#
# BioStudio functions
#
=head1 NAME
Bio::BioStudio::Mask
=head1 VERSION
Version 2.10
=head1 DESCRIPTION
BioStudio functions
=head1 AUTHOR
Sarah Richardson <smrichardson@lbl.gov>.
=cut
use strict;
our $VERSION = '2.10';
=head1 CONSTRUCTORS
=head2 new
Title : new
Function:
Returns : a new Bio::BioStudio::Mask object
Args :
=cut
sub new
{
my ($class, @args) = @_;
my $self = $class->SUPER::new(@args);
bless $self, $class;
my ($seqobj, $offset) = $self->_rearrange([qw(SEQUENCE OFFSET)], @args);
$self->throw('No Bio::Seq provided') unless $seqobj;
my $ref = ref($seqobj);
$self->throw("object of class $ref is not the kind of object Mask can take")
unless ($seqobj->isa('Bio::Seq')
|| $seqobj->isa('Bio::SeqFeatureI')
|| $seqobj->isa('Bio::PrimarySeq'));
my $seq = $seqobj->seq;
$seq = $seq->seq if (ref $seq);
$self->{length} = length $seq;
$self->{seqid} = $seqobj->id;
#COMMENT THIS
my @mask = map { [{}, 0] } (undef) x $self->{length};
$self->{mask} = \@mask;
$self->{index} = {};
$self->{offset} = $offset || 0;
return $self;
}
=head1 Masking functions
=head2 add_to_mask()
Given an array reference full of L<SeqFeature|Bio::DB::SeqFeature>s,
fills the mask
=cut
sub add_to_mask
{
my ($self, $featlist) = @_;
my $mask = $self->{mask};
my $offset = $self->{offset};
foreach my $q (@{$featlist})
{
$self->throw('object ' . ref($q) . ' is not a Bio::SeqFeatureI')
unless ($q->isa('Bio::SeqFeatureI'));
my $name = $q->display_name || $q->primary_tag . q{_} . $q->start;
my $pid = $q->primary_id || $name;
$self->{index}->{$name} = $pid;
$self->{feature}->{$name} = $q;
my $start = $q->start() - ($offset);
my $end = $q->end() - ($offset);
for my $x ($start - 1 .. $end - 1)
{
$mask->[$x]->[0]->{$name}++;
$mask->[$x]->[1]++;
}
}
return $self;
}
=head2 remove_from_mask()
=cut
sub remove_from_mask
{
my ($self, $feature) = @_;
my $mask = $self->{mask};
my $offset = $self->{offset};
$self->throw('object ' . ref($feature) . ' is not a Bio::SeqFeatureI')
unless ($feature->isa('Bio::SeqFeatureI'));
my $name = $feature->display_name;
delete $self->{index}->{$name};
my $start = $feature->start - 1 - $offset;
my $end = $feature->end - 1 - $offset;
for my $x ($start .. $end)
{
print "Removing $feature from mask at $x\n";
delete $mask->[$x]->[0]->{$name};
$mask->[$x]->[1]--;
}
return $self;
}
=head2 insert_sequence()
=cut
sub insert_sequence
{
my ($self, $feat) = @_;
my $mask = $self->{mask};
my $offset = $self->{offset};
my $name = $feat->display_name;
$self->{index}->{$name} = $feat->primary_id;
my $start = $feat->start - $offset;
my $end = $feat->end - $offset;
my $len = $end - $start + 1;
my %list = $self->what_overlaps($start);
my @insert = map { [{}, 0] } (undef) x $len;
splice @{$mask}, $start - 1, 0, @insert;
for my $x ($start - 1 .. $end - 1)
{
my %insy = map {$_ => 1} values %list;
$mask->[$x]->[0] = \%insy;
$mask->[$x]->[0]->{$name}++;
$mask->[$x]->[1]++;
}
$self->{length} += $len;
return $self;
}
=head2 remove_sequence()
=cut
sub remove_sequence
{
my ($self, $start, $end) = @_;
$self->_sanity_check($start, $start - $end + 1);
my $mask = $self->{mask};
my $len = $end - $start + 1;
splice @{$mask}, $start - 1, $len;
$self->{length} -= $len;
return $self;
}
=head2 find_deserts()
=cut
sub find_deserts
{
my ($self) = @_;
my @ranges;
my $len = $self->{length};
my $mask = $self->{mask};
# stat will track if we are in a feature or a desert
my $stat = $mask->[0]->[1];
my $start = $stat == 0 ? 1 : undef;
my $end = $stat == 0 ? 0 : 1;
for my $x (0 .. $len - 1)
{
$stat = $mask->[$x]->[1];
#moving from feature to desert
if ($stat == 0 && $end != 0)
{
$start = $x + 1;
}
#moving from desert to feature
elsif ($end == 0 && $stat != 0)
{
push @ranges, Bio::SeqFeature::Generic->new(
-start => $start,
-end => $x,
-display_name => "$start..$x",
-primary_tag => 'desert',
);
}
$end = $stat;
}
# end case - finish on a desert
if ($stat == 0)
{
push @ranges, Bio::SeqFeature::Generic->new(
-start => $start,
-end => $len,
-display_name => "$start..$len",
-primary_tag => 'desert',
);
}
return \@ranges;
}
=head2 find_overlaps()
=cut
sub find_overlaps
{
my ($self) = @_;
my @ranges;
my $len = $self->{length};
my $mask = $self->{mask};
my $seqid = $self->{seqid};
my $init = $mask->[0]->[1];
my $start = $init > 1 ? $init : undef;
my $end = $init > 1 ? $init : 1;
my $flag = $init > 1 ? $init : 0;
my %list = ();
for my $x (0 .. $len - 1)
{
my $stat = $mask->[$x]->[1];
#moving from non overlap to overlap
if ($stat > 1 && $end <= 1)
{
$start = $x+1;
$flag = 1;
$list{$_} = [$x+1, $x+1] foreach keys %{$mask->[$x]->[0]};
}
#moving from overlap to non overlap
elsif ($end > 1 && $stat <= 1)
{
my $lapfeat = Bio::SeqFeature::Generic->new(
-start => $start,
-end => $x,
-display_name => "$start..$x",
-primary_tag => 'overlap',
-seq_id => $seqid
);
foreach my $featid (keys %list)
{
my ($fstart, $fstop) = @{$list{$featid}};
my $subfeat = Bio::SeqFeature::Generic->new(
-start => $fstart,
-end => $fstop,
-display_name => $featid,
-seq_id => $seqid,
-tag => {
-length => $fstop - $fstart + 1,
-featname => $featid
}
);
$lapfeat->add_SeqFeature($subfeat);
}
push @ranges, $lapfeat;
%list = ();
$flag = 0;
}
#inside an overlap
elsif ($flag == 1)
{
foreach my $featid (keys %{$mask->[$x]->[0]})
{
if (exists $list{$featid})
{
$list{$featid}->[1] = $x+1;
}
else
{
$list{$featid} = [$x+1, $x+1];
}
}
}
$end = $stat;
}
return \@ranges;
}
=head2 what_overlaps()
=cut
sub what_overlaps
{
my ($self, $coordinate) = @_;
my $start = $coordinate - $self->{offset};
$self->_sanity_check($start);
my $poshash = $self->{mask}->[$start - 1]->[0];
my @names = keys %{$poshash};
my %feats = ();
foreach my $name (@names)
{
$feats{$name} = $self->{index}->{$name};
}
return %feats;
}
=head2 what_objects_overlap()
=cut
sub what_objects_overlap
{
my ($self, $coordinate) = @_;
my $start = $coordinate - $self->{offset};
$self->_sanity_check($start);
my $poshash = $self->{mask}->[$start - 1]->[0];
my @names = keys %{$poshash};
my %feats = ();
foreach my $name (@names)
{
$feats{$name} = $self->{feature}->{$name};
}
return %feats;
}
=head2 overlap_extents()
=cut
sub overlap_extents
{
my ($self, $start, $size) = @_;
$self->_sanity_check($start, $size);
my $mask = $self->{mask};
my $cstart = $start - 1;
my %extents;
for my $x ($cstart .. $cstart + $size - 1)
{
my @here = keys %{$mask->[$x]->[0]};
foreach my $name (@here)
{
my $id = $self->{index}->{$name};
if (! exists $extents{$id})
{
$extents{$id} = [$x + 1, $x + 1];
}
else
{
$extents{$id}->[1] = $x + 1;
}
}
}
return \%extents;
}
=head2 occlusion
=cut
sub occlusion
{
my ($self, $start, $size) = @_;
$self->_sanity_check($start, $size);
my $mask = $self->{mask};
my %feats;
my $cstart = $start - 1;
for my $x ($cstart .. $cstart + $size - 1)
{
my @here = keys %{$mask->[$x]->[0]};
$feats{$_}++ foreach @here;
}
my %percs = map {$_ => sprintf "%.1f", $feats{$_} / $size} keys %feats;
return %percs;
}
=head2 count_features()
=cut
sub count_features
{
my ($self, $coordinate) = @_;
$self->_sanity_check($coordinate);
my $stat = $self->{mask}->[$coordinate - 1]->[1];
return $stat;
}
=head2 count_features_in_range
=cut
sub count_features_in_range
{
my ($self, $coordinate, $size) = @_;
my $start = $coordinate - $self->{offset};
$self->_sanity_check($start, $size);
my %feats;
my $mask = $self->{mask};
my $cstart = $start - 1;
for my $x ($cstart .. $cstart + $size - 1)
{
my @here = keys %{$mask->[$x]->[0]};
$feats{$_}++ foreach @here;
}
return scalar values %feats;
}
=head2 features_in_range
=cut
sub features_in_range
{
my ($self, $start, $size) = @_;
$self->_sanity_check($start, $size);
my %feats;
my $mask = $self->{mask};
my $cstart = $start - 1;
for my $x ($cstart .. $cstart + $size - 1)
{
my @here = keys %{$mask->[$x]->[0]};
$feats{$_}++ foreach @here;
}
my @results = map {$self->{index}->{$_}} keys %feats;
return @results;
}
=head2 feature_objects_in_range
=cut
sub feature_objects_in_range
{
my ($self, $start, $size) = @_;
$self->_sanity_check($start, $size);
my %feats;
my $mask = $self->{mask};
my $cstart = $start - 1;
for my $x ($cstart .. $cstart + $size - 1)
{
my @here = keys %{$mask->[$x]->[0]};
$feats{$_}++ foreach @here;
}
my @results = map {$self->{feature}->{$_}} keys %feats;
return @results;
}
=head2 range_string
=cut
sub range_string
{
my ($self, $start, $size) = @_;
$self->_sanity_check($start, $size);
my $string;
my $mask = $self->{mask};
my $cstart = $start - 1;
for my $x ($cstart .. $cstart + $size - 1)
{
my $stat = $mask->[$x]->[1];
$string .= $stat;
}
return $string;
}
=head1 ACCESSORS
=head2 seqid
=cut
sub seqid
{
my ($self) = @_;
return $self->{seqid};
}
=head2 len
=cut
sub len
{
my ($self) = @_;
return $self->{length};
}
=head2 feature_index
=cut
sub feature_index
{
my ($self) = @_;
return $self->{index};
}
=head1 PRIVATE
=head2 _sanity_check
=cut
sub _sanity_check
{
my ($self, $start, $size) = @_;
my $cstart = $start - 1;
if ($cstart < 0)
{
$self->throw('Start argument to mask is not a positive index');
}
my $len = $self->{length};
if ($cstart > $len)
{
$self->throw("Start argument $cstart is greater than mask length $len");
}
if ($size && $cstart + $size - 1 > $len)
{
warn("Size argument $size puts index greater than mask length $len\n");
}
return;
}
1;
__END__
=head1 COPYRIGHT AND LICENSE
Copyright (c) 2015, BioStudio developers
All rights reserved.
Redistribution and use in source and binary forms, with or without modification,
are permitted provided that the following conditions are met:
* Redistributions of source code must retain the above copyright notice, this
list of conditions and the following disclaimer.
* Redistributions in binary form must reproduce the above copyright notice, this
list of conditions and the following disclaimer in the documentation and/or
other materials provided with the distribution.
* The names of Johns Hopkins, the Joint Genome Institute, the Joint BioEnergy
Institute, the Lawrence Berkeley National Laboratory, the Department of Energy,
and the BioStudio developers may not be used to endorse or promote products
derived from this software without specific prior written permission.
THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
DISCLAIMED. IN NO EVENT SHALL THE DEVELOPERS BE LIABLE FOR ANY DIRECT, INDIRECT,
INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR
PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF
LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE
OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
=cut