# $Id: RichSeq.pm 16123 2009-09-17 12:57:27Z cjfields $ # # BioPerl module for Bio::Seq::RichSeq # # Please direct questions and support issues to # # Cared for by Ewan Birney # # Copyright Ewan Birney # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::Seq::RichSeq - Module implementing a sequence created from a rich sequence database entry =head1 SYNOPSIS See L and documentation of methods. =head1 DESCRIPTION This module implements Bio::Seq::RichSeqI, an interface for sequences created from or created for entries from/of rich sequence databanks, like EMBL, GenBank, and SwissProt. Methods added to the Bio::SeqI interface therefore focus on databank-specific information. Note that not every rich databank format may use all of the properties provided. =head1 Implemented Interfaces This class implementes the following interfaces. =over 4 =item Bio::Seq::RichSeqI Note that this includes implementing Bio::PrimarySeqI and Bio::SeqI. =item Bio::IdentifiableI =item Bio::DescribableI =item Bio::AnnotatableI =back =head1 FEEDBACK =head2 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 =head2 Support Please direct usage questions or support issues to the mailing list: I 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. =head2 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: http://bugzilla.open-bio.org/ =head1 AUTHOR - Ewan Birney Email birney@ebi.ac.uk =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::Seq::RichSeq; use vars qw($AUTOLOAD); use strict; use base qw(Bio::Seq Bio::Seq::RichSeqI); =head2 new Title : new Usage : $seq = Bio::Seq::RichSeq->new( -seq => 'ATGGGGGTGGTGGTACCCT', -id => 'human_id', -accession_number => 'AL000012', ); Function: Returns a new seq object from basic constructors, being a string for the sequence and strings for id and accession_number Returns : a new Bio::Seq::RichSeq object =cut sub new { # standard new call.. my($caller,@args) = @_; my $self = $caller->SUPER::new(@args); $self->{'_dates'} = []; $self->{'_secondary_accession'} = []; my ($dates, $xtra, $sv, $keywords, $pid, $mol, $division ) = $self->_rearrange([qw(DATES SECONDARY_ACCESSIONS SEQ_VERSION KEYWORDS PID MOLECULE DIVISION )], @args); defined $division && $self->division($division); defined $mol && $self->molecule($mol); if(defined($keywords)) { if(ref($keywords) && (ref($keywords) eq "ARRAY")) { $self->add_keyword(@$keywords); } else { # got a string - use the old API $self->keywords($keywords); } } defined $sv && $self->seq_version($sv); defined $pid && $self->pid($pid); if( defined $dates ) { if( ref($dates) eq "ARRAY" ) { foreach ( @$dates) { $self->add_date($_); } } else { $self->add_date($dates); } } if( defined $xtra ) { if( ref($xtra) eq "ARRAY" ) { foreach ( @$xtra) { $self->add_secondary_accession($_); } } else { $self->add_secondary_accession($xtra); } } return $self; } =head2 division Title : division Usage : $obj->division($newval) Function: Returns : value of division Args : newvalue (optional) =cut sub division { my $obj = shift; if( @_ ) { my $value = shift; $obj->{'_division'} = $value; } return $obj->{'_division'}; } =head2 molecule Title : molecule Usage : $obj->molecule($newval) Function: Returns : type of molecule (DNA, mRNA) Args : newvalue (optional) =cut sub molecule { my $obj = shift; if( @_ ) { my $value = shift; $obj->{'_molecule'} = $value; } return $obj->{'_molecule'}; } =head2 add_date Title : add_date Usage : $self->add_date($datestr) Function: adds one or more dates This implementation stores dates as keyed annotation, the key being 'date_changed'. You can take advantage of this fact when accessing the annotation collection directly. Example : Returns : Args : a date string or an array of such strings =cut sub add_date { return shift->_add_annotation_value('date_changed',@_); } =head2 get_dates Title : get_dates Usage : my @dates = $seq->get_dates; Function: Get the dates of the sequence (usually, when it was created and changed. Returns : an array of date strings Args : =cut sub get_dates{ return shift->_get_annotation_values('date_changed'); } =head2 pid Title : pid Usage : my $pid = $seq->pid(); Function: Get (and set, depending on the implementation) the PID property for the sequence. Returns : a string Args : =cut sub pid{ my $self = shift; return $self->{'_pid'} = shift if @_; return $self->{'_pid'}; } =head2 accession Title : accession Usage : $obj->accession($newval) Function: Whilst the underlying sequence object does not have an accession, so we need one here. In this implementation this is merely a synonym for accession_number(). Example : Returns : value of accession Args : newvalue (optional) =cut sub accession { my ($obj,@args) = @_; return $obj->accession_number(@args); } =head2 add_secondary_accession Title : add_secondary_accession Usage : $self->add_domment($ref) Function: adds a secondary_accession This implementation stores secondary accession numbers as keyed annotation, the key being 'secondary_accession'. You can take advantage of this fact when accessing the annotation collection directly. Example : Returns : Args : a string or an array of strings =cut sub add_secondary_accession { return shift->_add_annotation_value('secondary_accession',@_); } =head2 get_secondary_accessions Title : get_secondary_accessions Usage : my @acc = $seq->get_secondary_accessions(); Function: Get the secondary accession numbers as strings. Returns : An array of strings Args : none =cut sub get_secondary_accessions{ return shift->_get_annotation_values('secondary_accession'); } =head2 seq_version Title : seq_version Usage : $obj->seq_version($newval) Function: Get/set the sequence version Returns : value of seq_version (a scalar) Args : on set, new value (a scalar or undef, optional) =cut sub seq_version{ my $self = shift; return $self->{'_seq_version'} = shift if @_; return $self->{'_seq_version'}; } =head2 add_keyword Title : add_keyword Usage : $obj->add_keyword($newval) Function: Add a new keyword to the annotation of the sequence. This implementation stores keywords as keyed annotation, the key being 'keyword'. You can take advantage of this fact when accessing the annotation collection directly. Returns : Args : value to be added (optional) (a string) =cut sub add_keyword { return shift->_add_annotation_value('keyword',@_); } =head2 get_keywords Title : get_keywords Usage : $obj->get_keywords($newval) Function: Get the keywords for this sequence as an array of strings. Returns : an array of strings Args : =cut sub get_keywords { return shift->_get_annotation_values('keyword'); } =head1 Private methods and synonyms for backward compatibility =cut =head2 _add_annotation_value Title : _add_annotation_value Usage : Function: Adds a value to the annotation collection under the specified key. Note that this is not a public method. Returns : Args : key (a string), value(s) (one or more scalars) =cut sub _add_annotation_value{ my $self = shift; my $key = shift; foreach my $val (@_) { $self->annotation->add_Annotation( Bio::Annotation::SimpleValue->new(-tagname => $key, -value => $val) ); } } =head2 _get_annotation_values Title : _get_annotation_values Usage : Function: Gets the values of a specific annotation as identified by the key from the annotation collection. Note that this is not a public method. Example : Returns : an array of strings Args : the key (a string) =cut sub _get_annotation_values{ my $self = shift; return map { $_->value(); } $self->annotation->get_Annotations(shift); } # ## ### Deprecated methods kept for ease of transition ## # sub keywords { my $self = shift; # have we been called in set mode? if(@_) { # yes; translate to the new API foreach my $kwd (@_) { $self->add_keyword(split(/\s*;\s*/,$kwd)); } } else { # no; translate read-only to the new API return join("; ",$self->get_keywords()); } } sub each_date { my ($self) = @_; $self->warn("Deprecated method... please use get_dates"); return $self->get_dates; } sub each_secondary_accession { my ($self) = @_; $self->warn("each_secondary_accession - deprecated method. use get_secondary_accessions"); return $self->get_secondary_accessions; } sub sv { my ($obj,$value) = @_; $obj->warn("sv - deprecated method. use seq_version"); $obj->seq_version($value); } 1;