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package Bio::Graphics::Browser2::DataLoader::bed;
# $Id$
use strict;
use Bio::DB::SeqFeature::Store;
use Carp 'croak';
use File::Basename 'basename';
use base 'Bio::Graphics::Browser2::DataLoader::generic';
use constant TOO_SMALL_FOR_SUMMARY_MODE => 10000; # don't go into summary mode
my @COLORS = qw(blue red orange brown mauve peach
green cyan black yellow cyan papayawhip coral);
sub Loader {
return 'Bio::DB::SeqFeature::Store::BedLoader';
}
sub load_line {
my $self = shift;
my $line = shift;
my $prefix = $self->strip_prefix;
chomp $line;
push @{$self->{conflines}},$line if $line =~ /^track/;
$line =~ s/^$prefix// if $prefix;
$self->loader->load_line($line);
}
sub finish_load {
my $self = shift;
my $line_count = shift;
$self->set_status('creating database');
$self->loader->finish_load();
my $db = $self->loader->store;
my $conf = $self->conf_fh;
my $trackname = $self->track_name;
my $dsn = $self->dsn;
my $backend = $self->backend;
$self->write_gff3($db,$dsn) if $backend eq 'memory';
my $loadid = $self->loadid;
my $summary = $line_count < TOO_SMALL_FOR_SUMMARY_MODE ? 'show summary = 0' : '';
eval {
$self->set_status('calculating summary statistics');
$self->loader->build_summary;
} unless $line_count < TOO_SMALL_FOR_SUMMARY_MODE;
warn $@ if $@;
$self->set_status('creating configuration');
my @lines = @{$self->{conflines}}; # correspond to a track line in the bed file
for (my $trackno=0; $trackno<@lines; $trackno++) {
my %options = $self->loader->parse_track_line($lines[$trackno]);
# Hacky special case for a remote BigWig track
next unless $options{type} eq 'bigWig'&& $options{bigDataUrl};
my $dbid = "$loadid.$trackno";
print $conf <<END;
[$dbid:database]
db_adaptor = Bio::DB::BigWig
db_args = -bigwig $options{bigDataUrl}
search options = none
END
}
print $conf <<END;
[$loadid:database]
db_adaptor = Bio::DB::SeqFeature::Store
db_args = -adaptor $backend
-dsn $dsn
#>>>>>>>>>> cut here <<<<<<<<
END
;
unless (@lines) {
my $track_label = $self->new_track_label;
my $track_name = $self->track_name;
my $key = $track_name;
my $bgcolor = $COLORS[rand @COLORS];
my $glyph = 'gene';
my @types = $self->loader->loaded_types;
my $category = $self->category;
print $conf <<END;
[$track_label]
database = $loadid
category = $category
glyph = $glyph
feature = @types
key = $key
decorate_introns = 1
thin_utr = 1
utr_color= $bgcolor
fgcolor = $bgcolor
bgcolor = $bgcolor
$summary
END
;
}
for (my $trackno=0; $trackno<@lines; $trackno++) {
my %options = $self->loader->parse_track_line($lines[$trackno]);
my $track_label = $self->new_track_label;
my $track_name = $self->track_name;
my $key = $options{name};
my $description= $options{description};
my $glyph = 'gene';
$options{visibility} ||= 'pack';
my $bump = $options{visibility} eq 'dense' ? 0
: $options{visibility} eq 'pack' ? 1
: $options{visibility} eq 'full' ? 2
: 1;
my $bgcolor = $options{itemRGB} ? 'featureRGB'
:$options{useScore} ? 'featureScore'
:$options{color} ? "rgb($options{color})"
:$COLORS[rand @COLORS];
# Hacky special case for a remote BigWig track
if ($options{type} eq 'bigWig'&& $options{bigDataUrl}) {
my $dbid = "$loadid.$trackno";
print $conf <<END;
[$track_label]
database = $dbid
feature = summary
glyph = wiggle_whiskers
max_color = lightgrey
min_color = lightgrey
mean_color = black
stdev_color = grey
stdev_color_neg = grey
height = 50
citation = $description
key = $key
END
} else { # conventional BED database
print $conf <<END;
[$track_label]
database = $loadid
category = My Tracks:Uploaded Tracks:$track_name
glyph = $glyph
feature = mRNA:$key region:$key
key = $key
citation = $description
decorate_introns = 1
thin_utr = 1
utr_color = $bgcolor
fgcolor = $bgcolor
bump = $bump
bgcolor = $bgcolor
$summary
END
}
}
}
1;
|
