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package Bio::Graphics::Browser2::DataLoader::bigbed;
# $Id$
use strict;
use base 'Bio::Graphics::Browser2::DataLoader';
use Bio::DB::BigBed;
use File::Basename 'basename','dirname';
my @COLORS = qw(blue red orange brown mauve peach
green cyan yellow coral);
sub new {
my $class = shift;
my $self = $class->SUPER::new(@_);
$self->{default_track_name} = 'track000';
$self;
}
sub default_track_name {
my $self = shift;
return $self->{default_track_name}++;
}
sub load {
my $self = shift;
my ($initial_lines,$fh) = @_;
$self->flag_busy(1);
eval {
$self->open_conf;
$self->set_status('starting load');
mkdir $self->sources_path or die $!;
$self->{bigbed} = File::Spec->catfile($self->sources_path,$self->track_name);
my $source_file = IO::File->new($self->{bigbed},'>');
warn "sourcefile=$self->{bigbed}";
$self->start_load;
$self->set_status('load data');
my $bytes_loaded = 0;
foreach (@$initial_lines) {
$source_file->print($_);
$bytes_loaded += length $_;
}
my $buffer;
while ((my $bytes = read($fh,$buffer,8192) > 0)) {
$source_file->print($buffer);
$bytes_loaded += length $ buffer;
$self->set_status("loaded $bytes_loaded bytes") if $bytes++ % 10000;
}
$source_file->close();
$self->finish_load;
$self->close_conf;
$self->set_processing_complete;
};
$self->flag_busy(0);
die $@ if $@;
return $self->tracks;
}
sub finish_load {
my $self = shift;
my $loadid = $self->loadid;
$self->set_status('creating configuration');
my $conf = $self->conf_fh;
my $dbid = $self->new_track_label;
my $bigbed = $self->{bigbed} or die "no bigbed file defined";
print $conf <<END;
[$dbid:database]
db_adaptor = Bio::DB::BigBed
db_args = -bigbed '$bigbed'
END
;
print $conf "#>>>>>>>>>> cut here <<<<<<<<\n";
my $color = $COLORS[rand @COLORS];
my $name = $self->track_name;
print $conf <<END
[$dbid]
database = $dbid
feature = region
glyph = segments
label density = 50
feature_limit = 500
bump = fast
stranded = 1
height = 4
bgcolor = $color
fgcolor = $color
key = $name segments
description =
[$dbid\_coverage]
database = $dbid
feature = summary
glyph = wiggle_whiskers
fgcolor = black
height = 50
autoscale = chromosome
key = $name coverage
description =
END
;
# We are defining two separate tracks rather than using semantic zoom
# because of the flexible nature of the bigBed format. It can be used
# as a Bam substitute where coverage is the best glyph, or it can be used
# for sparse intervals of interest where segments is the best glyph.
# Onus is on the user to select the most appropriate one.
}
1;
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