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Commit ecba7548 authored by Andreas Kusalananda Kähäri's avatar Andreas Kusalananda Kähäri
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Remove deprecated modules scheduled for removal in release 60.

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modules/Bio/EnsEMBL/Collection.pm deleted 100644 → 0
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View file @ 3bbeece2
=head1 LICENSE
Copyright (c) 1999-2010 The European Bioinformatics Institute and
Genome Research Limited. All rights reserved.
This software is distributed under a modified Apache license.
For license details, please see
http://www.ensembl.org/info/about/code_licence.html
=head1 CONTACT
Please email comments or questions to the public Ensembl
developers list at <ensembl-dev@ebi.ac.uk>.
Questions may also be sent to the Ensembl help desk at
<helpdesk@ensembl.org>.
=cut
=head1 NAME
Bio::EnsEMBL::Collection - Abstract base class for feature collection
classes.
=head1 SYNOPSIS
# Create an exon collection adaptor.
my $collection =
$registry->get_adaptor( 'Human', 'Core', 'ExonCollection' );
# Create a slice.
my $slice =
$slice_adaptor->fetch_by_region( 'Chromosome', '2', 1, 300_000 );
# Fetch the exons, represented as simple arrays of attributes, on
# the slice.
my @exons = @{ $collection->fetch_all_by_Slice($slice) };
# Fetch the exons on the slice and count them into 50 bins (each
# bin contains the number of exons overlapping that bin).
my @bins = @{
$collection->fetch_bins_by_Slice( -slice => $slice,
-nbins => 50,
-method => 'density'
) };
# Fetch the exons on the slice and calculate the coverage of 50
# bins (each bin contains the coverage of that bin by any exon as
# a number between 0 and 1).
my @bins = @{
$collection->fetch_bins_by_Slice( -slice => $slice,
-nbins => 50,
-method => 'coverage'
) };
=head1 DESCRIPTION
This is the abstract base class for feature collections.
In short, this class replaces the object creation routines in
Bio::EnsEMBL::DBSQL::BaseFeatureAdaptor with routines that creates
flat arrays. It also provides a way of binning features on a slice in
various different ways (see below).
A feature collection provides a compact representation of features of
a particular type on a slice. Each feature is represented by a short
array of attribute data. This data is divided into two halfs:
=over 4
=item 1.
Basic feature representation.
=item 2.
Extended feature representation.
=back
=head2 Basic feature representation
The basic feature representation is common to all features of any type
and consists of a minimal set of values. Each feature is represented by
an array that contains at least the following data (in this order)
=over 4
=item 1.
Ensembl internal database ID.
=item 2.
Ensembl internal sequence region ID.
=item 3.
Feature start position.
=item 4.
Feature end position.
=item 5.
Feature strand.
=back
The module defines a number of constants that may be used in place
of the index numbers 0 to 4: FEATURE_DBID, FEATURE_SEQREGIONID,
FEATURE_START, FEATURE_END, FEATURE_STRAND. For a feature $f,
$f->[Bio::EnsEMBL::Collection::FEATURE_END] will thus be the end
position for the feature that the array @{$f} represents.
The position of the feature is in the same coordinate system as the
slice used to fetch the features.
=head2 Extended feature representation
A sub-class of this abstract base class will specify further
data to be added to the features in order to account for the
particular feature type. A feature from a gene feature collection
(Bio::EnsEMBL::Collection::Gene) might, for example, contain the Ensembl
Stable ID of the gene.
The extended feature representation is defined by the method
_create_feature() or _create_feature_fast() which is implemented by the
sub-class. The extended representation is also documented in the POD of
each sub-class.
=head2 Light-weight features
A light-weight feature is a feature whose representation does not
contain the extended feature representation.
Light-weight features may be fetched by setting the lightweight
attribute using the lightweight() method before calling e.g.
fetch_all_by_Slice().
=cut
package Bio::EnsEMBL::Collection;
use strict;
use warnings;
use Bio::EnsEMBL::Utils::Argument ('rearrange');
use Bio::EnsEMBL::Utils::Exception ( 'throw', 'deprecate' );
deprecate( "The Bio::EnsEMBL::Collection module is deprecated\n"
. "and will be removed in Ensembl release 60.\n" );
use constant BASIC_SLOTS => 5;
use constant { FEATURE_DBID => 0,
FEATURE_SEQREGIONID => 1,
FEATURE_START => 2,
FEATURE_END => 3,
FEATURE_STRAND => 4 };
our %VALID_BINNING_METHODS = (
'count' => 0,
'density' => 0, # Same as 'count'.
'fractional_count' => 3,
'weight' => 3, # Same as 'fractional_count'.
'coverage' => 4 );
# ======================================================================
# The public interface added by Feature Collection
sub lightweight {
my ( $this, $value ) = @_;
if ( defined($value) ) {
$this->{'lightweight'} = ( $value != 0 );
}
return $this->{'lightweight'} || 0;
}
sub fetch_bins_by_Slice {
my ( $this, @args ) = @_;
my ( $slice, $method, $nbins, $logic_name, $lightweight ) =
rearrange( [ 'SLICE', 'METHOD', 'NBINS', 'LOGIC_NAME' ], @args );
# Temporarily set the colleciton to be lightweight.
my $old_value = $this->lightweight();
$this->lightweight(1);
my $bins =
$this->_bin_features(
-slice => $slice,
-nbins => $nbins,
-method => $method,
-features => $this->fetch_all_by_Slice( $slice, $logic_name )
);
# Reset the lightweightness to whatever it was before.
$this->lightweight($old_value);
return $bins;
}
# ======================================================================
# Specialization of methods in Bio::EnsEMBL::DBSQL::BaseFeatureAdaptor
sub _remap {
my ( $this, $features, $mapper, $slice ) = @_;
if ( scalar( @{$features} ) > 0 ) {
if ( $slice->get_seq_region_id() !=
$features->[0][FEATURE_SEQREGIONID] )
{
throw( '_remap() in Bio::EnsEMBL::Collection '
. 'was unexpectedly expected to be intelligent' );
}
}
return $features;
}
sub _create_feature {
my ( $this, $feature_type, $args ) = @_;
my ( $dbid, $start, $end, $strand, $slice ) =
rearrange( [ 'DBID', 'START', 'END', 'STRAND', 'SLICE' ],
%{$args} );
my $feature =
[ $dbid, $slice->get_seq_region_id(), $start, $end, $strand ];
return $feature;
}
sub _create_feature_fast {
my ( $this, $feature_type, $args ) = @_;
if ( !defined( $this->{'recent_slice'} )
|| $this->{'recent_slice'} ne $args->{'slice'} )
{
$this->{'recent_slice'} = $args->{'slice'};
$this->{'recent_slice_seq_region_id'} =
$args->{'slice'}->get_seq_region_id();
}
my $feature = [ $args->{'dbID'},
$this->{'recent_slice_seq_region_id'},
$args->{'start'},
$args->{'end'},
$args->{'strand'} ];
return $feature;
}
# ======================================================================
# Private methods
sub _bin_features {
my ( $this, @args ) = @_;
my ( $slice, $nbins, $method_name, $features ) =
rearrange( [ 'SLICE', 'NBINS', 'METHOD', 'FEATURES' ], @args );
if ( !defined($features) || !@{$features} ) { return [] }
if ( !defined($nbins) ) {
throw('Missing NBINS argument');
} elsif ( $nbins <= 0 ) {
throw('Negative or zero NBINS argument');
}
$method_name ||= 'count';
if ( !exists( $VALID_BINNING_METHODS{$method_name} ) ) {
throw(
sprintf(
"Invalid binning method '%s', valid methods are:\n\t%s\n",
$method_name,
join( "\n\t", sort( keys(%VALID_BINNING_METHODS) ) ) ) );
}
my $method = $VALID_BINNING_METHODS{$method_name};
my $slice_start = $slice->start();
my $bin_length = ( $slice->end() - $slice_start + 1 )/$nbins;
my @bins;
if ( $method == 0 || # 'count' or 'density'
$method == 3 || # 'fractional_count' or 'weight'
$method == 4 # 'coverage'
)
{
# For binning methods where each bin contain numerical values.
@bins = map( 0, 1 .. $nbins );
} else {
# For binning methods where each bin does not contain numerical
# values.
@bins = map( undef, 1 .. $nbins );
}
my $feature_index = 0;
my @bin_masks;
foreach my $feature ( @{$features} ) {
my $start_bin =
int( ( $feature->[FEATURE_START] - $slice_start )/$bin_length );
my $end_bin =
int( ( $feature->[FEATURE_END] - $slice_start )/$bin_length );
if ( $end_bin >= $nbins ) {
# This might happen for the very last entry.
$end_bin = $nbins - 1;
}
if ( $method == 0 ) {
# ----------------------------------------------------------------
# For 'count' and 'density'.
for ( my $bin_index = $start_bin;
$bin_index <= $end_bin;
++$bin_index )
{
++$bins[$bin_index];
}
}
# Method 1 & 2 were deleted.
elsif ( $method == 3 ) {
# ----------------------------------------------------------------
# For 'fractional_count' and 'weight'.
if ( $start_bin == $end_bin ) {
++$bins[$start_bin];
} else {
my $feature_length =
$feature->[FEATURE_END] - $feature->[FEATURE_START] + 1;
# The first bin...
$bins[$start_bin] +=
( ( $start_bin + 1 )*$bin_length -
( $feature->[FEATURE_START] - $slice_start ) )/
$feature_length;
# The intermediate bins (if there are any)...
for ( my $bin_index = $start_bin + 1;
$bin_index <= $end_bin - 1;
++$bin_index )
{
$bins[$bin_index] += $bin_length/$feature_length;
}
# The last bin...
$bins[$end_bin] +=
( ( $feature->[FEATURE_END] - $slice_start ) -
$end_bin*$bin_length +
1 )/$feature_length;
} ## end else [ if ( $start_bin == $end_bin)
} elsif ( $method == 4 ) {
# ----------------------------------------------------------------
# For 'coverage'.
my $feature_start = $feature->[FEATURE_START] - $slice_start;
my $feature_end = $feature->[FEATURE_END] - $slice_start;
if ( !defined( $bin_masks[$start_bin] )
|| ( defined( $bin_masks[$start_bin] )
&& $bin_masks[$start_bin] != 1 ) )
{
# Mask the $start_bin from the start of the feature to the end
# of the bin, or to the end of the feature (whichever occurs
# first).
my $bin_start = int( $start_bin*$bin_length );
my $bin_end = int( ( $start_bin + 1 )*$bin_length - 1 );
for ( my $pos = $feature_start;
$pos <= $bin_end && $pos <= $feature_end;
++$pos )
{
$bin_masks[$start_bin][ $pos - $bin_start ] = 1;
}
}
for ( my $bin_index = $start_bin + 1;
$bin_index <= $end_bin - 1;
++$bin_index )
{
# Mark the middle bins between $start_bin and $end_bin as fully
# masked out.
$bin_masks[$bin_index] = 1;
}
if ( $end_bin != $start_bin ) {
if ( !defined( $bin_masks[$end_bin] )
|| ( defined( $bin_masks[$end_bin] )
&& $bin_masks[$end_bin] != 1 ) )
{
# Mask the $end_bin from the start of the bin to the end of
# the feature, or to the end of the bin (whichever occurs
# first).
my $bin_start = int( $end_bin*$bin_length );
my $bin_end = int( ( $end_bin + 1 )*$bin_length - 1 );
for ( my $pos = $bin_start;
$pos <= $feature_end && $pos <= $bin_end;
++$pos )
{
$bin_masks[$end_bin][ $pos - $bin_start ] = 1;
}
}
}
} ## end elsif ( $method == 4 )
} ## end foreach my $feature ( @{$features...
if ( $method == 4 ) {
# ------------------------------------------------------------------
# For the 'coverage' method: Finish up by going through @bin_masks
# and sum up the arrays.
for ( my $bin_index = 0; $bin_index < $nbins; ++$bin_index ) {
if ( defined( $bin_masks[$bin_index] ) ) {
if ( !ref( $bin_masks[$bin_index] ) ) {
$bins[$bin_index] = 1;
} else {
$bins[$bin_index] =
scalar( grep ( defined($_), @{ $bin_masks[$bin_index] } ) )/
$bin_length;
}
}
}
}
return \@bins;
} ## end sub _bin_features
1;
modules/Bio/EnsEMBL/Collection/Exon.pm deleted 100644 → 0
+ 0
− 143
View file @ 3bbeece2
=head1 LICENSE
Copyright (c) 1999-2010 The European Bioinformatics Institute and
Genome Research Limited. All rights reserved.
This software is distributed under a modified Apache license.
For license details, please see
http://www.ensembl.org/info/about/code_licence.html
=head1 CONTACT
Please email comments or questions to the public Ensembl
developers list at <ensembl-dev@ebi.ac.uk>.
Questions may also be sent to the Ensembl help desk at
<helpdesk@ensembl.org>.
=cut
package Bio::EnsEMBL::Collection::Exon;
=head1 NAME
Bio::EnsEMBL::Collection::Exon - Feature collection implementation for
exon features.
=head1 DESCRIPTION
=head2 Extended feature representation
An exon is represented by the basic feature representation (see
documentation of Bio::EnsEMBL::Collection) and by the following extended
feature representation:
=over 4
=item 1.
Phase
=item 2.
End phase
=item 3.
Is-current
=item 4.
Stable ID
=item 5.
Version
=item 6.
Created date
=item 7.
Modified date
=back
=cut
use strict;
use warnings;
use Bio::EnsEMBL::Utils::Argument ('rearrange');
use Bio::EnsEMBL::Utils::Exception ('throw');
use base( 'Bio::EnsEMBL::Collection',
'Bio::EnsEMBL::DBSQL::ExonAdaptor' );
sub _create_feature {
my ( $this, $feature_type, $args ) = @_;
my $feature = $this->SUPER::_create_feature( $feature_type, $args );
if ( !$this->lightweight() ) {
my ( $phase, $end_phase, $is_current, $stable_id, $version,
$created_date, $modified_date )
= rearrange( [ 'PHASE', 'END_PHASE',
'IS_CURRENT', 'STABLE_ID',
'VERSION', 'CREATED_DATE',
'MODIFIED_DATE'
],
%{$args} );
push( @{$feature},
$phase, $end_phase, $is_current, $stable_id, $version,
$created_date, $modified_date );
}
return $feature;
}
sub _create_feature_fast {
my ( $this, $feature_type, $args ) = @_;
throw( '_create_feature_fast() '
. 'is not implemented for '
. 'exon collections' );
}
sub _tables {
my ($this) = @_;
my @tables = $this->SUPER::_tables();
if ( $this->lightweight() ) { return ( $tables[0] ) }
return @tables;
}
sub _columns {
my ($this) = @_;
my @columns = $this->SUPER::_columns();
if ( $this->lightweight() ) {
@columns[ Bio::EnsEMBL::Collection::BASIC_SLOTS .. $#columns ] =
map( 1, Bio::EnsEMBL::Collection::BASIC_SLOTS .. $#columns );
}
return @columns;
}
sub _default_where_clause {
my ($this) = @_;
if ( $this->lightweight() ) { return '' }
return $this->SUPER::_default_where_clause();
}
1;
# $Id$
modules/Bio/EnsEMBL/Collection/Gene.pm deleted 100644 → 0
+ 0
− 184
View file @ 3bbeece2
=head1 LICENSE
Copyright (c) 1999-2010 The European Bioinformatics Institute and
Genome Research Limited. All rights reserved.
This software is distributed under a modified Apache license.
For license details, please see
http://www.ensembl.org/info/about/code_licence.html
=head1 CONTACT
Please email comments or questions to the public Ensembl
developers list at <ensembl-dev@ebi.ac.uk>.
Questions may also be sent to the Ensembl help desk at
<helpdesk@ensembl.org>.
=cut
package Bio::EnsEMBL::Collection::Gene;
=head1 NAME
Bio::EnsEMBL::Collection::Gene - Feature collection implementation
for gene features.
=head1 DESCRIPTION
=head2 Extended feature representation
A gene is represented by the basic feature representation (see
documentation of Bio::EnsEMBL::Collection) and by the following extended
feature representation:
=over 4
=item 1.
Display label (display ID of the display Xref), if defined, otherwise
undef.
=item 2.
Biotype
=item 3.
Status
=item 4.
Is-current
=item 5.
Stable ID
=item 6.
Version
=item 7.
Created date
=item 8.
Modified date
=item 9.
Description
=item 10.
Confidence.
=item 11.
External name
=item 12.
External database name
=item 13.
External status
=item 14.
Source
=back
=cut
use strict;
use warnings;
use Bio::EnsEMBL::Utils::Argument ('rearrange');
use Bio::EnsEMBL::Utils::Exception ('throw');
use base( 'Bio::EnsEMBL::Collection',
'Bio::EnsEMBL::DBSQL::GeneAdaptor' );
sub _create_feature {
my ( $this, $feature_type, $args ) = @_;
my $feature = $this->SUPER::_create_feature( $feature_type, $args );
if ( !$this->lightweight() ) {
my ( $stable_id, $version, $external_name,
$type, $external_db, $external_status,
$display_xref, $description, $created_date,
$modified_date, $confidence, $biotype,
$source, $status, $is_current )
= rearrange( [ 'STABLE_ID', 'VERSION',
'EXTERNAL_NAME', 'TYPE',
'EXTERNAL_DB', 'EXTERNAL_STATUS',
'DISPLAY_XREF', 'DESCRIPTION',
'CREATED_DATE', 'MODIFIED_DATE',
'CONFIDENCE', 'BIOTYPE',
'SOURCE', 'STATUS',
'IS_CURRENT'
],
%{$args} );
push( @{$feature},
$display_xref->display_id() || undef, $biotype || $type,
$status, $is_current,
$stable_id, $version,
$created_date, $modified_date,
$description, $confidence,
$external_name, $external_db,
$external_status, $source );
}
return $feature;
}
sub _create_feature_fast {
my ( $this, $feature_type, $args ) = @_;
throw( '_create_feature_fast() '
. 'is not implemented for '
. 'gene collections' );
}
sub _tables {
my ($this) = @_;
my @tables = $this->SUPER::_tables();
if ( $this->lightweight() ) { return ( $tables[0] ) }
return @tables;
}
sub _columns {
my ($this) = @_;
my @columns = $this->SUPER::_columns();
if ( $this->lightweight() ) {
@columns[ Bio::EnsEMBL::Collection::BASIC_SLOTS .. $#columns ] =
map( 1, Bio::EnsEMBL::Collection::BASIC_SLOTS .. $#columns );
}
return @columns;
}
sub _default_where_clause {
my ($this) = @_;
if ( $this->lightweight() ) { return '' }
return $this->SUPER::_default_where_clause();
}
1;
# $Id$
modules/Bio/EnsEMBL/Collection/RepeatFeature.pm deleted 100644 → 0
+ 0
− 129
View file @ 3bbeece2
=head1 LICENSE
Copyright (c) 1999-2010 The European Bioinformatics Institute and
Genome Research Limited. All rights reserved.
This software is distributed under a modified Apache license.
For license details, please see
http://www.ensembl.org/info/about/code_licence.html
=head1 CONTACT
Please email comments or questions to the public Ensembl
developers list at <ensembl-dev@ebi.ac.uk>.
Questions may also be sent to the Ensembl help desk at
<helpdesk@ensembl.org>.
=cut
package Bio::EnsEMBL::Collection::RepeatFeature;
=head1 NAME
Bio::EnsEMBL::Collection::Exon - Feature collection implementation for
repeat features.
=head1 DESCRIPTION
=head2 Extended feature representation
A repeat feature is represented by the basic feature representation (see
documentation of Bio::EnsEMBL::Collection) and by the following extended
feature representation:
=over 4
=item 1.
Repeat start
=item 2.
Repeat end
=item 3.
Repeat consensus internal ID
=item 4.
Analysis internal ID
=item 5.
Score
=back
=cut
use strict;
use warnings;
use Bio::EnsEMBL::Utils::Argument ('rearrange');
use Bio::EnsEMBL::Utils::Exception ('throw');
use base( 'Bio::EnsEMBL::Collection',
'Bio::EnsEMBL::DBSQL::RepeatFeatureAdaptor' );
sub _create_feature {
my ( $this, $feature_type, $args ) = @_;
throw( '_create_feature() '
. 'is not implemented for '
. 'repeat feature collections' );
}
sub _create_feature_fast {
my ( $this, $feature_type, $args ) = @_;
my $feature =
$this->SUPER::_create_feature_fast( $feature_type, $args );
if ( !$this->lightweight() ) {
push( @{$feature},
$args->{'hstart'}, $args->{'hend'},
$args->{'repeat_consensus'}->dbID(),
$args->{'analysis'}->dbID(),
$args->{'score'} );
}
return $feature;
}
sub _tables {
my ($this) = @_;
my @tables = $this->SUPER::_tables();
if ( $this->lightweight() ) { return ( $tables[0] ) }
return @tables;
}
sub _columns {
my ($this) = @_;
my @columns = $this->SUPER::_columns();
if ( $this->lightweight() ) {
@columns[ Bio::EnsEMBL::Collection::BASIC_SLOTS .. $#columns ] =
map( 1, Bio::EnsEMBL::Collection::BASIC_SLOTS .. $#columns );
}
return @columns;
}
sub _default_where_clause {
my ($this) = @_;
if ( $this->lightweight() ) { return '' }
return $this->SUPER::_default_where_clause();
}
1;
# $Id$
modules/Bio/EnsEMBL/Collection/Transcript.pm deleted 100644 → 0
+ 0
− 179
View file @ 3bbeece2
=head1 LICENSE
Copyright (c) 1999-2010 The European Bioinformatics Institute and
Genome Research Limited. All rights reserved.
This software is distributed under a modified Apache license.
For license details, please see
http://www.ensembl.org/info/about/code_licence.html
=head1 CONTACT
Please email comments or questions to the public Ensembl
developers list at <ensembl-dev@ebi.ac.uk>.
Questions may also be sent to the Ensembl help desk at
<helpdesk@ensembl.org>.
=cut
=head1 NAME
Bio::EnsEMBL::Collection::Transcript - Feature collection implementation
for transcript features.
=head1 DESCRIPTION
=head2 Extended feature representation
A transcript is represented by the basic feature representation (see
documentation of Bio::EnsEMBL::Collection) and by the following extended
feature representation:
=over 4
=item 1.
Display label (display ID of the display Xref), if defined, otherwise
undef.
=item 2.
Biotype
=item 3.
Status
=item 4.
Is-current
=item 5.
Stable ID
=item 6.
Version
=item 7.
Created date
=item 8.
Modified date
=item 9.
Description
=item 10.
Confidence.
=item 11.
External name
=item 12.
External database name
=item 13.
External status
=back
=cut
package Bio::EnsEMBL::Collection::Transcript;
use strict;
use warnings;
use Bio::EnsEMBL::Utils::Argument ('rearrange');
use Bio::EnsEMBL::Utils::Exception ('throw');
use base( 'Bio::EnsEMBL::Collection',
'Bio::EnsEMBL::DBSQL::TranscriptAdaptor' );
sub _create_feature {
my ( $this, $feature_type, $args ) = @_;
my $feature = $this->SUPER::_create_feature( $feature_type, $args );
if ( !$this->lightweight() ) {
my ( $stable_id, $version, $external_name,
$external_db, $external_status, $display_xref,
$created_date, $modified_date, $description,
$biotype, $confidence, $status,
$is_current )
= rearrange( [ 'STABLE_ID', 'VERSION',
'EXTERNAL_NAME', 'EXTERNAL_DB',
'EXTERNAL_STATUS', 'DISPLAY_XREF',
'CREATED_DATE', 'MODIFIED_DATE',
'DESCRIPTION', 'BIOTYPE',
'CONFIDENCE', 'STATUS',
'IS_CURRENT'
],
%{$args} );
push( @{$feature},
$display_xref->display_id() || undef, $biotype,
$status, $is_current,
$stable_id, $version,
$created_date, $modified_date,
$description, $confidence,
$external_name, $external_db,
$external_status );
}
return $feature;
}
sub _create_feature_fast {
my ( $this, $feature_type, $args ) = @_;
throw( '_create_feature_fast() '
. 'is not implemented for '
. 'transcript collections' );
}
sub _tables {
my ($this) = @_;
my @tables = $this->SUPER::_tables();
if ( $this->lightweight() ) { return ( $tables[0] ) }
return @tables;
}
sub _columns {
my ($this) = @_;
my @columns = $this->SUPER::_columns();
if ( $this->lightweight() ) {
@columns[ Bio::EnsEMBL::Collection::BASIC_SLOTS .. $#columns ] =
map( 1, Bio::EnsEMBL::Collection::BASIC_SLOTS .. $#columns );
}
return @columns;
}
sub _default_where_clause {
my ($this) = @_;
if ( $this->lightweight() ) { return '' }
return $this->SUPER::_default_where_clause();
}
1;
# $Id$
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