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package Bio::Graphics::Browser2::DataLoader::wiggle;
# $Id$
use strict;
use base 'Bio::Graphics::Browser2::DataLoader';
use File::Basename 'basename','dirname';
use IO::String;
my $HASBIGWIG;
sub start_load {
my $self = shift;
my $loader = Bio::Graphics::Wiggle::Loader::Nosample->new(
$self->data_path,
$self->track_name,
);
$loader->status_setter($self);
$self->wigloader($loader);
}
# we are doing nothing during load_line except letting the
# base class make a copy of the file in SOURCES. finish_load()
# will do all the work
sub load_line { }
sub finish_load {
my $self = shift;
my $wigloader = $self->wigloader;
my $sourcefh = IO::File->new($self->source_file,'<');
$self->set_status('indexing data');
$wigloader->load($sourcefh);
$self->set_status('creating config file');
$self->close_conf; # the featurefile loader will handle the conf for us
my $featurefiledata = $wigloader->featurefile('featurefile');
eval "require Bio::Graphics::Browser2::DataLoader::featurefile"
unless Bio::Graphics::Browser2::DataLoader::featurefile->can('new');
my $ff_loader = Bio::Graphics::Browser2::DataLoader::featurefile->new(
$self->track_name,
$self->data_path,
$self->conf_path,
$self->settings,
$self->loadid,
);
$ff_loader->open_conf;
$ff_loader->start_load;
my @ff_lines = split "\n",$featurefiledata;
$ff_loader->load_line($_) foreach @ff_lines;
$ff_loader->finish_load;
$ff_loader->close_conf;
$self->add_track($_) foreach $ff_loader->tracks;
$self->wigloader(undef); # to avoid memory leak
}
sub wigloader {
my $self = shift;
my $d = $self->{wigloader};
$self->{wigloader} = shift if @_;
return $d;
}
# overload wiggle loader so that we don't go to genome-wide statistics
# on very large files. Always explicitly calculate stats for file.
package Bio::Graphics::Wiggle::Loader::Nosample;
use base 'Bio::Graphics::Wiggle::Loader';
sub status_setter {
my $self = shift;
$self->{__status_setter} = shift;
}
sub set_status {
my $self = shift;
my $msg = shift;
my $ss = $self->{__status_setter} or return;
$ss->set_status($msg);
}
sub report_status {
my $self = shift;
return unless $self->{__linecount}++ % 10000 == 0;
$self->set_status("Indexed ",$self->{__linecount}-1," lines");
}
sub load {
my $self = shift;
$self->{__linecount} = 0;
$self->SUPER::load(@_);
}
sub minmax {
my $self = shift;
my ($infh,$bedline) = @_;
local $_;
my $transform = $self->get_transform;
my $seqids = ($self->current_track->{seqids} ||= {});
my $chrom = $self->{track_options}{chrom};
$self->set_status('calculating descriptive statistics');
my %stats;
if ($bedline) { # left-over BED line
my @tokens = split /\s+/,$bedline;
my $seqid = $tokens[0];
my $value = $tokens[-1];
$value = $transform->($self,$value) if $transform;
$stats{$seqid} ||= Statistics::Descriptive::Sparse->new();
$stats{$seqid}->add_data($value);
}
my $count;
while (<$infh>) {
last if /^track|fixedStep|variableStep/;
next if /^\#/;
my @tokens = split(/\s+/,$_) or next;
my $seqid = @tokens > 3 ? $tokens[0] : $chrom;
$self->set_status("chromosome $seqid: line $count") if $count++ % 1000 == 0;
my $value = $tokens[-1];
$value = $transform->($self,$value) if $transform;
$stats{$seqid} ||= Statistics::Descriptive::Sparse->new();
$stats{$seqid}->add_data($value);
}
for my $seqid (keys %stats) {
$seqids->{$seqid}{min} = $stats{$seqid}->min();
$seqids->{$seqid}{max} = $stats{$seqid}->max();
$seqids->{$seqid}{mean} = $stats{$seqid}->mean();
$seqids->{$seqid}{stdev} = $stats{$seqid}->standard_deviation();
}
}
sub process_bed {
my $self = shift;
$self->report_status;
$self->SUPER::process_bed(@_);
}
sub process_fixedline {
my $self = shift;
$self->report_status;
$self->SUPER::process_fixedline(@_);
}
sub process_variableline {
my $self = shift;
$self->report_status;
$self->SUPER::process_variableline(@_);
}
1;
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