Bio::Seq
RichSeq
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Summary
Bio::Seq::RichSeq - Module implementing a sequence created from a rich
sequence database entry
Package variables
No package variables defined.
Inherit
Synopsis
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.
For more information, please see the relevant
Methods
Methods description
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 |
Title : division Usage : $obj->division($newval) Function: Returns : value of division Args : newvalue (optional) |
Title : molecule Usage : $obj->molecule($newval) Function: Returns : type of molecule (DNA, mRNA) Args : newvalue (optional) |
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 |
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 : |
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 : |
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) |
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 |
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 |
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) Note : this differs from Bio::PrimarySeq version() in that this explicitly refers to the sequence record version one would find in a typical sequence file. |
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) |
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 : |
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) |
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) |
Methods code
sub new
{ 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 {
$self->keywords($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; } |
sub division
{ my $obj = shift;
if( @_ ) {
my $value = shift;
$obj->{'_division'} = $value;
}
return $obj->{'_division'};} |
sub molecule
{ my $obj = shift;
if( @_ ) {
my $value = shift;
$obj->{'_molecule'} = $value;
}
return $obj->{'_molecule'};} |
sub add_date
{ return shift->_add_annotation_value('date_changed',@_);} |
sub get_dates
{ return shift->_get_annotation_values('date_changed');} |
sub pid
{ my $self = shift;
return $self->{'_pid'} = shift if @_;
return $self->{'_pid'};} |
sub accession
{ my ($obj,@args) = @_;
return $obj->accession_number(@args); } |
sub add_secondary_accession
{ return shift->_add_annotation_value('secondary_accession',@_);} |
sub get_secondary_accessions
{ return shift->_get_annotation_values('secondary_accession');} |
sub seq_version
{ my $self = shift;
return $self->{'_seq_version'} = shift if @_;
return $self->{'_seq_version'};} |
sub add_keyword
{ return shift->_add_annotation_value('keyword',@_);} |
sub get_keywords
{ return shift->_get_annotation_values('keyword');} |
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)
);
}} |
sub _get_annotation_values
{ my $self = shift;
return map { $_->value(); } $self->annotation->get_Annotations(shift);
}
} |
sub keywords
{ my $self = shift;
if(@_) {
foreach my $kwd (@_) {
$self->add_keyword(split(/\s*;\s*/,$kwd));
}
} else {
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;} |
General documentation
| Implemented Interfaces | Top |
This class implementes the following interfaces.
Note that this includes implementing
Bio::PrimarySeqI and
Bio::SeqI,
specifically via
Bio::Seq and
Bio::PrimarySeq. Please review the
documentation for those modules on implementation details relevant to those
interfaces, as well as the ones below.
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
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.
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/
The rest of the documentation details each of the object
methods. Internal methods are usually preceded with a _
| Private methods and synonyms for backward compatibility | Top |