#
# BioPerl module for Bio::SeqFeature::Generic
#
# Please direct questions and support issues to <bioperl-l@bioperl.org>
#
# Cared for by mark Fiers <m.w.e.j.fiers@plant.wag-ur.nl>
#
# Copyright Ewan Birney, Mark Fiers
#
# You may distribute this module under the same terms as perl itself
# POD documentation - main docs before the code
=head1 NAME
Bio::SeqFeature::Computation - Computation SeqFeature
=head1 SYNOPSIS
$feat = Bio::SeqFeature::Computation->new(
-start => 10,
-end => 100,
-strand => -1,
-primary => 'repeat',
-program_name => 'GeneMark',
-program_date => '12-5-2000',
-program_version => 'x.y',
-database_name => 'Arabidopsis',
-database_date => '12-dec-2000',
-computation_id => 2231,
-score => { no_score => 334 }
);
=head1 DESCRIPTION
Bio::SeqFeature::Computation extends the Generic seqfeature object with
a set of computation related fields and a more flexible set of storing
more types of score and subseqfeatures. It is compatible with the Generic
SeqFeature object.
The new way of storing score values is similar to the tag structure in the
Generic object. For storing sets of subseqfeatures the array containg the
subseqfeatures is now a hash which contains arrays of seqfeatures
Both the score and subSeqfeature methods can be called in exactly the same
way, the value's will be stored as a 'default' score or subseqfeature.
=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<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.
=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:
https://redmine.open-bio.org/projects/bioperl/
=head1 AUTHOR - Ewan Birney, Mark Fiers
Ewan Birney E<lt>birney@sanger.ac.ukE<gt>
Mark Fiers E<lt>m.w.e.j.fiers@plant.wag-ur.nlE<gt>
=head1 DEVELOPERS
This class has been written with an eye out of inheritance. The fields
the actual object hash are:
_gsf_sub_hash = reference to a hash containing sets of sub arrays
_gsf_score_hash= reference to a hash for the score values
=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::SeqFeature::Computation;
use strict;
use base qw(Bio::SeqFeature::Generic);
sub new {
my ( $class, @args) = @_;
my $self = $class->SUPER::new(@args);
my ( $computation_id, $program_name, $program_date, $program_version,
$database_name, $database_date, $database_version) =
$self->_rearrange([qw( COMPUTATION_ID
PROGRAM_NAME
PROGRAM_DATE
PROGRAM_VERSION
DATABASE_NAME
DATABASE_DATE
DATABASE_VERSION )],@args);
$program_name && $self->program_name($program_name);
$program_date && $self->program_date($program_date);
$program_version && $self->program_version($program_version);
$database_name && $self->database_name($database_name);
$database_date && $self->database_date($database_date);
$database_version && $self->database_version($database_version);
$computation_id && $self->computation_id($computation_id);
return $self;
}
=head2 has_score
Title : has_score
Usage : $value = $self->has_score('some_score')
Function: Tests wether a feature contains a score
Returns : TRUE if the SeqFeature has the score,
and FALSE otherwise.
Args : The name of a score
=cut
sub has_score {
my ($self, $score) = @_;
return unless defined $score;
return exists $self->{'_gsf_score_hash'}->{$score};
}
=head2 add_score_value
Title : add_score_value
Usage : $self->add_score_value('P_value',224);
Returns : TRUE on success
Args : score (string) and value (any scalar)
=cut
sub add_score_value {
my ($self, $score, $value) = @_;
if( ! defined $score || ! defined $value ) {
$self->warn("must specify a valid $score and $value to add_score_value");
return 0;
}
if ( !defined $self->{'_gsf_score_hash'}->{$score} ) {
$self->{'_gsf_score_hash'}->{$score} = [];
}
push(@{$self->{'_gsf_score_hash'}->{$score}},$value);
}
=head2 score
Title : score
Usage : $value = $comp_obj->score()
$comp_obj->score($value)
Function: Returns the 'default' score or sets the 'default' score
This method exist for compatibility options
It would equal ($comp_obj->each_score_value('default'))[0];
Returns : A value
Args : (optional) a new value for the 'default' score
=cut
sub score {
my ($self, $value) = @_;
my @v;
if (defined $value) {
if( ref($value) =~ /HASH/i ) {
while( my ($t,$val) = each %{ $value } ) {
$self->add_score_value($t,$val);
}
} else {
@v = $value;
$self->add_score_value('default', $value);
}
} else {
@v = $self->each_score_value('default');
}
return $v[0];
}
=head2 each_score_value
Title : each_score_value
Usage : @values = $gsf->each_score_value('note');
Function: Returns a list of all the values stored
under a particular score.
Returns : A list of scalars
Args : The name of the score
=cut
sub each_score_value {
my ($self, $score) = @_;
if ( ! exists $self->{'_gsf_score_hash'}->{$score} ) {
$self->warn("asking for score value that does not exist $score");
return;
}
return @{$self->{'_gsf_score_hash'}->{$score}};
}
=head2 all_scores
Title : all_scores
Usage : @scores = $feat->all_scores()
Function: Get a list of all the scores in a feature
Returns : An array of score names
Args : none
=cut
sub all_scores {
my ($self, @args) = @_;
return keys %{$self->{'_gsf_score_hash'}};
}
=head2 remove_score
Title : remove_score
Usage : $feat->remove_score('some_score')
Function: removes a score from this feature
Returns : nothing
Args : score (string)
=cut
sub remove_score {
my ($self, $score) = @_;
if ( ! exists $self->{'_gsf_score_hash'}->{$score} ) {
$self->warn("trying to remove a score that does not exist: $score");
}
delete $self->{'_gsf_score_hash'}->{$score};
}
=head2 computation_id
Title : computation_id
Usage : $computation_id = $feat->computation_id()
$feat->computation_id($computation_id)
Function: get/set on program name information
Returns : string
Args : none if get, the new value if set
=cut
sub computation_id {
my ($self,$value) = @_;
if (defined($value)) {
$self->{'_gsf_computation_id'} = $value;
}
return $self->{'_gsf_computation_id'};
}
=head2 program_name
Title : program_name
Usage : $program_name = $feat->program_name()
$feat->program_name($program_name)
Function: get/set on program name information
Returns : string
Args : none if get, the new value if set
=cut
sub program_name {
my ($self,$value) = @_;
if (defined($value)) {
$self->{'_gsf_program_name'} = $value;
}
return $self->{'_gsf_program_name'};
}
=head2 program_date
Title : program_date
Usage : $program_date = $feat->program_date()
$feat->program_date($program_date)
Function: get/set on program date information
Returns : date (string)
Args : none if get, the new value if set
=cut
sub program_date {
my ($self,$value) = @_;
if (defined($value)) {
$self->{'_gsf_program_date'} = $value;
}
return $self->{'_gsf_program_date'};
}
=head2 program_version
Title : program_version
Usage : $program_version = $feat->program_version()
$feat->program_version($program_version)
Function: get/set on program version information
Returns : date (string)
Args : none if get, the new value if set
=cut
sub program_version {
my ($self,$value) = @_;
if (defined($value)) {
$self->{'_gsf_program_version'} = $value;
}
return $self->{'_gsf_program_version'};
}
=head2 database_name
Title : database_name
Usage : $database_name = $feat->database_name()
$feat->database_name($database_name)
Function: get/set on program name information
Returns : string
Args : none if get, the new value if set
=cut
sub database_name {
my ($self,$value) = @_;
if (defined($value)) {
$self->{'_gsf_database_name'} = $value;
}
return $self->{'_gsf_database_name'};
}
=head2 database_date
Title : database_date
Usage : $database_date = $feat->database_date()
$feat->database_date($database_date)
Function: get/set on program date information
Returns : date (string)
Args : none if get, the new value if set
=cut
sub database_date {
my ($self,$value) = @_;
if (defined($value)) {
$self->{'_gsf_database_date'} = $value;
}
return $self->{'_gsf_database_date'};
}
=head2 database_version
Title : database_version
Usage : $database_version = $feat->database_version()
$feat->database_version($database_version)
Function: get/set on program version information
Returns : date (string)
Args : none if get, the new value if set
=cut
sub database_version {
my ($self,$value) = @_;
if (defined($value)) {
$self->{'_gsf_database_version'} = $value;
}
return $self->{'_gsf_database_version'};
}
=head2 get_SeqFeature_type
Title : get_SeqFeature_type
Usage : $SeqFeature_type = $feat->get_SeqFeature_type()
$feat->get_SeqFeature_type($SeqFeature_type)
Function: Get SeqFeature type which is automatically set when adding
a computation (SeqFeature) to a computation object
Returns : SeqFeature_type (string)
Args : none if get, the new value if set
=cut
sub get_SeqFeature_type {
my ($self, $value) = @_;
if (defined($value)) {
$self->{'_gsf_sub_SeqFeature_type'} = $value;
}
return $self->{'_gsf_sub_SeqFeature_type'};
}
=head2 get_all_SeqFeature_types
Title : get_all_SeqFeature_types
Usage : @all_SeqFeature_types = $comp->get_all_SeqFeature_types();
Function: Returns an array with all subseqfeature types
Returns : An array
Args : none
=cut
sub get_all_SeqFeature_types {
my ($self) = @_;
return keys ( %{$self->{'gsf_sub_hash'}} );
}
=head2 get_SeqFeatures
Title : get_SeqFeatures('feature_type')
Usage : @feats = $feat->get_SeqFeatures();
@feats = $feat->get_SeqFeatures('feature_type');
Function: Returns an array of sub Sequence Features of a specific
type or, if the type is ommited, all sub Sequence Features
Returns : An array
Args : (optional) a SeqFeature type (ie exon, pattern)
=cut
sub get_SeqFeatures {
my ($self, $ssf_type) = @_;
my (@return_array) = ();
if ($ssf_type eq '') {
#return all SeqFeatures
foreach (keys ( %{$self->{'gsf_sub_hash'}} )){
push @return_array, @{$self->{'gsf_sub_hash'}->{$_}};
}
return @return_array;
} else {
if (defined ($self->{'gsf_sub_hash'}->{$ssf_type})) {
return @{$self->{'gsf_sub_hash'}->{$ssf_type}};
} else {
$self->warn("$ssf_type is not a valid sub SeqFeature type");
}
}
}
=head2 add_SeqFeature
Title : add_SeqFeature
Usage : $feat->add_SeqFeature($subfeat);
$feat->add_SeqFeature($subfeat,'seqfeature_type')
$feat->add_SeqFeature($subfeat,'EXPAND')
$feat->add_SeqFeature($subfeat,'EXPAND','seqfeature_type')
Function: adds a SeqFeature into a specific subSeqFeature array.
with no 'EXPAND' qualifer, subfeat will be tested
as to whether it lies inside the parent, and throw
an exception if not.
If EXPAND is used, the parents start/end/strand will
be adjusted so that it grows to accommodate the new
subFeature,
optionally a seqfeature type can be defined.
Returns : nothing
Args : An object which has the SeqFeatureI interface
(optional) 'EXPAND'
(optional) 'SeqFeature_type'
=cut
sub add_SeqFeature{
my ($self,$feat,$var1, $var2) = @_;
$var1 = '' unless( defined $var1);
$var2 = '' unless( defined $var2);
my ($expand, $ssf_type) = ('', $var1 . $var2);
$expand = 'EXPAND' if ($ssf_type =~ s/EXPAND//);
if ( !$feat->isa('Bio::SeqFeatureI') ) {
$self->warn("$feat does not implement Bio::SeqFeatureI. Will add it anyway, but beware...");
}
if($expand eq 'EXPAND') {
$self->_expand_region($feat);
} else {
if ( !$self->contains($feat) ) {
$self->throw("$feat is not contained within parent feature, and expansion is not valid");
}
}
$ssf_type = 'default' if ($ssf_type eq '');
if (!(defined ($self->{'gsf_sub_hash'}->{$ssf_type}))) {
@{$self->{'gsf_sub_hash'}->{$ssf_type}} = ();
}
$feat->get_SeqFeature_type($ssf_type);
push @{$self->{'gsf_sub_hash'}->{$ssf_type}}, $feat;
}
=head2 remove_SeqFeatures
Title : remove_SeqFeatures
Usage : $sf->remove_SeqFeatures
$sf->remove_SeqFeatures('SeqFeature_type');
Function: Removes all sub SeqFeature or all sub SeqFeatures of a specified type
(if you want to remove a more specific subset, take an array of them
all, flush them, and add back only the guys you want)
Example :
Returns : none
Args : none
=cut
sub remove_SeqFeatures {
my ($self, $ssf_type) = @_;
if ($ssf_type) {
if ((defined ($self->{'gsf_sub_hash'}->{$ssf_type}))) {
delete $self->{'gsf_sub_hash'}->{$ssf_type};
} else {
$self->warn("$ssf_type is not a valid sub SeqFeature type");
}
} else {
$self->{'_gsf_sub_hash'} = {}; # zap the complete hash implicitly.
}
}
# Aliases to better match Bio::SeqFeature function names
*sub_SeqFeature_type = \&get_SeqFeature_type;
*all_sub_SeqFeature_types = \&get_all_SeqFeature_types;
*sub_SeqFeature = \&get_SeqFeatures;
*add_sub_SeqFeature = \&add_SeqFeature;
*flush_sub_SeqFeatures = \&remove_SeqFeatures;
*flush_sub_SeqFeature = \&remove_SeqFeatures;
1;