Bio::EnsEMBL::Compara
ConservationScore
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Summary
Bio::EnsEMBL::Compara::ConservationScore - Stores conservation scores
Package variables
Privates (from "my" definitions)
$pack_type = "f"
$pack_size = 4
Included modules
Synopsis
use Bio::EnsEMBL::Compara::ConservationScore;
my $conservation_score = new Bio::EnsEMBL::Compara::ConservationScore(
-genomic_align_block => $gab,
-window_size => $win_size,
-position => $pos,
-observed_score => $obs_scores,
-expected_score => $exp_scores,
-diff_score => $diff_scores);
SET VALUES
$conservation_score->genomic_align_block($gab);
$conservation_score->window_size(10);
$conservation_score->position(1);
$conservation_score->observed_score($observed_scores);
$conservation_score->expected_score($expected_scores);
$conservation_score->diff_score($diff_scores);
$conservation_score->y_axis_min(0);
$conservation_score->y_axis_max(100);
GET VALUES
$gab = $conservation_score->genomic_align_block;
$win_size = $conservation_score->window_size;
$pos = $conservation_score->position;
$obs_scores = $conservation_score->observed_score;
$exp_scores = $conservation_score->expected_score;
$diff_scores = $conservation_score->diff_score;
$y_axis_min = $conservation_score->y_axis_min;
$y_axis_max = $conservation_score->y_axis_max;
Description
Object for storing conservation scores. The scores are averaged over different
window sizes to speed up drawing over large regions. The scores are packed as
floats and stored in a string. The scores can be stored and retrieved in
either a packed or unpacked format. The unpacked format is as a space delimited
string eg ("0.123 0.456 0.789"). The packed format is a single precision float
(4 bytes). It is recommended to use the unpacked format.
Methods
Methods description
Example : $conservation_score->_print;
Description: print the contents of the ConservationScore object
Returntype : none
Exceptions : none
Caller : general
Status : At risk |
Arg [1] : string $score_str (string of scores)
Arg [2] : int $num_scores (number of scores in the string)
Arg [3] : boolean $packed (whether the scores are packed or not)
Example : _reverse_score($self->expected_score, $num_scores, $self->packed)
Description: internal method used by reverse to reverse the score strings
Returntype : string
Exceptions : none
Caller : general
Status : At risk |
Arg [1] : Bio::EnsEMBL::DBSQL::ConservationScoreAdaptor $adaptor
Example : $conservation_score->adaptor($adaptor);
Description: Getter/Setter for the adaptor this object used for database
interaction
Returntype : Bio::EnsEMBL::DBSQL::ConservationScoreAdaptor object
Exceptions : thrown if the argument is not a
Bio::EnsEMBL::DBSQL::ConservationScoreAdaptor object
Caller : general
Status : At risk |
Arg [1] : (opt) string of difference scores (expected - observed)
(can be either packed or space delimited)
Example : $conservation_score->diff_score("1.85 -2.54 1.56");
Example : my $diff_score = $conservation_score->diff_score();
Description: Getter/Setter for the difference score string
Returntype : string (either packed or space delimited)
Exceptions : none
Caller : general
Status : At risk |
Example : $conservation_score->end();
Description: wrapper around position
Returntype : integer. Return 1 if value not defined
Exceptions : none
Caller : general
Status : At risk |
Arg [1] : (opt) string of expected scores (can be either packed or space
delimited)
Example : $conservation_score->expected_score("3.85 2.54 1.56");
Example : my $exp_score = $conservation_score->expected_score();
Description: Getter/Setter for the expected score string
Returntype : string (either packed or space delimited)
Exceptions : none
Caller : general
Status : At risk |
Arg [1] : Bio::EnsEMBL::Compara::GenomicAlignBlock $genomic_align_block
Example : my $genomic_align_block = $conservation_score->genomic_align_block();
Example : $conservation_score->genomic_align_block($genomic_align_block);
Description: Getter/Setter for the genomic_align_block attribute
Returntype : Bio::EnsEMBL::Compara::GenomicAlignBlock object. If no
argument is given, the genomic_align_block is not defined but
if both the genomic_align_block_id and the adaptor are, it tries
to fetch the data using the genomic_align_block_id.
Exceptions : thrown if $genomic_align_block is not a
Bio::EnsEMBL::Compara::GenomicAlignBlock object or if
$genomic_align_block does not match a previously defined
genomic_align_block_id
Warning : warns if getting data from other sources fails.
Caller : general
Status : At risk |
Arg [1] : (opt) integer genomic_align_block_id
Example : my $genomic_align_block_id = $conservation_score->genomic_align_block_id();
Example : $conservation_score->genomic_align_block_id($genomic_align_block_id);
Description: Getter/Setter for the genomic_align_block_id attribute. If no
argument is given and the genomic_align_block_id is not defined,
it tries to get the data from other sources like the
corresponding Bio::EnsEMBL::Compara::GenomicAlignBlock object or
the database using the dbID of the Bio::EnsEMBL::Compara::GenomicAlign object.
Returntype : integer
Exceptions : thrown if $genomic_align_block_id does not match a previously
defined genomic_align_block
Warning : warns if getting data from other sources fails.
Caller : general
Status : At risk |
Arg [-ADAPTOR]
: Bio::EnsEMBL::Compara::DBSQL::ConservationScore $adaptor
(the adaptor for connecting to the database)
Arg [-GENOMIC_ALIGN_BLOCK] (opt)
: Bio::EnsEMBL::Compara::DBSQL::GenomicAlignBlock $genomic_align_block
(the Bio::EnsEMBL::Compara::DBSQL::GenomicAlignBlock of the multiple
alignment)
Arg [-GENOMIC_ALIGN_BLOCK_ID] (opt)
: int $genomic_align_block_id
(the database internal ID of the $genomic_align_block)
Arg [-WINDOW_SIZE] (opt)
: int $window_size
(window size used to average the scores over)
Arg [-POSITION] (opt)
: int $position
(position of the first score in alignment coordinates)
Arg [-SEQ_REGION_POS] (opt)
: int $seq_region_pos
(position of the first score in species coordinates)
Arg [-EXPECTED_SCORE]
: string $expected_score
(packed or unpacked string of expected scores)
Arg [-DIFF_SCORE]
: string $diff_score
(packed or unpacked string of the difference between the observed and
expected scores)
Arg [-PACKED] (opt)
: boolean $packed
(whether the scores are packed (1) or unpacked (0))
Arg [Y_AXIS_MIN] (opt)
: float $y_axis_min
(minimum score value used for display)
Arg [Y_AXIS_MAX] (opt)
: float $y_axis_max
(maximum score value used for display)
Example :
my $conservation_score = new Bio::EnsEMBL::Compara::ConservationScore(
-genomic_align_block => $gab,
-window_size => $win_size,
-position => $pos,
-expected_score => $exp_scores,
-diff_score => $diff_scores);
Description: Creates a new ConservationScore object
Returntype : Bio::EnsEMBL::Compara::ConservationScore
Exceptions : none
Caller : general
Status : At risk |
Arg [1] : hash reference $hashref
Example : none
Description: This is an ultra fast constructor which requires knowledge of
the objects internals to be used.
Returntype :
Exceptions : none
Caller :
Status : At risk |
Example : my $obs_score = $conservation_score->observed_score();
Description: Getter for the observed score string (no setter functionality)
Returntype : double
Exceptions : none
Caller : general
Status : At risk |
Arg [1] : (opt) boolean
Example : $conservation_score->packed(1);
Example : $packed = $conservation_score->packed;
Description: Getter/Setter for the whether the scores are packed or space
delimited
Returntype : boolean
Exceptions : none
Caller : general
Status : At risk |
Arg [1] : (opt) integer
Example : $conservation_score->position(1);
Description: Getter/Setter for the alignment position of the first score
Returntype : integer. Return 1 if value not defined
Exceptions : none
Caller : general
Status : At risk |
Example : $conservation_score->reverse;
Description: reverse scores and position in the ConservationScore object
Returntype : none
Exceptions : none
Caller : general
Status : At risk |
Arg [1] : (opt) string of difference scores (expected - observed)
(can be either packed or space delimited)
Example : $conservation_score->diff_score("1.85 -2.54 1.56");
Example : my $diff_score = $conservation_score->diff_score();
Description: alias for diff score
Returntype : string (either packed or space delimited)
Exceptions : none
Caller : general
Status : At risk |
Arg [1] : (opt) integer
Example : $conservation_score->seq_region_pos(1);
Description: Getter/Setter for the species position of the first score
Returntype : integer.
Exceptions : none
Caller : general
Status : At risk |
Example : $conservation_score->start();
Description: Wrapper round position call
Returntype : integer. Return 1 if value not defined
Exceptions : none
Caller : general
Status : At risk |
Arg [1] : (opt) integer window_size
Example : my $window_size = $conservation_score->window_size();
Example : $conservation_score->window_size(1);
Description: Getter/Setter for the window_size of this conservation score
Returntype : integer, Returns 1 if value not defined
Exceptions : none
Caller : general
Status : At risk |
Arg [1] : (opt) float
Example : $conservation_score->y_axis_max(2.45);
Example : $y_axis_max = $conservation_score->y_axis_min;
Description: Getter/Setter for the maximum score
Returntype : float
Exceptions : none
Caller : general
Status : At risk |
Arg [1] : (opt) float
Example : $conservation_score->y_axis_min(-0.5);
Example : $y_axis_min = $conservation_score->y_axis_min;
Description: Getter/Setter for the minimum score
Returntype : float
Exceptions : none
Caller : general
Status : At risk |
Methods code
sub _print
{ my ($self, $FILEH) = @_;
my $exp_score = 0;
if ($self->expected_score) {
$exp_score = $self->expected_score;
}
$FILEH ||=\* STDOUT;
print $FILEH
"Bio::EnsEMBL::Compara::GenomicAlignBlock object ($self)
genomic_align_block = " . ($self->genomic_align_block) . "
genomic_align_block_id = " . ($self->genomic_align_block_id) . "
window_size = " . ($self->window_size) . "
position = " . ($self->position) . "
seq_region_pos = " . ($self->seq_region_pos) . "
diff_score = " . ($self->diff_score) . "
expected_score = $exp_score\n ";
}
1; } | sub _reverse_score
{ my ($score_str, $num_scores, $packed) = @_;
my $rev_str;
if ($packed) {
for (my $i = $num_scores-1; $i >=0; $i--) {
my $value = substr $score_str, $i*$pack_size, $pack_size;
$rev_str .= $value;
}
} else {
my @scores = split ' ', $score_str;
my $rev_str;
for (my $i = $num_scores-1; $i >= 0; $i--) {
$rev_str .= $scores[$i];
}
}
return $rev_str;} | sub adaptor
{ my ( $self, $adaptor ) = @_;
if (defined($adaptor)) {
throw("$adaptor is not a Bio::EnsEMBL::Compara::DBSQL::ConservationScoreAdaptor object")
unless ($adaptor->isa("Bio::EnsEMBL::Compara::DBSQL::ConservationScoreAdaptor"));
$self->{'adaptor'} = $adaptor;
}
return $self->{'adaptor'};} | sub diff_score
{ my ($self, $diff_score) = @_;
if (defined $diff_score) {
$self->{'diff_score'} = $diff_score;
}
return $self->{'diff_score'};} | sub end
{ my $self = shift;
return $self->position; } | sub expected_score
{ my ($self, $expected_score) = @_;
if (defined $expected_score) {
$self->{'expected_score'} = $expected_score;
}
return $self->{'expected_score'};} | sub genomic_align_block
{ my ($self, $genomic_align_block) = @_;
if (defined($genomic_align_block)) {
throw("$genomic_align_block is not a Bio::EnsEMBL::Compara::GenomicAlignBlock object")
unless ($genomic_align_block->isa("Bio::EnsEMBL::Compara::GenomicAlignBlock"));
if ($self->{'genomic_align_block_id'}) {
throw("dbID of genomic_align_block object does not match previously defined".
" genomic_align_block_id. If you want to override a".
" Bio::EnsEMBL::Compara::ConservationScore object, you can reset the ".
"genomic_align_block_id using\$ conservation_score->genomic_align_block_id(0)")
if ($self->{'genomic_align_block'}->dbID != $self->{'genomic_align_block_id'});
}
$self->{'genomic_align_block'} = $genomic_align_block;
} elsif (!defined($self->{'genomic_align_block'})) {
if (defined($self->genomic_align_block_id) and defined($self->{'adaptor'})) {
my $genomic_align_block_adaptor = $self->{'adaptor'}->db->get_GenomicAlignBlockAdaptor;
$self->{'genomic_align_block'} = $genomic_align_block_adaptor->fetch_by_dbID(
$self->{'genomic_align_block_id'});
} else {
warning("Fail to get data from other sources in Bio::EnsEMBL::Compara::GenomicAlign->genomic_align_block".
" You either have to specify more information (see perldoc for".
" Bio::EnsEMBL::Compara::GenomicAlign) or to set it up directly");
}
}
return $self->{'genomic_align_block'};} | sub genomic_align_block_id
{ my ($self, $genomic_align_block_id) = @_;
if (defined($genomic_align_block_id)) {
$self->{'genomic_align_block_id'} = ($genomic_align_block_id or undef);
if (defined($self->{'genomic_align_block'}) and $self->{'genomic_align_block_id'}) {
warning("Defining both genomic_align_block_id and genomic_align_block");
throw("genomic_align_block_id does not match previously defined genomic_align_block object")
if ($self->{'genomic_align_block'} and
$self->{'genomic_align_block'}->dbID != $self->{'genomic_align_block_id'});
}
} elsif (!($self->{'genomic_align_block_id'})) {
if (defined($self->{'genomic_align_block'}) and defined($self->{'genomic_align_block'}->dbID)) {
$self->{'genomic_align_block_id'} = $self->{'genomic_align_block'}->dbID;
} elsif (defined($self->{'adaptor'}) and defined($self->{'dbID'})) {
$self->adaptor->retrieve_all_direct_attributes($self);
} else {
warning("Fail to get data from other sources in Bio::EnsEMBL::Compara::GenomicAlign->genomic_align_block_id".
" You either have to specify more information (see perldoc for".
" Bio::EnsEMBL::Compara::GenomicAlign) or to set it up directly");
}
}
return $self->{'genomic_align_block_id'};} | sub new
{
my($class, @args) = @_;
my $self = {};
bless $self,$class;
my ($adaptor, $genomic_align_block, $genomic_align_block_id,
$window_size, $position, $seq_region_pos,
$expected_score, $diff_score, $packed, $y_axis_min, $y_axis_max) =
rearrange([qw(
ADAPTOR GENOMIC_ALIGN_BLOCK GENOMIC_ALIGN_BLOCK_ID
WINDOW_SIZE POSITION SEQ_REGION_POS
EXPECTED_SCORE DIFF_SCORE PACKED Y_AXIS_MIN
Y_AXIS_MAX)],
@args);
$self->adaptor($adaptor) if (defined($adaptor));
$self->genomic_align_block($genomic_align_block) if (defined($genomic_align_block));
$self->genomic_align_block_id($genomic_align_block_id) if (defined($genomic_align_block_id));
$self->window_size($window_size) if (defined($window_size));
$self->position($position) if (defined($position));
$self->seq_region_pos($seq_region_pos) if (defined($seq_region_pos));
$self->expected_score($expected_score) if (defined($expected_score));
$self->diff_score($diff_score) if (defined($diff_score));
$self->y_axis_min($y_axis_min) if (defined($y_axis_min));
$self->y_axis_max($y_axis_max) if (defined($y_axis_max));
if (defined($packed)) {
$self->packed($packed);
} else {
$self->packed(0);
}
return $self;} | sub new_fast
{ my ($class, $hashref) = @_;
return bless $hashref, $class; } | sub observed_score
{ my ($self) = @_;
return ($self->expected_score - $self->diff_score);} | sub packed
{ my ($self, $packed) = @_;
if($packed) {
$self->{'packed'} = $packed;
}
return $self->{'packed'};} | sub position
{ my ($self, $position) = @_;
if(defined $position) {
$self->{'position'} = $position;
}
$self->{'position'}='1' unless(defined($self->{'position'}));
return $self->{'position'};} | sub reverse
{ my ($self, $genomic_align_block_length) = @_;
my $num_scores = 0;
return if (!defined($self->score));
if ($self->packed) {
$num_scores = length($self->score)/$pack_size;
} else {
my @scores = split ' ', $self->score;
$num_scores = scalar(@scores);
}
my $end = $self->position + (($num_scores - 1) * $self->window_size);
if (!defined($genomic_align_block_length)) {
$genomic_align_block_length = $self->genomic_align_block->length;
}
$self->position($genomic_align_block_length - $end + 1);
if (defined $self->seq_region_pos) {
$end = $self->seq_region_pos + (($num_scores - 1) * $self->window_size);
$self->seq_region_pos($self->genomic_align_block->length - $end + 1);
}
$self->expected_score(_reverse_score($self->expected_score, $num_scores, $self->packed));
$self->diff_score(_reverse_score($self->diff_score, $num_scores, $self->packed));} | sub score
{ my ($self, $diff_score) = @_;
return $self->diff_score($diff_score);} | sub seq_region_pos
{ my ($self, $seq_region_pos) = @_;
if(defined $seq_region_pos) {
$self->{'seq_region_pos'} = $seq_region_pos;
}
return $self->{'seq_region_pos'};} | sub start
{ my $self = shift;
return $self->position; } | sub window_size
{ my ($self, $window_size) = @_;
if(defined $window_size) {
$self->{'window_size'} = $window_size;
}
$self->{'window_size'}='1' unless(defined($self->{'window_size'}));
return $self->{'window_size'};} | sub y_axis_max
{ my ($self, $y_axis_max) = @_;
if (defined $y_axis_max) {
$self->{'y_axis_max'} = $y_axis_max;
}
return $self->{'y_axis_max'};} | sub y_axis_min
{ my ($self, $y_axis_min) = @_;
if (defined $y_axis_min) {
$self->{'y_axis_min'} = $y_axis_min;
}
return $self->{'y_axis_min'};} | General documentation
This modules is part of the EnsEMBL project (
)
Questions can be posted to the ensembl-dev mailing list:
ensembl-dev@ebi.ac.ukThe rest of the documentation details each of the object methods. Internal methods are usually preceded with a _