bio::updateableseqi(3pm) [debian man page]
Bio::UpdateableSeqI(3pm) User Contributed Perl Documentation Bio::UpdateableSeqI(3pm) NAME
Bio::UpdateableSeqI - Descendant of Bio::SeqI that allows updates SYNOPSIS
See Bio::SeqI for most of the documentation. See the documentation of the methods for further details. DESCRIPTION
Bio::UpdateableSeqI is an interface for Sequence objects which are expected to allow users to perform basic editing functions (update/delete) on their component SeqFeatures. 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 - David Block Email dblock@gene.pbi.nrc.ca CONTRIBUTORS
Ewan Birney forced me to this... APPENDIX
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ delete_feature Title : delete_feature Usage : my $orphanlist=$self->delete_feature($feature,$transcript,$gene); Function: deletes the specified $feature from the given transcript, if $transcript is sent and exists and $feature is a feature of $transcript, or from $gene if the $feature is a feature of $gene, or from $self if $transcript and $gene are not sent. Keeps track of the features of the $gene object that may be left as orphans and returns them as a listref. Example : I want to delete transcript 'abc' of gene 'def', with three exons, leaving only transcript 'ghi' with two exons. This will leave exons 1 and 3 part of 'ghi', but exon 2 will become an orphan. my $orphanlist=$seq->delete_feature($transcript{'abc'},undef,$gene{'def'}); $orphanlist is a reference to a list containing $exon{'2'}; Returns : a listref of orphaned features after the deletion of $feature (optional) Args : $feature - the feature to be deleted $transcript - the transcript containing the $feature, so that a $feature can be removed from only one transcript when there are multiple transcripts in a gene. $gene - the gene containing the $transcript and/or the $feature perl v5.14.2 2012-03-02 Bio::UpdateableSeqI(3pm)
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Bio::SeqFeature::Gene::GeneStructureI(3pm) User Contributed Perl Documentation Bio::SeqFeature::Gene::GeneStructureI(3pm) NAME
Bio::SeqFeature::Gene::GeneStructureI - A feature representing an arbitrarily complex structure of a gene SYNOPSIS
#documentation needed DESCRIPTION
A feature representing a gene structure. 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 _ transcripts Title : transcripts() Usage : @transcripts = $gene->transcripts(); Function: Get the transcript features/sites of this gene structure. See Bio::SeqFeature::Gene::TranscriptI for properties of the returned objects. Returns : An array of Bio::SeqFeature::Gene::TranscriptI implementing objects representing the promoter regions or sites. Args : promoters Title : promoters() Usage : @prom_sites = $gene->promoters(); Function: Get the promoter features/sites of this gene structure. 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 = $gene->exons(); @inital = $gene->exons('Initial'); Function: Get all exon features or all exons of specified type of this gene structure. Refer to the documentation of the class that produced this gene structure 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 representing the exon regions. Args : An optional string specifying the type of the exon. introns Title : introns() Usage : @introns = $gene->introns(); Function: Get all introns of this gene structure. Returns : An array of Bio::SeqFeatureI implementing objects representing the introns. Args : poly_A_sites Title : poly_A_sites() Usage : @polyAsites = $gene->poly_A_sites(); Function: Get the poly-adenylation features/sites of this gene structure. Returns : An array of Bio::SeqFeatureI implementing objects representing the poly-adenylation regions or sites. Args : utrs Title : utrs() Usage : @utr_sites = $gene->utrs(); Function: Get the UTR features/sites of this gene structure. See Bio::SeqFeature::Gene::ExonI for properties of the returned objects. Returns : An array of Bio::SeqFeature::Gene::ExonI implementing objects representing the UTR regions or sites. Args : perl v5.14.2 2012-03-02 Bio::SeqFeature::Gene::GeneStructureI(3pm)