[Bioperl-l] (no subject)
Laure.Durufle at serono.com
Laure.Durufle at serono.com
Mon Jul 12 13:00:53 EDT 2004
Hi,
I noticed something : in the the package embl.pm, the method species
returns only the last organism : but in embl, one entry can belong to 2
organisms.
I write a method get_species to obtain all organisms in RichSeq.pm and in
embl.pm, we add push @{$params{'-species'}},$species ; instead
$params{'-species'} = $species ;
# $Id: RichSeq.pm,v 1.9 2002/11/11 18:16:31 lapp Exp $
#
# BioPerl module for Bio::Seq::RichSeq
#
# Cared for by Ewan Birney <birney at ebi.ac.uk>
#
# 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 Bio::Seq::RichSeqI 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 at bioperl.org - General discussion
http://bio.perl.org/MailList.html - About the mailing lists
=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 email or the web:
bioperl-bugs at bio.perl.org
http://bugzilla.bioperl.org/
=head1 AUTHOR - Ewan Birney
Email birney at ebi.ac.uk
Describe contact details here
=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 @ISA);
use strict;
# Object preamble - inherits from Bio::Root::Object
use Bio::Seq;
use Bio::Seq::RichSeqI;
use Data::Denter;
@ISA = 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, at args) = @_;
my $self = $caller->SUPER::new(@args);
$self->{'_dates'} = [];
$self->{'_secondary_accession'} = [];
$self->{'_species'} = [];
my ($dates, $xtra, $sv,
$keywords, $pid, $mol,
$division,$species ) = $self->_rearrange([qw(DATES
SECONDARY_ACCESSIONS
SEQ_VERSION
KEYWORDS
PID
MOLECULE
DIVISION
SPECIES
)],
@args);
defined $division && $self->division($division);
defined $mol && $self->molecule($mol);
defined $keywords && $self->keywords($keywords);
defined $sv && $self->seq_version($sv);
defined $pid && $self->pid($pid);
#defined $pid && $self->species($pid);
if( defined $dates ) {
if( ref($dates) =~ /array/i ) {
foreach ( @$dates) {
$self->add_date($_);
}
} else {
$self->add_date($dates);
}
}
if( defined $species ) {
if( ref($species) =~ /array/i ) {
foreach ( @$species) {
$self->add_species($_);
}
} else {
$self->add_species($species);
}
}
if( defined $xtra ) {
if( ref($xtra) =~ /array/i ) {
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_species
Title : add_species
Usage : $self->add_species($species)
Function: adds a species
Example :
Returns : an array of such strings
Args :
=cut
sub add_species {
my ($self, at species) = @_;
foreach my $dt ( @species ) {
push(@{$self->{'_species'}},$dt);
}
}
=head2 get_species
Title : get_species
Usage :
Function:
Example :
Returns : an array of strings
Args :
=cut
sub get_species{
my ($self) = @_;
return @{$self->{'_species'}};
}
=head2 add_date
Title : add_date
Usage : $self->add_date($datestr)
Function: adds a date
Example :
Returns : a date string or an array of such strings
Args :
=cut
sub add_date {
my ($self, at dates) = @_;
foreach my $dt ( @dates ) {
push(@{$self->{'_dates'}},$dt);
}
}
=head2 get_dates
Title : get_dates
Usage :
Function:
Example :
Returns : an array of date strings
Args :
=cut
sub get_dates{
my ($self) = @_;
return @{$self->{'_dates'}};
}
=head2 pid
Title : pid
Usage :
Function: Get (and set, depending on the implementation) the PID property
for the sequence.
Example :
Returns : a string
Args :
=cut
sub pid {
my ($self,$pid) = @_;
if(defined($pid)) {
$self->{'_pid'} = $pid;
}
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, at args) = @_;
return $obj->accession_number(@args);
}
=head2 add_secondary_accession
Title : add_secondary_accession
Usage : $self->add_domment($ref)
Function: adds a secondary_accession
Example :
Returns :
Args : a string or an array of strings
=cut
sub add_secondary_accession {
my ($self) = shift;
foreach my $dt ( @_ ) {
push(@{$self->{'_secondary_accession'}},$dt);
}
}
=head2 get_secondary_accessions
Title : get_secondary_accessions
Usage :
Function:
Example :
Returns : An array of strings
Args :
=cut
sub get_secondary_accessions{
my ($self, at args) = @_;
return @{$self->{'_secondary_accession'}};
}
=head2 seq_version
Title : seq_version
Usage : $obj->seq_version($newval)
Function:
Example :
Returns : value of seq_version
Args : newvalue (optional)
=cut
sub seq_version{
my ($obj,$value) = @_;
if( defined $value) {
$obj->{'_seq_version'} = $value;
}
return $obj->{'_seq_version'};
}
=head2 keywords
Title : keywords
Usage : $obj->keywords($newval)
Function:
Returns : value of keywords (a string)
Args : newvalue (optional) (a string)
=cut
sub keywords {
my $obj = shift;
if( @_ ) {
my $value = shift;
$obj->{'_keywords'} = $value;
}
return $obj->{'_keywords'};
}
#
##
### Deprecated methods kept for ease of transtion
##
#
sub each_date {
my ($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;
Best regards
Laure Durufle
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