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1 =head1 LICENSE
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2
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3 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
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4 Copyright [2016-2018] EMBL-European Bioinformatics Institute
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5
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6 Licensed under the Apache License, Version 2.0 (the "License");
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7 you may not use this file except in compliance with the License.
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8 You may obtain a copy of the License at
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9
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10 http://www.apache.org/licenses/LICENSE-2.0
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11
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12 Unless required by applicable law or agreed to in writing, software
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13 distributed under the License is distributed on an "AS IS" BASIS,
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14 WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
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15 See the License for the specific language governing permissions and
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16 limitations under the License.
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17
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18 =head1 CONTACT
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19
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20 Ensembl <http://www.ensembl.org/info/about/contact/index.html>
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21
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22 =cut
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23
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24 =head1 NAME
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25
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26 Draw
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27
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28 =head1 SYNOPSIS
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29
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30 mv Draw.pm ~/.vep/Plugins
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31 ./vep -i variations.vcf --plugin Draw
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32
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33 =head1 DESCRIPTION
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34
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35 A VEP plugin that draws pictures of the transcript model showing the
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36 variant location. Can take five optional paramters:
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37
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38 1) File name stem for images
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39 2) Image width in pixels (default: 1000px)
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40 3) Image height in pixels (default: 100px)
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41 4) Transcript ID - only draw images for this transcript
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42 5) Variant ID - only draw images for this variant
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43
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44 e.g.
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45
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46 ./vep -i variations.vcf --plugin Draw,myimg,2000,100
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47
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48 Images are written to [file_stem]_[transcript_id]_[variant_id].png
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49
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50 Requires GD library installed to run.
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51
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52 =cut
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53
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54 package Draw;
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55
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56 use strict;
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57 use warnings;
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58
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59 use Bio::EnsEMBL::Variation::Utils::BaseVepPlugin;
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60
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61 # GD libraries for image creating
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62 use GD;
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63 use GD::Polygon;
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64
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65 use Bio::EnsEMBL::Variation::Utils::VariationEffect qw(MAX_DISTANCE_FROM_TRANSCRIPT);
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66
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67 use base qw(Bio::EnsEMBL::Variation::Utils::BaseVepPlugin);
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68
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69
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70 sub new {
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71 my $class = shift;
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72
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73 my $self = $class->SUPER::new(@_);
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74
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75 # configure
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76 my @params = @{$self->params};
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77
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78 $self->{prefix} = $params[0] || $self->{config}->{output_file};
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79 $self->{width} = $params[1] || 1000;
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80 $self->{height} = $params[2] || 100;
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81 $self->{transcript} = $params[3] || undef;
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82 $self->{variant} = $params[4] || undef;
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83
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84 return $self;
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85 }
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86
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87 sub version {
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88 return '2.4';
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89 }
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90
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91 sub feature_types {
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92 return ['Transcript'];
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93 }
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94
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95 sub variant_feature_types {
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96 return ['BaseVariationFeature'];
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97 }
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98
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99 sub get_header_info {
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100 return {};
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101 }
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102
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103 sub run {
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104 my ($self, $tva) = @_;
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105
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106 my $main_tr = $tva->feature;
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107 my $vf = $tva->base_variation_feature;
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108
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109 return {} if defined($self->{transcript}) && $main_tr->stable_id ne $self->{transcript};
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110 return {} if defined($self->{variant}) && $vf->variation_name ne $self->{variant};
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111
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112 # if we're showing a gene fusion, get
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113 my $second_tr = $tva->{_fusion_transcripts}->[0] if grep {$_->SO_term =~ /gene_fusion/} @{$tva->get_all_OverlapConsequences};
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114
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115 # set up scales etc
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116 my $width = $main_tr->feature_Slice->length + (2 * MAX_DISTANCE_FROM_TRANSCRIPT);
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117 my $tr_start = $main_tr->start - MAX_DISTANCE_FROM_TRANSCRIPT;
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118 my $tr_end = $main_tr->end + MAX_DISTANCE_FROM_TRANSCRIPT;
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119
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120 if(defined($second_tr)) {
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121 $width = (max(($main_tr->end, $second_tr->end)) - min(($main_tr->start, $second_tr->start))) + 1 + (2 * MAX_DISTANCE_FROM_TRANSCRIPT);
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122 $tr_start = min(($main_tr->start, $second_tr->start)) - MAX_DISTANCE_FROM_TRANSCRIPT;
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123 $tr_end = max(($main_tr->end, $second_tr->end)) + MAX_DISTANCE_FROM_TRANSCRIPT;
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124 }
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125
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126 my $x_scale = ($self->{width} - 20) / $width;
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127 my $y_scale = ($self->{height} - 30) / 100;
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128 my $x_off = 10;
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129 my $y_off = 20;
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130
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131 # create GD image object
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132 my $img = GD::Image->new($self->{width}, $self->{height});
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133
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134 # set up some colours
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135 my %colours = (
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136 white => $img->colorAllocate(255,255,255),
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137 black => $img->colorAllocate(0,0,0),
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138 grey => $img->colorAllocate(200,200,200),
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139 darkgrey => $img->colorAllocate(150,150,150),
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140 vlightgrey => $img->colorAllocate(235,235,235),
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141 blue => $img->colorAllocate(0,0,200),
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142 lightblue => $img->colorAllocate(200,200,255),
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143 red => $img->colorAllocate(200,0,0),
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144 lightred => $img->colorAllocate(255,200,200),
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145 green => $img->colorAllocate(0,200,0),
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146 lightgreen => $img->colorAllocate(220,255,220),
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147 yellow => $img->colorAllocate(236,164,26),
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148 purple => $img->colorAllocate(195,50,212),
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149 );
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150
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151 # scale bar
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152 my $zero_string = '0' x (length(int(100 / $x_scale)) - 1);
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153 my $bases_per_bar = '1'.$zero_string;
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154
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155 my $start = int($tr_start / $bases_per_bar) * $bases_per_bar;
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156 my $end = (int($tr_start / $bases_per_bar) + 1) * $bases_per_bar;
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157 my $colour = 0;
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158
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159 while($start < $tr_end) {
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160 my $method = $colour ? 'rectangle' : 'filledRectangle';
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161
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162 $img->$method(
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163 $x_off + (($start - $tr_start) * $x_scale),
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164 $self->{height} - 15,
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165 $x_off + (($end - $tr_start) * $x_scale),
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166 $self->{height} - 10,
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167 $colours{grey},
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168 );
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169
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170 # tick and label
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171 if($start =~ /(5|0)$zero_string$/) {
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172 my $string = $start;
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173 1 while $string =~ s/^(-?\d+)(\d\d\d)/$1,$2/;
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174
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175 $img->string(
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176 gdTinyFont,
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177 $x_off + (($start - $tr_start) * $x_scale) + 2,
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178 $self->{height} - 8,
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179 $string,
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180 $colours{black}
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181 );
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182
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183 $img->line(
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184 $x_off + (($start - $tr_start) * $x_scale),
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185 $self->{height} - 15,
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186 $x_off + (($start - $tr_start) * $x_scale),
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187 $self->{height},
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188 $start =~ /5$zero_string$/ ? $colours{grey} : $colours{black}
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189 );
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190
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191 $img->dashedLine(
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192 $x_off + (($start - $tr_start) * $x_scale),
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193 0,
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194 $x_off + (($start - $tr_start) * $x_scale),
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195 $self->{height} - 15,
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196 $start =~ /5$zero_string$/ ? $colours{vlightgrey} : $colours{grey}
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197 )
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198 }
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199
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200 $colour = 1 - $colour;
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201 $start += $bases_per_bar;
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202 $end += $bases_per_bar;
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203 }
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204
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205 # render transcripts
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206 foreach my $tr($main_tr, $second_tr) {
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207 next unless defined($tr);
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208
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209 # render introns
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210 foreach my $intron(@{$tr->get_all_Introns}) {
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211 $img->line(
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212 $x_off + (($intron->start - $tr_start) * $x_scale),
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213 $y_off + (20 * $y_scale),
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214 $x_off + (((($intron->start + $intron->end) / 2) - $tr_start) * $x_scale),
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215 $y_off + (10 * $y_scale),
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216 $colours{lightblue}
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217 );
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218
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219 $img->line(
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220 $x_off + (((($intron->start + $intron->end) / 2) - $tr_start) * $x_scale),
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221 $y_off + (10 * $y_scale),
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222 $x_off + (($intron->end - $tr_start) * $x_scale),
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223 $y_off + (20 * $y_scale),
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224 $colours{lightblue}
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225 );
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226 }
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227
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228 # render exons
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229 foreach my $exon(@{$tr->get_all_Exons}) {
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230
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231 # non-coding part
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232 $img->rectangle(
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233 $x_off + (($exon->start - $tr_start) * $x_scale),
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234 $y_off + (10 * $y_scale),
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235 $x_off + (($exon->end - $tr_start) * $x_scale),
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236 $y_off + (30 * $y_scale),
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237 $colours{lightblue}
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238 );
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239
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240 # coding part
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241 $img->filledRectangle(
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242 $x_off + (($exon->coding_region_start($tr) - $tr_start) * $x_scale),
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243 $y_off + (0 * $y_scale),
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244 $x_off + (($exon->coding_region_end($tr) - $tr_start) * $x_scale),
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245 $y_off + (40 * $y_scale),
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246 $colours{blue}
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247 ) if defined $exon->coding_region_start($tr) && defined $exon->coding_region_end($tr);
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248 }
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249
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250 # add transcript direction indicator
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251 if($tr->strand == 1) {
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252
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253 # vertical line
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254 $img->line(
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255 $x_off + (($tr->start - $tr_start) * $x_scale),
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256 $y_off + (-5 * $y_scale),
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257 $x_off + (($tr->start - $tr_start) * $x_scale),
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258 $y_off + (20 * $y_scale),
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259 $colours{lightblue},
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260 );
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261
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262 # horizontal line
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263 $img->line(
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264 $x_off + (($tr->start - $tr_start) * $x_scale),
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265 $y_off + (-5 * $y_scale),
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266 $x_off + (($tr->start - $tr_start) * $x_scale) + 20,
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267 $y_off + (-5 * $y_scale),
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268 $colours{lightblue},
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269 );
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270
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271 # top arrow part
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272 $img->line(
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273 $x_off + (($tr->start - $tr_start) * $x_scale) + 17,
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274 $y_off + (-8 * $y_scale),
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275 $x_off + (($tr->start - $tr_start) * $x_scale) + 20,
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276 $y_off + (-5 * $y_scale),
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277 $colours{lightblue},
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278 );
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279
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280 # bottom arrow part
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281 $img->line(
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282 $x_off + (($tr->start - $tr_start) * $x_scale) + 17,
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283 $y_off + (-1 * $y_scale),
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284 $x_off + (($tr->start - $tr_start) * $x_scale) + 20,
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285 $y_off + (-5 * $y_scale),
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286 $colours{lightblue},
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287 );
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288
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289 # label
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290 $img->string(gdTinyFont, $x_off + (($tr->start - $tr_start) * $x_scale) + 25, $y_off + (-12 * $y_scale), $tr->stable_id, $colours{blue});
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291 }
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292
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293 else {
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294
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295 # vertical line
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296 $img->line(
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297 $x_off + (($tr->end - $tr_start) * $x_scale),
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298 $y_off + (20 * $y_scale),
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299 $x_off + (($tr->end - $tr_start) * $x_scale),
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300 $y_off + (47 * $y_scale),
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301 $colours{lightblue},
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302 );
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303
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304 # horizontal line
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305 $img->line(
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306 $x_off + (($tr->end - $tr_start) * $x_scale),
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307 $y_off + (47 * $y_scale),
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308 $x_off + (($tr->end - $tr_start) * $x_scale) - 20,
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309 $y_off + (47 * $y_scale),
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310 $colours{lightblue},
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311 );
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312
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313 # top arrow part
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314 $img->line(
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315 $x_off + (($tr->end - $tr_start) * $x_scale) - 17,
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316 $y_off + (50 * $y_scale),
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317 $x_off + (($tr->end - $tr_start) * $x_scale) - 20,
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318 $y_off + (47 * $y_scale),
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319 $colours{lightblue},
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320 );
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321
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322 # bottom arrow part
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323 $img->line(
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324 $x_off + (($tr->end - $tr_start) * $x_scale) - 17,
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325 $y_off + (43 * $y_scale),
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326 $x_off + (($tr->end - $tr_start) * $x_scale) - 20,
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327 $y_off + (47 * $y_scale),
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328 $colours{lightblue},
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329 );
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330
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331 # label
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332 $img->string(gdTinyFont, $x_off + (($tr->end - $tr_start) * $x_scale) - 100, $y_off + (43 * $y_scale), $tr->stable_id, $colours{blue});
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333 }
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334 }
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335
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336 # render variant
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337 my $var_colour = 'green';
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338
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339 if($vf->class_SO_term =~ /deletion/) {
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340 $var_colour = 'red';
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341 }
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342
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343 $img->filledRectangle(
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344 $x_off + (($vf->start - $tr_start) * $x_scale),
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345 $y_off + (60 * $y_scale),
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346 $x_off + (($vf->end - $tr_start) * $x_scale),
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347 $y_off + (70 * $y_scale),
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348 $colours{$var_colour},
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349 );
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350
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351 # variant label
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352 $img->string(
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353 gdTinyFont,
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354 $x_off + (($vf->start - $tr_start) * $x_scale),
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355 $y_off + (75 * $y_scale),
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356 $vf->variation_name,
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357 $colours{$var_colour}
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358 );
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359
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360 my $vname = $vf->variation_name;
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361 $vname =~ s/\//\_/g;
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362 my $file = $self->{prefix}."_".$main_tr->stable_id."_".(defined($second_tr) ? $second_tr->stable_id."_" : "").$vname."\.png";
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363
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364 # check we're allowed to write to it
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365 if(!defined($self->{config}->{force_overwrite}) && -e $file) {
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366 die "ERROR: Image file $file already exists - choose a different file name stem or use --force_overwrite\n";
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367 return;
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368 }
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369
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370 open IM, ">$file" or die "ERROR: Could not write to file $file\n";
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371 binmode IM;
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372 print IM $img->png;
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373 close IM;
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374
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375 return {};
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376 }
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377
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378 sub max {
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379 return (sort {$a <=> $b} @_)[-1];
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380 }
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381
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382 sub min {
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383 return (sort {$a <=> $b} @_)[0];
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384 }
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385
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386 1;
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387
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