. Refer to the documentation of the class that produced this transcript object for information about the possible types. See Bio::SeqFeature::Gene::ExonI for properties of the returned objects. Returns : An array of Bio::SeqFeature::Gene::ExonI implementing objects Args : An optional string specifying the type of the exon. introns Title : introns() Usage : @introns = $transcript->introns(); Function: Get all introns this transcript comprises of. Returns : An array of Bio::SeqFeatureI implementing objects representing the introns. Args : poly_A_site Title : poly_A_site() Usage : $polyAsite = $transcript->poly_A_site(); Function: Get the poly-adenylation site of this transcript. Returns : A Bio::SeqFeatureI implementing object. Args : utrs Title : utrs() Usage : @utr_sites = $transcript->utrs(); Function: Get the UTR regions this transcript comprises of. See Bio::SeqFeature::Gene::ExonI for properties of the returned objects. Returns : An array of Bio::SeqFeature::Gene::ExonI implementing objects Args : mrna Title : mrna() Usage : $mrna = $transcript->mrna(); Function: Get the mRNA of the transcript as a sequence object. Returns : A Bio::PrimarySeqI implementing object. Args : cds Title : cds() Usage : $cds = $transcript->cds(); Function: Get the CDS (coding sequence) of the transcript as a sequence object. Returns : A Bio::PrimarySeqI implementing object. Args : protein Title : protein() Usage : $protein = $transcript->protein(); Function: Get the protein encoded by the transcript as a sequence object. Returns : A Bio::PrimarySeqI implementing object. Args : parent Title : parent Usage : $obj->parent($newval) Function: get the parent gene of the transcript Returns : value of parent - a Bio::SeqFeature::Gene::GeneStructureI-compliant object Args : a Bio::SeqFeature::Gene::GeneStructureI-compliant object (optional) perl v5.14.2 2012-03-02 Bio::SeqFeature::Gene::TranscriptI(3pm)