05-18-2014
well, the id field in the exon rows may not always be of that form. It happens so in this case but they may be represented differently. the 'true gene id' is always in the gene row.
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LEARN ABOUT DEBIAN
bio::seqfeature::gene::genestructurei
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)