bio::liveseq::gene(3pm) [debian man page]
Bio::LiveSeq::Gene(3pm) User Contributed Perl Documentation Bio::LiveSeq::Gene(3pm) NAME
Bio::LiveSeq::Gene - Range abstract class for LiveSeq SYNOPSIS
# documentation needed DESCRIPTION
This is used as storage for all object references concerning a particular gene. AUTHOR - Joseph A.L. Insana Email: Insana@ebi.ac.uk, jinsana@gmx.net APPENDIX
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ new Title : new Usage : $gene = Bio::LiveSeq::Gene->new(-name => "name", -features => $hashref -upbound => $min -downbound => $max); Function: generates a new Bio::LiveSeq::Gene Returns : reference to a new object of class Gene Errorcode -1 Args : one string and one hashreference containing all features defined for the Gene and the references to the LiveSeq objects for those features. Two labels for defining boundaries of the gene. Usually the boundaries will reflect max span of transcript, exon... features, while the DNA sequence will be created with some flanking regions (e.g. with the EMBL_SRS::gene2liveseq routine). If these two labels are not given, they will default to the start and end of the DNA object. Note : the format of the hash has to be like DNA => reference to LiveSeq::DNA object Transcripts => reference to array of transcripts objrefs Transclations => reference to array of transcripts objrefs Exons => .... Introns => .... Prim_Transcripts => .... Repeat_Units => .... Repeat_Regions => .... Only DNA and Transcripts are mandatory verbose Title : verbose Usage : $self->verbose(0) Function: Sets verbose level for how ->warn behaves -1 = silent: no warning 0 = reduced: minimal warnings 1 = default: all warnings 2 = extended: all warnings + stack trace dump 3 = paranoid: a warning becomes a throw and the program dies Note: a quick way to set all LiveSeq objects at the same verbosity level is to change the DNA level object, since they all look to that one if their verbosity_level attribute is not set. But the method offers fine tuning possibility by changing the verbose level of each object in a different way. So for example, after $loader= and $gene= have been retrieved by a program, the command $gene->verbose(0); would set the default verbosity level to 0 for all objects. Returns : the current verbosity level Args : -1,0,1,2 or 3 perl v5.14.2 2012-03-02 Bio::LiveSeq::Gene(3pm)
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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)