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VEPbrowse.pm
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VEPbrowse.pm
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=head1 LICENSE
Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
Copyright [2016] EMBL-European Bioinformatics Institute
Licensed under the Apache License, Version 2.0 (the "License");
you may not use this file except in compliance with the License.
You may obtain a copy of the License at
http://www.apache.org/licenses/LICENSE-2.0
Unless required by applicable law or agreed to in writing, software
distributed under the License is distributed on an "AS IS" BASIS,
WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
See the License for the specific language governing permissions and
limitations under the License.
=head1 CONTACT
Will McLaren <wm2@ebi.ac.uk>
=cut
=head1 NAME
Draw
=head1 SYNOPSIS
mv VEPbrowse.pm ~/.vep/Plugins
perl variant_effect_predictor.pl -i variations.vcf --plugin VEPbrowse --individual JohnDoe
=head1 DESCRIPTION
A VEP plugin that generates HTML with an overview of an individual's mutations
across the genome, as well as a transcript-specific sequence view. This plugin
is under development, please expect bugs!!!
=cut
package VEPbrowse;
use strict;
use warnings;
use Bio::EnsEMBL::Variation::Utils::BaseVepPlugin;
use Bio::EnsEMBL::Variation::Utils::VariationEffect qw(MAX_DISTANCE_FROM_TRANSCRIPT overlap);
use Bio::EnsEMBL::Variation::Utils::Sequence qw(align_seqs);
use Bio::EnsEMBL::Utils::Sequence qw(reverse_comp);
use Bio::EnsEMBL::Utils::Exception qw(throw warning);
use Bio::SeqUtils;
use base qw(Bio::EnsEMBL::Variation::Utils::BaseVepPlugin);
my $ktbs;
sub new {
my $class = shift;
my $self = $class->SUPER::new(@_);
# configure
my @params = @{$self->params};
# initialize cache
$self->{cache} = {};
$self->{has_cache} = 1;
# force various options
$self->{config}->{prefetch} = 1;
$self->{config}->{hgnc} = 1;
return $self;
}
sub version {
return '2.5';
}
sub feature_types {
return ['Transcript'];
}
sub variant_feature_types {
return ['VariationFeature'];
}
sub get_header_info {
return {};
}
# the destroy method will be run as the script closes
# so we can use this to build the summary HTML page
sub DESTROY {
my $self = shift;
open OUT, ">index.html";
if(defined($self->{karyotype_bands})) {
my ($canvas_width, $canvas_height) = (1000, 500);
my $html =<<END;
<!DOCTYPE html>
<html>
<head>
</head>
<body onload="init();">
<div id="canvas_holder" style="border:1px solid #c3c3c3; width:${canvas_width}px;">
<canvas id="karyotype" width="$canvas_width" height="$canvas_height">
Your browser does not support the HTML5 canvas element.
</canvas>
</div>
<div id="info" style="width:${canvas_width}px;height:200px;overflow:auto;border:1px solid #c3c3c3; padding: 5px; font-family: arial, sans-serif;">
</div>
<script type="text/javascript">
var c, ctx, tool, genes, info;
var select_from, select_to;
var canvas_width, canvas_height;
var x_scale, x_off;
function init() {
c = document.getElementById("karyotype");
ctx = c.getContext("2d");
info = document.getElementById("info");
canvas_width = $canvas_width;
canvas_height = $canvas_height;
tool = new tool_pencil();
drawKaryotype();
c.addEventListener('mousedown', ev_canvas, false);
c.addEventListener('mousemove', ev_canvas, false);
c.addEventListener('mouseup', ev_canvas, false);
}
END
$html .= $self->karyotype_jscript();
$html .= $self->render_karyotype_html($canvas_width, $canvas_height);
$html .= "\n</script>\n</body>\n</html>";
print OUT $html;
}
else {
print OUT "<ul>";
foreach my $gene(keys %{$self->{genes}}) {
print OUT "<li>$gene<ul>\n";
foreach my $tr(@{$self->{genes}->{$gene}->{transcripts}}) {
print OUT "<li><a href='".$tr->{transcript}.".html'>$tr->{transcript}</a>";
print OUT " Mismatches: ".$tr->{mismatches}." Length ratio: ".$tr->{length_ratio};
print OUT "</li>";
}
print OUT "</ul></li>";
}
print OUT "</ul>";
}
close OUT;
}
sub run {
my ($self, $tva) = @_;
my $tr = $tva->transcript;
my $vf = $tva->base_variation_feature;
my $tr_stable_id = $tr->stable_id;
my $individual = $vf->{individual};
$self->get_karyotype_bands($self->config->{reg}->get_adaptor($self->config->{species}, 'core', 'slice')->db);
return {} unless defined($vf->{last_in_transcript}->{$tr_stable_id});
return {} unless defined $tr->{vfs} && scalar @{$tr->{vfs}};
my $exons = $tr->get_all_Exons();
return {} unless defined $exons && scalar @$exons;
$_->{slice} ||= $tr->{slice} for @$exons;
my $mapper = $tr->{_variation_effect_feature_cache}->{mapper};
return {} unless defined $mapper;
my $codon_table = $tr->{_variation_effect_feature_cache}->{codon_table};
return {} unless defined $tr->translation;
my $translateable_seq = $tr->{_variation_effect_feature_cache}->{translateable_seq};
# check if this transcript has any variants that change its sequence
my $ok = 0;
my $worst_con;
foreach my $vf(@{$tr->{vfs}}) {
foreach my $tv(@{$vf->get_all_TranscriptVariations([$tr])}) {
foreach my $tva(@{$tv->get_all_TranscriptVariationAlleles}) {
foreach my $oc(@{$tva->get_all_OverlapConsequences}) {
my $so_term = $oc->SO_term;
$worst_con = $oc if !defined($worst_con) || $oc->rank < $worst_con->rank;
if(
$so_term eq 'missense_variant' ||
$so_term eq 'stop_gained' ||
$so_term eq 'stop_lost' ||
$so_term eq 'transcript_ablation' ||
$so_term eq 'frameshift_variant' ||
$so_term eq 'initiator_codon_variant' ||
$so_term =~ /inframe_codon/
) {
$ok = 1;
last;
}
}
}
}
}
return {} unless $ok;
#$DBsingle = 1;
#print STDERR "\nDoing $tr_stable_id $individual\n";
#return {} unless $tr_stable_id eq 'ENST00000343703';
#print STDERR "Getting ref features\n";
# get ref features
my @ref_features = @{$self->get_ref_transcript_features($tr)};
# check ref features
die("ERROR: Ref features borked\n") unless grep {$_->{t} eq 'coding' && $_->{seq}} @ref_features;
#print STDERR "Getting ind features\n";
# get aligned individual features
# this also re-aligns the reference
my $features_arrayref = $self->get_individual_features($tr, \@ref_features);
my $var_features = pop @$features_arrayref;
#print STDERR "Getting translations\n";
# get peptides
my @peptides = map {$self->translate_features($_, $codon_table)} (\@ref_features, @$features_arrayref);
#print STDERR "Aligning ref peptide\n";
# align peptides to features
$self->align_pep_to_features($peptides[0], \@ref_features);
#print STDERR "Aligning ind peptides\n";
my $i = 1;
$self->align_pep_to_features($peptides[$i++], $_) for @$features_arrayref;
#print STDERR "Marking up codons\n";
# mark up codons
$self->markup_codons($_) for (\@ref_features, @$features_arrayref);
#print STDERR "Compiling sequences\n";
# construct seq from features
my $ref_tr_seq = "";
$ref_tr_seq .= $_->{marked_seq} for @ref_features;
# compile sequences, ref first, tr then pep
my @seqs = ($ref_tr_seq);
my $seq = "";
$seq .= $_->{pep} for @ref_features;
push @seqs, $seq;
for my $phase(@$features_arrayref) {
my $seq = "";
$seq .= $_->{marked_seq} for @{$phase};
push @seqs, $seq;
$seq = "";
$seq .= $_->{pep} for @{$phase};
push @seqs, $seq;
}
$seq = "";
$seq .= $_->{seq} for @$var_features;
push @seqs, $seq;
my $seqs = join ",", map {"'$_'"} @seqs;
# compare peptides
my $ref_pep = $seqs[1];
my ($worst_length_ratio, $worst_mismatches) = (100, 0);
for(my $i=3; $i<=$#seqs; $i+=2) {
my $pep = $seqs[$i];
# seq_differences
my ($tp1, $tp2) = ($ref_pep, $pep);
$tp1 =~ s/\-|\_//g;
$tp2 =~ s/\-|\_//g;
my $length_ratio = $tp1 ? 100 * (length($tp2) / length($tp1)) : 0;
$worst_length_ratio = $length_ratio if abs($length_ratio - 100) > abs($worst_length_ratio - 100);
my $mismatches = 0;
for(my $j=0; $j<length($tp1) && $j<length($tp2); $j+=3) {
$mismatches++ unless substr($tp1, $j, 3) eq substr($tp2, $j, 3);
}
$worst_mismatches = $mismatches if $mismatches > $worst_mismatches;
}
#my @seqs = ([map {$_->{marked_seq}} @ref_features],[map {$_->{pep_seq}} @ref_features]);
#
#foreach my $phase(@$features_arrayref) {
# push @seqs, [map {$_->{marked_seq}} @{$phase}];
# push @seqs, [map {$_->{pep_seq}} @{$phase}];
#}
#
#my $seqs = '[';
#
#foreach my $seq(@seqs) {
# $seqs .= '['.(join ",", map {"'$_'"} @$seq).'],';
#}
#
#$seqs =~ s/\,$//g;
#$seqs .= ']';
# log gaps in align
my @gaps = ('SHIFTMEOFF');
for my $i(0..(length($ref_tr_seq) - 1)) {
push @gaps, $i + 1 if substr($ref_tr_seq, $i, 1) eq '-';
}
my $gaps = join ",", map {"'$_'"} @gaps;
# parse VFs
my $vfs = $self->format_vfs($tr);
my $canvas_width = 1000;
my $canvas_height = 100;
my $x_scale = ($canvas_width - 20) / ($tr->end - $tr->start + 1);
my $y_scale = ($canvas_height - 20) / 100;
my $x_off = 10;
my $css = get_css();
my $html =<<END;
<!DOCTYPE html>
<html>
<head>
$css
</head>
<body onload="init();">
<div id="header" style="width:${canvas_width}px" class="header">
<div style="display: inline; float: right;"><img src="http://www.ensembl.org/img/vep_logo.png"></div>
<h1 style="display: inline; vertical-align: top;">$tr_stable_id</h1><br/>
<h2 style="display: inline; vertical-align: top;">$individual</h2>
<div style="font-size:small"><a href="index.html">Back to index</a></div>
</div>
<div id="canvas_holder" style="border:1px solid #c3c3c3; width:${canvas_width}px;">
<canvas id="transcript" width="$canvas_width" height="$canvas_height">
Your browser does not support the HTML5 canvas element.
</canvas>
</div>
<div id="control" style="width:${canvas_width}px" class="control">
<b>Selection: </b>
<a href="#" onClick="select_all();">Select all</a>
|
<a href="#" onClick="clear_selection();">Clear selection</a>
|
<b>Zoom: </b><a href="#" onClick="zoom(0.75);">+</a> / <a href="#" onClick="zoom(1.33);">-</a>
|
<b>Move: </b><a href="#" onClick="move(-0.5);"><<</a> / <a href="#" onClick="move(-0.1);"><</a> / <a href="#" onClick="move(0.1);">></a> / <a href="#" onClick="move(0.5);">>></a>
<hr class="control_spacer">
<b>Options: </b>
<input type="checkbox" name="coding_only_checkbox" id="coding_only_checkbox" onclick="coding_only=toggle_value(coding_only);render_seq();" checked=1/>
<span onClick="var c = document.getElementById('coding_only_checkbox'); c.checked =(! c.checked); coding_only=toggle_value(coding_only);render_seq();">Show coding sequence only</span>
<hr class="control_spacer">
<b>Sequences: </b>
Reference
<select name="ref_seqs_select" id="ref_seqs_select" onchange="ref_seqs=this.value;render_seq();">
<option value="tr_pep">Both</option>
<option value="tr">Transcript</option>
<option value="pep">Peptide</option>
<option value="none">None</option>
</select>
|
Phase 1
<select name="p1_seqs_select" id="p1_seqs_select" onchange="p1_seqs=this.value;render_seq();">
<option value="tr_pep">Both</option>
<option value="tr">Transcript</option>
<option value="pep">Peptide</option>
<option value="none">None</option>
</select>
|
Phase 2
<select name="p2_seqs_select" id="p2_seqs_select" onchange="p2_seqs=this.value;render_seq();">
<option value="tr_pep">Both</option>
<option value="tr">Transcript</option>
<option value="pep">Peptide</option>
<option value="none">None</option>
</select>
</div>
<div id="sequence" style="width:${canvas_width}px;height:400px;overflow:auto;border:1px solid #c3c3c3">
Click and drag to select a region of the transcript and show sequence.
</div>
<div id="debug" style="width:${canvas_width}px;height:150px;overflow:auto;border:1px solid #c3c3c3; font-size: small;"><h3>Debug</h3></div>
<script type="text/javascript">
var c, ctx, tool, s, debug_div, canvas_scale;
var select_from, select_to;
var seqs, vfs;
var coding_only, ref_seqs, p1_seqs, p2_seqs;
var seq_div_html;
var canvas_width, canvas_height;
var x_scale, x_off;
var gaps;
function init() {
c = document.getElementById("transcript");
ctx = c.getContext("2d");
s = document.getElementById("sequence");
debug_div = document.getElementById("debug");
canvas_width = $canvas_width;
canvas_height = $canvas_height;
x_scale = $x_scale;
x_off = $x_off;
gaps = new Array($gaps);
seqs = new Array($seqs);
vfs = $vfs;
// shift off first element
// bugfix for strange javascript behaviour when you try to create an array
// with one numeric element
gaps.shift();
drawTranscript();
canvas_scale = 1;
coding_only = 1;
ref_seqs = 'tr_pep';
p1_seqs = 'tr_pep';
p2_seqs = 'tr_pep';
seq_div_html = s.innerHTML;
tool = new tool_pencil();
c.addEventListener('mousedown', ev_canvas, false);
c.addEventListener('mousemove', ev_canvas, false);
c.addEventListener('mouseup', ev_canvas, false);
}
END
# add main jscript stuff
$html .= $self->jscript_html();
# add transcript render jscript
$html .= $self->render_transcript_html($tr, $canvas_width, $canvas_height);
# close javascript
$html .= "\n</script>\n";
$html .= "\n</body>\n</html>";
open OUT, ">".$tr->stable_id.".html";
print OUT $html;
close OUT;
# write transcript data to cache
my $gene = $tr->{_gene};
$self->{genes}->{$gene->stable_id} ||= {
coords => {
chr => $tr->slice->seq_region_name,
start => $gene->start,
end => $gene->end,
},
hgnc => $tr->{_gene_hgnc},
transcripts => [],
};
push @{$self->{genes}->{$gene->stable_id}->{transcripts}}, {
transcript => $tr->stable_id,
mismatches => $worst_mismatches,
length_ratio => $worst_length_ratio,
worst_con => $worst_con->label,
};
return {};
}
sub max {
return (sort {$a <=> $b} @_)[-1];
}
sub min {
return (sort {$a <=> $b} @_)[0];
}
sub print_aligned {
my $self = shift;
my ($s1, $s2) = @_;
my $width = 60;
while(1) {
my $c1 = substr($s1, 0, $width);
my $c2 = substr($s2, 0, $width);
#for my $i(0..(CORE::length($c1) - 1)) {
# substr($c2, $i, 1) = "." if substr($c2, $i, 1) eq substr($c1, $i, 1);
#}
#$c1 =~ s/([A-Z]{3})/$1 /g;
#$c2 =~ s/([A-Z]{3})/$1 /g;
print "$c1\n$c2\n\n";
last if CORE::length($s1) <= $width;
$s1 = substr($s1, $width);
$s2 = substr($s2, $width);
last unless $s1 && $s2;
}
}
sub get_ref_transcript_features {
my $self = shift;
my $tr = shift;
my $exons = $tr->get_all_Exons();
return {} unless defined $exons && scalar @$exons;
my $mapper = $tr->{_variation_effect_feature_cache}->{mapper};
return {} unless defined $mapper;
my $translateable_seq = $tr->{_variation_effect_feature_cache}->{translateable_seq};
#$DBsingle = 1;
my @features = ();
my $tr_seq = "";
my $prev_exon;
foreach my $exon(@$exons) {
# intron
if(defined($prev_exon)) {
my $seq = "_" x ($exon->start > $prev_exon->start ? $exon->start - $prev_exon->end : $prev_exon->start - $exon->end);
my $feat = {
t => 'intron',
s => length($tr_seq),
seq => $seq
};
$tr_seq .= $seq;
$feat->{e} = length($tr_seq);
push @features, $feat;
}
$prev_exon = $exon;
# map exon to CDS coords
my @coords = $mapper->genomic2cds($exon->start, $exon->end, $exon->strand);
foreach my $coord(@coords) {
# UTR
if($coord->isa('Bio::EnsEMBL::Mapper::Gap')) {
my $seq = '#' x $coord->length;
my $feat = {
t => 'utr',
s => length($tr_seq),
seq => $seq
};
$tr_seq .= $seq;
$feat->{e} = length($tr_seq);
push @features, $feat;
}
else {
my $seq = substr($translateable_seq, $coord->start - 1, $coord->length);
my $feat = {
t => 'coding',
s => length($tr_seq),
seq => $seq,
};
$tr_seq .= $seq;
$feat->{e} = length($tr_seq);
push @features, $feat;
}
}
}
return \@features;
}
sub get_individual_features {
my $self = shift;
my $tr = shift;
my $ref_features = shift;
# construct sequence from ref features
my $ref_tr_seq = "";
$ref_tr_seq .= $_->{seq} for @$ref_features;
# back up features
my @backup_features;
foreach(@$ref_features) {
push @backup_features, {
seq => $_->{seq},
t => $_->{t}
};
}
my @ind_features_array;
# copy features
foreach my $phase(0..1) {
my ($new_tr_seq, $new_features);
$new_tr_seq = $ref_tr_seq;
# clone features
foreach(@backup_features) {
push @$new_features, {
seq => $_->{seq},
t => $_->{t}
};
}
push @ind_features_array, $new_features;
}
# copy for var track
my @var_features;
foreach(@backup_features) {
push @var_features, {
'seq' => $_->{t} eq 'coding' ? (' ' x length($_->{seq})) : $_->{seq},
't' => $_->{t}
}
}
foreach my $vf(sort {$b->{start} <=> $a->{start}} @{$tr->{vfs}}) {
# get coords
my ($tr_vf_start, $tr_vf_end);
if($tr->strand == 1) {
$tr_vf_start = ($vf->start - $tr->start) + 1;
$tr_vf_end = ($vf->end - $tr->start) + 1;
}
else {
$tr_vf_start = ($tr->end - $vf->end) + 1;
$tr_vf_end = ($tr->end - $vf->start) + 1;
}
my $vf_length = ($vf->{end} - $vf->{start}) + 1;
# get alleles
next unless defined $vf->{genotype};
my @alleles = @{$vf->{genotype}};
next unless scalar @alleles;
# find longest
my $longest = (sort {length($a) <=> length($b)} @alleles)[-1];
my $longest_length = length($longest);
$longest_length = $vf_length if $vf_length > $longest_length;
# pad alleles
$_ .= "-" x ($longest_length - length($_)) for @alleles;
# replace sequence
for my $i(0..(scalar @$ref_features - 1)) {
my $ref_feat = $ref_features->[$i];
my $var_feat = $var_features[$i];
if(overlap($ref_feat->{s}, $ref_feat->{e}, $tr_vf_start, $tr_vf_end)) {
my ($s, $e) = ($tr_vf_start - $ref_feat->{s}, $tr_vf_end - $ref_feat->{s});
# pad ref sequence if necessary
if($longest_length > $vf_length) {
my $char = $ref_feat->{t} eq 'coding' ? '-' : ($ref_feat->{t} eq 'intron' ? '_' : '#');
substr($ref_feat->{seq}, $s, 0) = $char x ($longest_length - $vf_length);
substr($var_feat->{seq}, $s, 0) = ($ref_feat->{t} eq 'coding' ? 'i' : $char) x ($longest_length - $vf_length);
}
else {
substr($var_feat->{seq}, $s, ($e - $s) + 1) = ($vf->allele_string =~ /\-/ ? 'd' : 'v') x (($e - $s) + 1)
}
for my $phase(0..1) {
my $feat = $ind_features_array[$phase]->[$i];
my $tmp_allele = $alleles[$phase];
my ($s, $e) = ($tr_vf_start - $ref_feat->{s}, $tr_vf_end - $ref_feat->{s});
if($s < 0 && $tmp_allele ne '') {
$tmp_allele = substr($tmp_allele, 0 - $s);
$s = 0;
}
if($e > ($ref_feat->{e} - $ref_feat->{s})) {
$tmp_allele = substr($tmp_allele, 0, $e - ($ref_feat->{e} - $ref_feat->{s}));
$e = ($ref_feat->{e} - $ref_feat->{s});
}
$tmp_allele =~ s/./\_/g if $ref_feat->{t} eq 'intron';
$tmp_allele =~ s/./\#/g if $ref_feat->{t} eq 'utr';
substr($feat->{seq}, $s, ($e - $s) + 1) = $tmp_allele;
}
}
}
}
push @ind_features_array, \@var_features;
return \@ind_features_array;
}
sub markup_codons {
my $self = shift;
my $features = shift;
my $phase_adjust = 0;
my $tmp_phase = 0;
my $flipper = 1;
for my $i(0..(scalar @$features - 1)) {
my $feat = $features->[$i];
$feat->{marked_seq} = $feat->{seq};
if($feat->{t} eq 'coding') {
my $j = 0;
while($j < length($feat->{marked_seq})) {
my $l = 3 - $phase_adjust;
my $tl = $l;
die("Something's gone wrong in sequence markup\n") if $l < 0;
my $test = substr($feat->{marked_seq}, $j, $tl);
my $prev_length = length($test);
$test =~ s/\-//g;
my $t_length = length($test);
while($t_length < $l) {
$tl++;
$test = substr($feat->{marked_seq}, $j, $tl);
last if $prev_length == length($test);
$prev_length = length($test);
$test =~ s/\-//g;
$t_length = length($test);
}
if($flipper) {
$test = substr($feat->{marked_seq}, $j, $tl);
$test =~ tr/ACGT-/VWXYZ/;
substr($feat->{marked_seq}, $j, $tl) = $test;
}
$flipper = 1 - $flipper;
$j += $tl;
$phase_adjust = 0;
$tmp_phase = length($test) == 3 ? 0 : length($test);
}
$phase_adjust = $tmp_phase;
$flipper = 1 - $flipper if $phase_adjust;
}
}
}
sub translate_features {
my $self = shift;
my $features = shift;
my $codon_table = shift;
my $tr_seq = "";
$tr_seq .= $_->{seq} for @$features;
$tr_seq =~ s/\#|\_|n|i|\-//g;
my $pep_seq = Bio::Seq->new(-seq => $tr_seq)->translate(undef, undef, undef, $codon_table);
# get sequence as 3-letter AA codes
my $seq3 = Bio::SeqUtils->seq3($pep_seq);
# shorten the sequence if a new terminator has been introduced
while($seq3 =~ m/Ter/g) {
my $pos = pos($seq3);
substr($seq3, $pos) = "_" x (length($seq3) - $pos) if $pos < length($seq3);
last;
}
return $seq3;
}
sub align_pep_to_features {
my $self = shift;
my $pep = shift;
my $features = shift;
my $tmp_pep = $pep;
foreach my $f(@$features) {
if($f->{t} eq 'coding') {
my $tmp = $f->{seq};
$tmp =~ s/\-//g;
my $tmp2 = substr($tmp_pep, 0, length($tmp));
# re-insert gaps
for(my $i=0; $i < length($f->{seq}); $i++) {
substr($tmp2, $i, 0) = '-' if substr($f->{seq}, $i, 1) eq '-';
}
$f->{pep} = $tmp2;
# shorten tmp_pep
$tmp_pep = substr($tmp_pep, length($tmp)) unless length($tmp_pep) < length($tmp);
}
else {
$f->{pep} = "_" x length($f->{seq});
}
}
}
sub format_vfs {
my $self = shift;
my $tr = shift;
my @vfs;
foreach my $vf(@{$tr->{vfs}}) {
foreach my $tv(@{$vf->get_all_TranscriptVariations([$tr])}) {
foreach my $tva(@{$tv->get_all_TranscriptVariationAlleles}) {
push @vfs, [
$vf->variation_name,
$vf->{chr}, $vf->{start}, $vf->{end},
(join ",", map {$_->label} @{$tva->get_all_OverlapConsequences})
];
}
}
}
my $return = '[';
$return .= join ",", map {"[".(join ",", map {$_ =~ /^\d+$/ ? $_ : "'$_'"} @$_)."]"} @vfs;
$return .= ']';
#print $return."\n";
return $return;
}
sub get_karyotype_bands {
my $self = shift;
my $db = shift;
return if defined($self->{karyotype_bands});
my $config = $self->config;
my $ktba = $db->get_KaryotypeBandAdaptor;
my $sa = $db->get_SliceAdaptor;
if(!defined($ktba) || !defined($sa)) {
warn("WARNING: VEPbrowse plugin could not get karyotype bands");
$self->{karyotype_bands} = {};
return;
}
foreach my $slice(grep {$_->is_reference} @{$sa->fetch_all('chromosome')}) {
foreach my $ktb(@{$ktba->fetch_all_by_Slice($slice)}) {
push @{$self->{karyotype_bands}->{$slice->seq_region_name}}, {
start => $ktb->start,
end => $ktb->end,
stain => $ktb->stain,
};
}
}
}
sub jscript_html {
my $self = shift;
my $html =<<END;
function tool_pencil () {
var tool = this;
this.started = false;
var start_x;
// This is called when you start holding down the mouse button.
// This starts the pencil drawing.
this.mousedown = function (ev) {
start_x = ev._x;
tool.started = true;
};
// This function is called every time you move the mouse. Obviously, it only
// draws if the tool.started state is set to true (when you are holding down
// the mouse button).
this.mousemove = function (ev) {
if (tool.started) {
var x = start_x < ev._x ? start_x : ev._x;
var w = ev._x - start_x;
if(w < 0) {
w = 0 - w;
}
select_from = start_x < ev._x ? start_x : ev._x;
select_to = start_x > ev._x ? start_x : ev._x;
// clear canvas
ctx.clearRect(0, 0, canvas_width, canvas_height);
// redraw transcript
drawTranscript();
draw_box(x, w);
}
};
// This is called when you release the mouse button.
this.mouseup = function (ev) {
if (tool.started) {
tool.mousemove(ev);
tool.started = false;
render_seq();
}
}
}
function ev_canvas (ev) {
var element = c, offsetX = 0, offsetY = 0, div = document.getElementById('canvas_holder');
// Compute the total offset
if (element.offsetParent !== undefined) {
do {
offsetX += element.offsetLeft;
offsetY += element.offsetTop;
} while ((element = element.offsetParent));
}
// Add padding and border style widths to offset
// Also add the <html> offsets in case there's a position:fixed bar
//offsetX += div.stylePaddingLeft + div.styleBorderLeft + div.htmlLeft;
//offsetY += div.stylePaddingTop + div.styleBorderTop + div.htmlTop;
ev._x = ev.pageX - offsetX;
ev._y = ev.pageY - offsetY;
// old way
//if (ev.layerX || ev.layerX == 0) { // Firefox
// ev._x = ev.layerX;
// ev._y = ev.layerY;
//} else if (ev.offsetX || ev.offsetX == 0) { // Opera
// ev._x = ev.offsetX;
// ev._y = ev.offsetY;
//}