bio::variation::allele(3pm) [debian man page]
Bio::Variation::Allele(3pm) User Contributed Perl Documentation Bio::Variation::Allele(3pm) NAME
Bio::Variation::Allele - Sequence object with allele-specific attributes SYNOPSIS
$allele1 = Bio::Variation::Allele->new ( -seq => 'A', -id => 'AC00001.1', -alphabet => 'dna', -is_reference => 1 ); DESCRIPTION
List of alleles describe known sequence alternatives in a variable region. Alleles are contained in Bio::Variation::VariantI complying objects. See Bio::Variation::VariantI for details. Bio::Varation::Alleles are PrimarySeqI complying objects which can contain database cross references as specified in Bio::DBLinkContainerI interface, too. A lot of the complexity with dealing with Allele objects are caused by null alleles; Allele objects that have zero length sequence string. In addition describing the allele by its sequence , it possible to give describe repeat structure within the sequence. This done using methods repeat_unit (e.g. 'ca') and repeat_count (e.g. 7). 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 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 - Heikki Lehvaslaiho Email: heikki-at-bioperl-dot-org APPENDIX
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ is_reference Title : is_reference Usage : $obj->is_reference() Function: sets and returns boolean values. Unset values return false. Example : $obj->is_reference() Returns : boolean Args : optional true of false value add_DBLink Title : add_DBLink Usage : $self->add_DBLink($ref) Function: adds a link object Example : Returns : Args : each_DBLink Title : each_DBLink Usage : foreach $ref ( $self->each_DBlink() ) Function: gets an array of DBlink of objects Example : Returns : Args : repeat_unit Title : repeat_unit Usage : $obj->repeat_unit('ca'); Function: Sets and returns the sequence of the repeat_unit the allele is composed of. Example : Returns : string Args : string repeat_count Title : repeat_count Usage : $obj->repeat_count(); Function: Sets and returns the number of repeat units in the allele. Example : Returns : string Args : string count Title : count Usage : $obj->count(); Function: Sets and returns the number of times this allele was observed. Example : Returns : string Args : string frequency Title : frequency Usage : $obj->frequency(); Function: Sets and returns the frequency of the allele in the observed population. Example : Returns : string Args : string perl v5.14.2 2012-03-02 Bio::Variation::Allele(3pm)
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Bio::Variation::DNAMutation(3pm) User Contributed Perl Documentation Bio::Variation::DNAMutation(3pm) NAME
Bio::Variation::DNAMutation - DNA level mutation class SYNOPSIS
$dnamut = Bio::Variation::DNAMutation->new ('-start' => $start, '-end' => $end, '-length' => $len, '-upStreamSeq' => $upflank, '-dnStreamSeq' => $dnflank, '-proof' => $proof, '-isMutation' => 1, '-mut_number' => $mut_number ); $a1 = Bio::Variation::Allele->new; $a1->seq('a'); $dnamut->allele_ori($a1); my $a2 = Bio::Variation::Allele->new; $a2->seq('t'); $dnamut->add_Allele($a2); print "Restriction changes are ", $dnamut->restriction_changes, " "; # add it to a SeqDiff container object $seqdiff->add_Variant($dnamut); DESCRIPTION
The instantiable class Bio::Variation::DNAMutation describes basic sequence changes in genomic DNA level. It uses methods defined in superclass Bio::Variation::VariantI. See Bio::Variation::VariantI for details. If the variation described by a DNAMutation object is transcibed, link the corresponding Bio::Variation::RNAChange object to it using method RNAChange(). See Bio::Variation::RNAChange for more information. 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 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 - Heikki Lehvaslaiho Email: heikki-at-bioperl-dot-org APPENDIX
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ CpG Title : CpG Usage : $obj->CpG() Function: sets and returns boolean values for variation hitting a CpG site. Unset value return -1. Example : $obj->CpG() Returns : boolean Args : optional true of false value RNAChange Title : RNAChange Usage : $mutobj = $obj->RNAChange; : $mutobj = $obj->RNAChange($objref); Function: Returns or sets the link-reference to a mutation/change object. If there is no link, it will return undef Returns : an obj_ref or undef label Title : label Usage : $obj->label(); Function: Sets and returns mutation event label(s). If value is not set, or no argument is given returns false. Each instantiable subclass of L<Bio::Variation::VariantI> needs to implement this method. Valid values are listed in 'Mutation event controlled vocabulary' in http://www.ebi.ac.uk/mutations/recommendations/mutevent.html. Example : Returns : string Args : string sysname Title : sysname Usage : $self->sysname Function: This subroutine creates a string corresponding to the 'systematic name' of the mutation. Systematic name is specified in Antonorakis & MDI Nomenclature Working Group: Human Mutation 11:1-3, 1998. Returns : string perl v5.14.2 2012-03-02 Bio::Variation::DNAMutation(3pm)