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1 package Bio::EnsEMBL::Variation::Utils::Config;
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2
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3 use base qw(Exporter);
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4
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5 our @EXPORT_OK = qw(
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6 @ATTRIB_TYPES
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7 %ATTRIBS
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8 @ATTRIB_SETS
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9 @VARIATION_CLASSES
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10 @OVERLAP_CONSEQUENCES
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11 @FEATURE_TYPES
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12 $OVERLAP_CONSEQUENCE_CLASS
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13 $MAX_ATTRIB_CODE_LENGTH
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14 );
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15
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16 our $OVERLAP_CONSEQUENCE_CLASS = 'Bio::EnsEMBL::Variation::OverlapConsequence';
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17
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18 our $MAX_ATTRIB_CODE_LENGTH = 20;
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19
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20 our @short_names = qw(1kg_hct 1kg_hct_ceu 1kg_hct_yri 1kg_hce 1kg_hce_ceu 1kg_hce_chb
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21 1kg_hce_chd 1kg_hce_jpt 1kg_hce_lwk 1kg_hce_tsi 1kg_hce_yri 1kg_lc
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22 1kg_lc_ceu 1kg_lc_chb_jpt 1kg_lc_yri hapmap
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23 1kg 1kg_afr 1kg_amr 1kg_asn 1kg_eur 1kg_afr 1kg_amr_com 1kg_asn_com 1kg_eur_com
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24 ind_venter ind_watson ind_gill ind_ak1 ind_irish ind_angrist
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25 ind_gates_jr ind_gates_sr ind_kriek ind_quake ind_saqqaq ind_saqqaq_hc ind_sjk ind_yh
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26 fail_all fail_nonref fail_ambig fail_gt_fq fail_incons_map fail_mult_map
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27 fail_no_alleles fail_no_gt fail_no_map fail_no_seq fail_non_nt fail_mult_alleles fail_dbsnp_suspect
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28 ph_hgmd_pub ph_johnson_et_al ph_nhgri ph_omim ph_variants ph_uniprot
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29 ph_cosmic ph_ega precious hapmap_ceu hapmap_hcb hapmap_jpt hapmap_yri
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30 Affy_500K Affy_SNP6 Cardio-Metabo_Chip HumanOmni1-Quad Illumina_1M-duo Illumina_660Q
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31 );
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32
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33 our @dbsnp_clinical_significance_types = qw(
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34 unknown
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35 untested
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36 non-pathogenic
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37 probable-non-pathogenic
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38 probable-pathogenic
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39 pathogenic
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40 drug-response
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41 histocompatibility
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42 other
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43 );
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44
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45 our @dgva_clinical_significance_types = (
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46 'Not tested',
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47 'Benign',
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48 'Pathogenic',
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49 'Uncertain Significance',
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50 'Uncertain Significance: likely benign',
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51 'Uncertain Significance: likely pathogenic'
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52 );
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53
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54 our @VARIATION_CLASSES = (
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55 {
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56 SO_accession => 'SO:0001483',
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57 SO_term => 'SNV',
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58 display_term => 'SNP',
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59 somatic_display_term => 'somatic_SNV',
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60 },
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61 {
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62 SO_accession => 'SO:1000002',
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63 SO_term => 'substitution',
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64 },
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65 {
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66 SO_accession => 'SO:0001019',
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67 SO_term => 'copy_number_variation',
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68 display_term => 'CNV',
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69 },
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70 {
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71 SO_accession => 'SO:0000667',
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72 SO_term => 'insertion',
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73 },
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74 {
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75 SO_accession => 'SO:0000159',
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76 SO_term => 'deletion',
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77 },
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78 {
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79 SO_accession => 'SO:1000032',
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80 SO_term => 'indel',
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81 },
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82 {
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83 SO_accession => 'SO:0000705',
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84 SO_term => 'tandem_repeat',
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85 },
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86 {
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87 SO_accession => 'SO:0001059',
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88 SO_term => 'sequence_alteration',
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89 },
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90 # Structural variation classes
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91 {
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92 SO_accession => 'SO:0001537',
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93 SO_term => 'structural_variant',
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94 display_term => 'SV',
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95 },
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96 {
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97 SO_accession => 'SO:0000051',
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98 SO_term => 'probe',
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99 display_term => 'CNV_PROBE',
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100 },
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101 {
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102 SO_accession => 'SO:0001742',
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103 SO_term => 'copy_number_gain',
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104 display_term => 'Gain',
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105 },
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106 {
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107 SO_accession => 'SO:0001743',
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108 SO_term => 'copy_number_loss',
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109 display_term => 'Loss',
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110 },
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111 {
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112 SO_accession => 'SO:1000036',
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113 SO_term => 'inversion',
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114 },
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115 {
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116 SO_accession => 'SO:0001784',
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117 SO_term => 'complex_structural_alteration',
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118 display_term => 'Complex',
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119 },
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120 {
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121 SO_accession => 'SO:1000173',
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122 SO_term => 'tandem_duplication',
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123 display_term => 'Tandem duplication',
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124 },
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125 {
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126 SO_accession => 'SO:0001837',
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127 SO_term => 'mobile_element_insertion',
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128 display_term => 'Mobile element insertion',
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129 },
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130 {
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131 SO_accession => 'SO:0001873',
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132 SO_term => 'interchromosomal_breakpoint',
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133 display_term => 'Interchromosomal breakpoint',
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134 },
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135 {
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136 SO_accession => 'SO:0001874',
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137 SO_term => 'intrachromosomal_breakpoint',
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138 display_term => 'Intrachromosomal breakpoint',
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139 },
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140 {
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141 SO_accession => 'SO:0000199',
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142 SO_term => 'translocation',
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143 },
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144 {
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145 SO_accession => 'SO:1000035',
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146 SO_term => 'duplication',
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147 display_term => 'Duplication',
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148 },
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149 );
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150
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151 our @OVERLAP_CONSEQUENCES = (
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152 {
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153 SO_accession => 'SO:0001628',
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154 SO_term => 'intergenic_variant',
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155 display_term => 'INTERGENIC',
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156 rank => '38',
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157 tier => '4',
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158 description => 'A sequence variant located in the intergenic region, between genes',
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159 label => 'Intergenic variant',
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160 is_default => 1,
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161 },
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162 {
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163 SO_accession => 'SO:0001631',
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164 SO_term => 'upstream_gene_variant',
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165 display_term => 'UPSTREAM',
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166 feature_SO_term => 'transcript',
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167 feature_class => 'Bio::EnsEMBL::Transcript',
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168 variant_feature_class => 'Bio::EnsEMBL::Variation::BaseVariationFeature',
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169 rank => '24',
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170 tier => '3',
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171 predicate => 'Bio::EnsEMBL::Variation::Utils::VariationEffect::upstream',
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172 description => 'A sequence variant located 5\' of a gene',
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173 label => 'Upstream gene variant',
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174 },
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175 {
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176 SO_accession => 'SO:0001632',
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177 SO_term => 'downstream_gene_variant',
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178 display_term => 'DOWNSTREAM',
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179 feature_SO_term => 'transcript',
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180 feature_class => 'Bio::EnsEMBL::Transcript',
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181 variant_feature_class => 'Bio::EnsEMBL::Variation::BaseVariationFeature',
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182 rank => '25',
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183 tier => '3',
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184 predicate => 'Bio::EnsEMBL::Variation::Utils::VariationEffect::downstream',
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185 description => 'A sequence variant located 3\' of a gene',
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186 label => 'Downstream gene variant',
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187 },
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188 {
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189 SO_accession => 'SO:0001575',
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190 SO_term => 'splice_donor_variant',
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191 display_term => 'ESSENTIAL_SPLICE_SITE',
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192 NCBI_term => 'splice-5',
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193 feature_SO_term => 'primary_transcript',
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194 feature_class => 'Bio::EnsEMBL::Transcript',
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195 variant_feature_class => 'Bio::EnsEMBL::Variation::VariationFeature',
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196 rank => '3',
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197 tier => '3',
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198 predicate => 'Bio::EnsEMBL::Variation::Utils::VariationEffect::donor_splice_site',
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199 description => 'A splice variant that changes the 2 base region at the 5\' end of an intron',
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200 label => 'Splice donor variant',
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201 },
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202 {
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203 SO_accession => 'SO:0001574',
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204 SO_term => 'splice_acceptor_variant',
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205 display_term => 'ESSENTIAL_SPLICE_SITE',
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206 NCBI_term => 'splice-3',
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207 feature_SO_term => 'primary_transcript',
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208 feature_class => 'Bio::EnsEMBL::Transcript',
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209 variant_feature_class => 'Bio::EnsEMBL::Variation::VariationFeature',
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210 rank => '3',
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211 tier => '3',
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212 predicate => 'Bio::EnsEMBL::Variation::Utils::VariationEffect::acceptor_splice_site',
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213 description => 'A splice variant that changes the 2 base region at the 3\' end of an intron',
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214 label => 'Splice acceptor variant',
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215 },
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216 {
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217 SO_accession => 'SO:0001630',
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218 SO_term => 'splice_region_variant',
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219 display_term => 'SPLICE_SITE',
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220 feature_SO_term => 'primary_transcript',
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221 feature_class => 'Bio::EnsEMBL::Transcript',
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222 variant_feature_class => 'Bio::EnsEMBL::Variation::VariationFeature',
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223 rank => '13',
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224 tier => '3',
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225 predicate => 'Bio::EnsEMBL::Variation::Utils::VariationEffect::splice_region',
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226 description => 'A sequence variant in which a change has occurred within the region of the splice site, either within 1-3 bases of the exon or 3-8 bases of the intron',
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227 label => 'Splice region variant',
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228 },
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229 {
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230 SO_accession => 'SO:0001627',
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231 SO_term => 'intron_variant',
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232 display_term => 'INTRONIC',
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233 NCBI_term => 'intron',
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234 feature_SO_term => 'primary_transcript',
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235 feature_class => 'Bio::EnsEMBL::Transcript',
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236 variant_feature_class => 'Bio::EnsEMBL::Variation::BaseVariationFeature',
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237 rank => '20',
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238 tier => '3',
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239 predicate => 'Bio::EnsEMBL::Variation::Utils::VariationEffect::within_intron',
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240 description => 'A transcript variant occurring within an intron',
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241 label => 'Intron variant',
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242 },
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243 {
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244 SO_accession => 'SO:0001623',
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245 SO_term => '5_prime_UTR_variant',
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246 display_term => '5PRIME_UTR',
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247 NCBI_term => 'untranslated_5',
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248 feature_SO_term => 'mRNA',
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249 feature_class => 'Bio::EnsEMBL::Transcript',
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250 variant_feature_class => 'Bio::EnsEMBL::Variation::BaseVariationFeature',
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251 rank => '18',
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252 tier => '3',
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253 predicate => 'Bio::EnsEMBL::Variation::Utils::VariationEffect::within_5_prime_utr',
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254 description => 'A UTR variant of the 5\' UTR',
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255 label => '5 prime UTR variant',
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256 },
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257 {
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258 SO_accession => 'SO:0001624',
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259 SO_term => '3_prime_UTR_variant',
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260 display_term => '3PRIME_UTR',
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261 NCBI_term => 'untranslated_3',
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262 feature_SO_term => 'mRNA',
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263 feature_class => 'Bio::EnsEMBL::Transcript',
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264 variant_feature_class => 'Bio::EnsEMBL::Variation::BaseVariationFeature',
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265 rank => '19',
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266 tier => '3',
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267 predicate => 'Bio::EnsEMBL::Variation::Utils::VariationEffect::within_3_prime_utr',
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268 description => 'A UTR variant of the 3\' UTR',
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269 label => '3 prime UTR variant',
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270 },
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271 # {
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272 # SO_accession => 'SO:0001577',
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273 # SO_term => 'complex_change_in_transcript',
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274 # display_term => 'COMPLEX_INDEL',
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275 # feature_SO_term => 'primary_transcript',
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276 # feature_class => 'Bio::EnsEMBL::Transcript',
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277 # variant_feature_class => 'Bio::EnsEMBL::Variation::VariationFeature',
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278 # rank => '4',
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279 # tier => '3',
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280 # predicate => 'Bio::EnsEMBL::Variation::Utils::VariationEffect::complex_indel',
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281 # description => 'Insertion or deletion that spans an exon/intron or coding sequence/UTR border',
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282 # label => 'Complex change in transcript',
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283 # },
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284 {
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285 SO_accession => 'SO:0001819',
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286 SO_term => 'synonymous_variant',
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287 display_term => 'SYNONYMOUS_CODING',
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288 NCBI_term => 'cds-synon',
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289 feature_SO_term => 'mRNA',
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290 feature_class => 'Bio::EnsEMBL::Transcript',
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291 variant_feature_class => 'Bio::EnsEMBL::Variation::VariationFeature',
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292 rank => '15',
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293 tier => '3',
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294 predicate => 'Bio::EnsEMBL::Variation::Utils::VariationEffect::synonymous_variant',
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295 description => 'A sequence variant where there is no resulting change to the encoded amino acid',
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296 label => 'Synonymous variant',
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297 },
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298 {
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299 SO_accession => 'SO:0001583',
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300 SO_term => 'missense_variant',
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301 display_term => 'NON_SYNONYMOUS_CODING',
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302 NCBI_term => 'missense',
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303 feature_SO_term => 'mRNA',
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304 feature_class => 'Bio::EnsEMBL::Transcript',
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305 variant_feature_class => 'Bio::EnsEMBL::Variation::VariationFeature',
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306 rank => '12',
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307 tier => '3',
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308 predicate => 'Bio::EnsEMBL::Variation::Utils::VariationEffect::missense_variant',
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309 description => 'A sequence variant, where the change may be longer than 3 bases, and at least one base of a codon is changed resulting in a codon that encodes for a different amino acid',
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310 label => 'Missense variant',
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311 },
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312 {
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313 SO_accession => 'SO:0001821',
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314 SO_term => 'inframe_insertion',
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315 display_term => 'NON_SYNONYMOUS_CODING',
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316 feature_SO_term => 'mRNA',
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317 feature_class => 'Bio::EnsEMBL::Transcript',
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318 variant_feature_class => 'Bio::EnsEMBL::Variation::BaseVariationFeature',
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319 rank => '10',
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320 tier => '3',
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321 predicate => 'Bio::EnsEMBL::Variation::Utils::VariationEffect::inframe_insertion',
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322 description => 'An inframe non synonymous variant that inserts bases into in the coding sequence',
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323 label => 'Inframe insertion',
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324 },
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325 {
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326 SO_accession => 'SO:0001822',
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327 SO_term => 'inframe_deletion',
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328 display_term => 'NON_SYNONYMOUS_CODING',
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329 feature_SO_term => 'mRNA',
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330 feature_class => 'Bio::EnsEMBL::Transcript',
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331 variant_feature_class => 'Bio::EnsEMBL::Variation::BaseVariationFeature',
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332 rank => '11',
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333 tier => '3',
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334 predicate => 'Bio::EnsEMBL::Variation::Utils::VariationEffect::inframe_deletion',
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335 description => 'An inframe non synonymous variant that deletes bases from the coding sequence',
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336 label => 'Inframe deletion',
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337 },
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338 {
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339 SO_accession => 'SO:0001587',
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340 SO_term => 'stop_gained',
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341 display_term => 'STOP_GAINED',
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342 NCBI_term => 'nonsense',
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343 feature_SO_term => 'mRNA',
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344 feature_class => 'Bio::EnsEMBL::Transcript',
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345 variant_feature_class => 'Bio::EnsEMBL::Variation::VariationFeature',
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346 rank => '4',
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347 tier => '3',
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348 predicate => 'Bio::EnsEMBL::Variation::Utils::VariationEffect::stop_gained',
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349 description => 'A sequence variant whereby at least one base of a codon is changed, resulting in a premature stop codon, leading to a shortened transcript',
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350 label => 'Stop gained',
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351 },
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352 {
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353 SO_accession => 'SO:0001578',
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354 SO_term => 'stop_lost',
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355 display_term => 'STOP_LOST',
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356 feature_SO_term => 'mRNA',
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357 feature_class => 'Bio::EnsEMBL::Transcript',
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358 variant_feature_class => 'Bio::EnsEMBL::Variation::BaseVariationFeature',
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359 rank => '6',
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360 tier => '3',
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361 predicate => 'Bio::EnsEMBL::Variation::Utils::VariationEffect::stop_lost',
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362 description => 'A sequence variant where at least one base of the terminator codon (stop) is changed, resulting in an elongated transcript',
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363 label => 'Stop lost',
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364 },
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365 {
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366 SO_accession => 'SO:0001567',
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367 SO_term => 'stop_retained_variant',
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368 display_term => 'SYNONYMOUS_CODING',
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369 feature_SO_term => 'mRNA',
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370 feature_class => 'Bio::EnsEMBL::Transcript',
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371 variant_feature_class => 'Bio::EnsEMBL::Variation::VariationFeature',
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372 rank => '15',
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373 tier => '3',
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374 predicate => 'Bio::EnsEMBL::Variation::Utils::VariationEffect::stop_retained',
|
|
|
375 description => 'A sequence variant where at least one base in the terminator codon is changed, but the terminator remains',
|
|
|
376 label => 'Stop retained variant',
|
|
|
377 },
|
|
|
378 {
|
|
|
379 SO_accession => 'SO:0001582',
|
|
|
380 SO_term => 'initiator_codon_variant',
|
|
|
381 display_term => 'NON_SYNONYMOUS_CODING',
|
|
|
382 feature_SO_term => 'mRNA',
|
|
|
383 feature_class => 'Bio::EnsEMBL::Transcript',
|
|
|
384 variant_feature_class => 'Bio::EnsEMBL::Variation::BaseVariationFeature',
|
|
|
385 rank => '7',
|
|
|
386 tier => '3',
|
|
|
387 predicate => 'Bio::EnsEMBL::Variation::Utils::VariationEffect::affects_start_codon',
|
|
|
388 description => 'A codon variant that changes at least one base of the first codon of a transcript',
|
|
|
389 label => 'Initiator codon variant',
|
|
|
390 },
|
|
|
391 {
|
|
|
392 SO_accession => 'SO:0001589',
|
|
|
393 SO_term => 'frameshift_variant',
|
|
|
394 display_term => 'FRAMESHIFT_CODING',
|
|
|
395 NCBI_term => 'frameshift',
|
|
|
396 feature_SO_term => 'mRNA',
|
|
|
397 feature_class => 'Bio::EnsEMBL::Transcript',
|
|
|
398 variant_feature_class => 'Bio::EnsEMBL::Variation::BaseVariationFeature',
|
|
|
399 rank => '5',
|
|
|
400 tier => '3',
|
|
|
401 predicate => 'Bio::EnsEMBL::Variation::Utils::VariationEffect::frameshift',
|
|
|
402 description => 'A sequence variant which causes a disruption of the translational reading frame, because the number of nucleotides inserted or deleted is not a multiple of three',
|
|
|
403 label => 'Frameshift variant',
|
|
|
404 },
|
|
|
405 {
|
|
|
406 SO_accession => 'SO:0001626',
|
|
|
407 SO_term => 'incomplete_terminal_codon_variant',
|
|
|
408 display_term => 'PARTIAL_CODON',
|
|
|
409 feature_SO_term => 'mRNA',
|
|
|
410 feature_class => 'Bio::EnsEMBL::Transcript',
|
|
|
411 variant_feature_class => 'Bio::EnsEMBL::Variation::VariationFeature',
|
|
|
412 rank => '14',
|
|
|
413 tier => '3',
|
|
|
414 predicate => 'Bio::EnsEMBL::Variation::Utils::VariationEffect::partial_codon',
|
|
|
415 description => 'A sequence variant where at least one base of the final codon of an incompletely annotated transcript is changed',
|
|
|
416 label => 'Incomplete terminal codon variant',
|
|
|
417 },
|
|
|
418 {
|
|
|
419 SO_accession => 'SO:0001621',
|
|
|
420 SO_term => 'NMD_transcript_variant',
|
|
|
421 display_term => 'NMD_TRANSCRIPT',
|
|
|
422 feature_SO_term => 'mRNA',
|
|
|
423 feature_class => 'Bio::EnsEMBL::Transcript',
|
|
|
424 variant_feature_class => 'Bio::EnsEMBL::Variation::BaseVariationFeature',
|
|
|
425 rank => '21',
|
|
|
426 tier => '3',
|
|
|
427 predicate => 'Bio::EnsEMBL::Variation::Utils::VariationEffect::within_nmd_transcript',
|
|
|
428 description => 'A variant in a transcript that is the target of NMD',
|
|
|
429 label => 'NMD transcript variant',
|
|
|
430 },
|
|
|
431 {
|
|
|
432 SO_accession => 'SO:0001619',
|
|
|
433 SO_term => 'nc_transcript_variant',
|
|
|
434 display_term => 'WITHIN_NON_CODING_GENE',
|
|
|
435 feature_SO_term => 'ncRNA',
|
|
|
436 feature_class => 'Bio::EnsEMBL::Transcript',
|
|
|
437 variant_feature_class => 'Bio::EnsEMBL::Variation::BaseVariationFeature',
|
|
|
438 rank => '23',
|
|
|
439 tier => '3',
|
|
|
440 predicate => 'Bio::EnsEMBL::Variation::Utils::VariationEffect::within_non_coding_gene',
|
|
|
441 description => 'A transcript variant of a non coding RNA',
|
|
|
442 label => 'NC transcript variant',
|
|
|
443 },
|
|
|
444 {
|
|
|
445 SO_accession => 'SO:0001792',
|
|
|
446 SO_term => 'non_coding_exon_variant',
|
|
|
447 display_term => 'WITHIN_NON_CODING_GENE',
|
|
|
448 feature_SO_term => 'ncRNA',
|
|
|
449 feature_class => 'Bio::EnsEMBL::Transcript',
|
|
|
450 variant_feature_class => 'Bio::EnsEMBL::Variation::BaseVariationFeature',
|
|
|
451 rank => '22',
|
|
|
452 tier => '3',
|
|
|
453 predicate => 'Bio::EnsEMBL::Variation::Utils::VariationEffect::non_coding_exon_variant',
|
|
|
454 description => 'A sequence variant that changes non-coding exon sequence',
|
|
|
455 label => 'Non coding exon variant',
|
|
|
456 },
|
|
|
457 {
|
|
|
458 SO_accession => 'SO:0001620',
|
|
|
459 SO_term => 'mature_miRNA_variant',
|
|
|
460 display_term => 'WITHIN_MATURE_miRNA',
|
|
|
461 feature_SO_term => 'miRNA',
|
|
|
462 feature_class => 'Bio::EnsEMBL::Transcript',
|
|
|
463 variant_feature_class => 'Bio::EnsEMBL::Variation::BaseVariationFeature',
|
|
|
464 rank => '17',
|
|
|
465 tier => '2',
|
|
|
466 predicate => 'Bio::EnsEMBL::Variation::Utils::VariationEffect::within_mature_miRNA',
|
|
|
467 description => 'A transcript variant located with the sequence of the mature miRNA',
|
|
|
468 label => 'Mature miRNA variant',
|
|
|
469 },
|
|
|
470 {
|
|
|
471 SO_accession => 'SO:0001580',
|
|
|
472 SO_term => 'coding_sequence_variant',
|
|
|
473 display_term => 'CODING_UNKNOWN',
|
|
|
474 feature_SO_term => 'mRNA',
|
|
|
475 feature_class => 'Bio::EnsEMBL::Transcript',
|
|
|
476 variant_feature_class => 'Bio::EnsEMBL::Variation::BaseVariationFeature',
|
|
|
477 rank => '16',
|
|
|
478 tier => '3',
|
|
|
479 predicate => 'Bio::EnsEMBL::Variation::Utils::VariationEffect::coding_unknown',
|
|
|
480 description => 'A sequence variant that changes the coding sequence',
|
|
|
481 label => 'Coding sequence variant',
|
|
|
482 },
|
|
|
483 {
|
|
|
484 SO_accession => 'SO:0001566',
|
|
|
485 SO_term => 'regulatory_region_variant',
|
|
|
486 display_term => 'REGULATORY_REGION',
|
|
|
487 feature_SO_term => 'regulatory_region',
|
|
|
488 feature_class => 'Bio::EnsEMBL::Funcgen::RegulatoryFeature',
|
|
|
489 variant_feature_class => 'Bio::EnsEMBL::Variation::BaseVariationFeature',
|
|
|
490 rank => '36',
|
|
|
491 tier => '2',
|
|
|
492 predicate => 'Bio::EnsEMBL::Variation::Utils::VariationEffect::within_regulatory_feature',
|
|
|
493 description => 'A sequence variant located within a regulatory region',
|
|
|
494 label => 'Regulatory region variant',
|
|
|
495 },
|
|
|
496 # {
|
|
|
497 # SO_accession => 'SO:X000005',
|
|
|
498 # SO_term => 'pre_miRNA_variant',
|
|
|
499 # display_term => 'WITHIN_NON_CODING_GENE',
|
|
|
500 # feature_SO_term => 'miRNA',
|
|
|
501 # feature_class => 'Bio::EnsEMBL::Transcript',
|
|
|
502 # rank => '13',
|
|
|
503 # tier => '2',
|
|
|
504 # predicate => 'Bio::EnsEMBL::Variation::Utils::VariationEffect::within_miRNA',
|
|
|
505 # },
|
|
|
506 # {
|
|
|
507 # SO_accession => 'SO:X000004',
|
|
|
508 # SO_term => 'miRNA_target_site_variant',
|
|
|
509 # display_term => 'REGULATORY_REGION',
|
|
|
510 # feature_SO_term => 'binding_site',
|
|
|
511 # feature_class => 'Bio::EnsEMBL::Funcgen::ExternalFeature',
|
|
|
512 # rank => '13',
|
|
|
513 # tier => '2',
|
|
|
514 # predicate => 'Bio::EnsEMBL::Variation::Utils::VariationEffect::within_miRNA_target_site',
|
|
|
515 # description => 'In regulatory region annotated by Ensembl',
|
|
|
516 # label => 'Regulatory region',
|
|
|
517 # },
|
|
|
518 {
|
|
|
519 SO_accession => 'SO:0001782',
|
|
|
520 SO_term => 'TF_binding_site_variant',
|
|
|
521 display_term => 'REGULATORY_REGION',
|
|
|
522 feature_SO_term => 'TF_binding_site',
|
|
|
523 feature_class => 'Bio::EnsEMBL::Funcgen::MotifFeature',
|
|
|
524 variant_feature_class => 'Bio::EnsEMBL::Variation::BaseVariationFeature',
|
|
|
525 rank => '30',
|
|
|
526 tier => '2',
|
|
|
527 predicate => 'Bio::EnsEMBL::Variation::Utils::VariationEffect::within_motif_feature',
|
|
|
528 description => 'In regulatory region annotated by Ensembl',
|
|
|
529 label => 'A sequence variant located within a transcription factor binding site',
|
|
|
530 },
|
|
|
531
|
|
|
532 # {
|
|
|
533 # SO_accession => 'SO:X000002',
|
|
|
534 # SO_term => 'decreased_binding_affinity',
|
|
|
535 # display_term => 'REGULATORY_REGION',
|
|
|
536 # feature_SO_term => 'binding_site',
|
|
|
537 # feature_class => 'Bio::EnsEMBL::Funcgen::MotifFeature',
|
|
|
538 # rank => '47',
|
|
|
539 # tier => '2',
|
|
|
540 # predicate => 'Bio::EnsEMBL::Variation::Utils::VariationEffect::decreased_binding_affinity',
|
|
|
541 # },
|
|
|
542 # {
|
|
|
543 # SO_accession => 'SO:X000001',
|
|
|
544 # SO_term => 'increased_binding_affinity',
|
|
|
545 # display_term => 'REGULATORY_REGION',
|
|
|
546 # feature_SO_term => 'binding_site',
|
|
|
547 # feature_class => 'Bio::EnsEMBL::Funcgen::MotifFeature',
|
|
|
548 # rank => '48',
|
|
|
549 # tier => '2',
|
|
|
550 # predicate => 'Bio::EnsEMBL::Variation::Utils::VariationEffect::increased_binding_affinity',
|
|
|
551 # },
|
|
|
552
|
|
|
553
|
|
|
554 ## NEW FOR 68
|
|
|
555 #############
|
|
|
556
|
|
|
557 {
|
|
|
558 SO_accession => 'SO:0001893',
|
|
|
559 SO_term => 'transcript_ablation',
|
|
|
560 feature_SO_term => 'mRNA',
|
|
|
561 feature_class => 'Bio::EnsEMBL::Transcript',
|
|
|
562 variant_feature_class => 'Bio::EnsEMBL::Variation::BaseVariationFeature',
|
|
|
563 rank => '1',
|
|
|
564 tier => '1',
|
|
|
565 predicate => 'Bio::EnsEMBL::Variation::Utils::VariationEffect::feature_ablation',
|
|
|
566 description => 'A feature ablation whereby the deleted region includes a transcript feature',
|
|
|
567 label => 'Transcript ablation',
|
|
|
568 },
|
|
|
569 # {
|
|
|
570 # SO_accession => 'SO:0001886',
|
|
|
571 # SO_term => 'transcript_fusion',
|
|
|
572 # feature_SO_term => 'mRNA',
|
|
|
573 # feature_class => 'Bio::EnsEMBL::Transcript',
|
|
|
574 # variant_feature_class => 'Bio::EnsEMBL::Variation::BaseVariationFeature',
|
|
|
575 # rank => '2',
|
|
|
576 # tier => '2',
|
|
|
577 # predicate => 'Bio::EnsEMBL::Variation::Utils::VariationEffect::transcript_fusion',
|
|
|
578 # description => 'A feature fusion where the deletion brings together transcript regions',
|
|
|
579 # label => 'Transcript fusion',
|
|
|
580 # },
|
|
|
581 {
|
|
|
582 SO_accession => 'SO:0001889',
|
|
|
583 SO_term => 'transcript_amplification',
|
|
|
584 feature_SO_term => 'mRNA',
|
|
|
585 feature_class => 'Bio::EnsEMBL::Transcript',
|
|
|
586 variant_feature_class => 'Bio::EnsEMBL::Variation::BaseVariationFeature',
|
|
|
587 rank => '8',
|
|
|
588 tier => '1',
|
|
|
589 predicate => 'Bio::EnsEMBL::Variation::Utils::VariationEffect::feature_amplification',
|
|
|
590 description => 'A feature amplification of a region containing a transcript',
|
|
|
591 label => 'Transcript amplification',
|
|
|
592 },
|
|
|
593 # {
|
|
|
594 # SO_accession => 'SO:0001883',
|
|
|
595 # SO_term => 'transcript_translocation',
|
|
|
596 # feature_SO_term => 'mRNA',
|
|
|
597 # feature_class => 'Bio::EnsEMBL::Transcript',
|
|
|
598 # variant_feature_class => 'Bio::EnsEMBL::Variation::BaseVariationFeature',
|
|
|
599 # rank => '9',
|
|
|
600 #tier => '2',
|
|
|
601 # predicate => 'Bio::EnsEMBL::Variation::Utils::VariationEffect::transcript_translocation',
|
|
|
602 # description => 'A feature translocation where the region contains a transcript',
|
|
|
603 # label => 'Transcript translocation',
|
|
|
604 # },
|
|
|
605 {
|
|
|
606 SO_accession => 'SO:0001895',
|
|
|
607 SO_term => 'TFBS_ablation',
|
|
|
608 feature_SO_term => 'TF_binding_site',
|
|
|
609 feature_class => 'Bio::EnsEMBL::Funcgen::MotifFeature',
|
|
|
610 variant_feature_class => 'Bio::EnsEMBL::Variation::BaseVariationFeature',
|
|
|
611 rank => '26',
|
|
|
612 tier => '2',
|
|
|
613 predicate => 'Bio::EnsEMBL::Variation::Utils::VariationEffect::feature_ablation',
|
|
|
614 description => 'A feature ablation whereby the deleted region includes a transcription factor binding site',
|
|
|
615 label => 'TFBS ablation',
|
|
|
616 },
|
|
|
617 # {
|
|
|
618 # SO_accession => 'SO:0001888',
|
|
|
619 # SO_term => 'TFBS_fusion',
|
|
|
620 # feature_SO_term => 'TF_binding_site',
|
|
|
621 # feature_class => 'Bio::EnsEMBL::Funcgen::MotifFeature',
|
|
|
622 # variant_feature_class => 'Bio::EnsEMBL::Variation::BaseVariationFeature',
|
|
|
623 # rank => '27',
|
|
|
624 #tier => '2',
|
|
|
625 # predicate => 'Bio::EnsEMBL::Variation::Utils::VariationEffect::motif_feature_fusion',
|
|
|
626 # description => 'A fusion where the deletion brings together transcription factor binding sites',
|
|
|
627 # label => 'TFBS fusion',
|
|
|
628 # },
|
|
|
629 {
|
|
|
630 SO_accession => 'SO:0001892',
|
|
|
631 SO_term => 'TFBS_amplification',
|
|
|
632 feature_SO_term => 'TF_binding_site',
|
|
|
633 feature_class => 'Bio::EnsEMBL::Funcgen::MotifFeature',
|
|
|
634 variant_feature_class => 'Bio::EnsEMBL::Variation::BaseVariationFeature',
|
|
|
635 rank => '28',
|
|
|
636 tier => '2',
|
|
|
637 predicate => 'Bio::EnsEMBL::Variation::Utils::VariationEffect::feature_amplification',
|
|
|
638 description => 'A feature amplification of a region containing a transcription factor binding site',
|
|
|
639 label => 'TFBS amplification',
|
|
|
640 },
|
|
|
641 # {
|
|
|
642 # SO_accession => 'SO:0001885',
|
|
|
643 # SO_term => 'TFBS_translocation',
|
|
|
644 # feature_SO_term => 'TF_binding_site',
|
|
|
645 # feature_class => 'Bio::EnsEMBL::Funcgen::MotifFeature',
|
|
|
646 # variant_feature_class => 'Bio::EnsEMBL::Variation::BaseVariationFeature',
|
|
|
647 # rank => '29',
|
|
|
648 #tier => '2',
|
|
|
649 # predicate => 'Bio::EnsEMBL::Variation::Utils::VariationEffect::motif_feature_translocation',
|
|
|
650 # description => 'A feature translocation where the region contains a transcription factor binding site',
|
|
|
651 # label => 'TFBS translocation',
|
|
|
652 # },
|
|
|
653 {
|
|
|
654 SO_accession => 'SO:0001894',
|
|
|
655 SO_term => 'regulatory_region_ablation',
|
|
|
656 feature_SO_term => 'TF_binding_site',
|
|
|
657 feature_class => 'Bio::EnsEMBL::Funcgen::RegulatoryFeature',
|
|
|
658 variant_feature_class => 'Bio::EnsEMBL::Variation::BaseVariationFeature',
|
|
|
659 rank => '31',
|
|
|
660 tier => '2',
|
|
|
661 predicate => 'Bio::EnsEMBL::Variation::Utils::VariationEffect::feature_ablation',
|
|
|
662 description => 'A feature ablation whereby the deleted region includes a regulatory region',
|
|
|
663 label => 'Regulatory region ablation',
|
|
|
664 },
|
|
|
665 # {
|
|
|
666 # SO_accession => 'SO:0001887',
|
|
|
667 # SO_term => 'regulatory_region_fusion',
|
|
|
668 # feature_SO_term => 'TF_binding_site',
|
|
|
669 # feature_class => 'Bio::EnsEMBL::Funcgen::RegulatoryFeature',
|
|
|
670 # variant_feature_class => 'Bio::EnsEMBL::Variation::BaseVariationFeature',
|
|
|
671 # rank => '32',
|
|
|
672 #tier => '2',
|
|
|
673 # predicate => 'Bio::EnsEMBL::Variation::Utils::VariationEffect::regulatory_feature_fusion',
|
|
|
674 # description => 'A fusion where the deletion brings together regulatory regions',
|
|
|
675 # label => 'Regulatory region fusion',
|
|
|
676 # },
|
|
|
677 {
|
|
|
678 SO_accession => 'SO:0001891',
|
|
|
679 SO_term => 'regulatory_region_amplification',
|
|
|
680 feature_SO_term => 'TF_binding_site',
|
|
|
681 feature_class => 'Bio::EnsEMBL::Funcgen::RegulatoryFeature',
|
|
|
682 variant_feature_class => 'Bio::EnsEMBL::Variation::BaseVariationFeature',
|
|
|
683 rank => '33',
|
|
|
684 tier => '2',
|
|
|
685 predicate => 'Bio::EnsEMBL::Variation::Utils::VariationEffect::feature_amplification',
|
|
|
686 description => 'A feature amplification of a region containing a regulatory region',
|
|
|
687 label => 'Regulatory region amplification',
|
|
|
688 },
|
|
|
689 # {
|
|
|
690 # SO_accession => 'SO:0001884',
|
|
|
691 # SO_term => 'regulatory_region_translocation',
|
|
|
692 # feature_SO_term => 'TF_binding_site',
|
|
|
693 # feature_class => 'Bio::EnsEMBL::Funcgen::RegulatoryFeature',
|
|
|
694 # variant_feature_class => 'Bio::EnsEMBL::Variation::BaseVariationFeature',
|
|
|
695 # rank => '34',
|
|
|
696 #tier => '2',
|
|
|
697 # predicate => 'Bio::EnsEMBL::Variation::Utils::VariationEffect::regulatory_feature_translocation',
|
|
|
698 # description => 'A feature translocation where the region contains a regulatory region',
|
|
|
699 # label => 'Regulatory region translocation',
|
|
|
700 # },
|
|
|
701 {
|
|
|
702 SO_accession => 'SO:0001907',
|
|
|
703 SO_term => 'feature_elongation',
|
|
|
704 feature_class => 'Bio::EnsEMBL::Feature',
|
|
|
705 variant_feature_class => 'Bio::EnsEMBL::Variation::BaseVariationFeature',
|
|
|
706 rank => '36',
|
|
|
707 tier => '3',
|
|
|
708 predicate => 'Bio::EnsEMBL::Variation::Utils::VariationEffect::feature_elongation',
|
|
|
709 description => 'A sequence variant that causes the extension of a genomic feature, with regard to the reference sequence',
|
|
|
710 label => 'Feature elongation',
|
|
|
711 },
|
|
|
712 {
|
|
|
713 SO_accession => 'SO:0001906',
|
|
|
714 SO_term => 'feature_truncation',
|
|
|
715 feature_class => 'Bio::EnsEMBL::Feature',
|
|
|
716 variant_feature_class => 'Bio::EnsEMBL::Variation::BaseVariationFeature',
|
|
|
717 rank => '37',
|
|
|
718 tier => '3',
|
|
|
719 predicate => 'Bio::EnsEMBL::Variation::Utils::VariationEffect::feature_truncation',
|
|
|
720 description => 'A sequence variant that causes the reduction of a genomic feature, with regard to the reference sequence',
|
|
|
721 label => 'Feature truncation',
|
|
|
722 },
|
|
|
723 );
|
|
|
724
|
|
|
725 our @FEATURE_TYPES = (
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726 {
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727 SO_accession => 'SO:0000234',
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728 SO_term => 'mRNA',
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|
|
729 ens_feature_class => 'Bio::EnsEMBL::Transcript',
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730 ens_feature_subtype => 'protein_coding',
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|
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731 ens_variant_class => 'Bio::EnsEMBL::Variation::TranscriptVariation',
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|
|
732 },
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|
|
733 {
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734 SO_accession => 'SO:0000673',
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|
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735 SO_term => 'transcript',
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736 ens_feature_class => 'Bio::EnsEMBL::Transcript',
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737 ens_variant_class => 'Bio::EnsEMBL::Variation::TranscriptVariation',
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|
|
738 },
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|
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739 {
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|
740 SO_accession => 'SO:0000185',
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|
|
741 SO_term => 'primary_transcript',
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|
|
742 ens_feature_class => 'Bio::EnsEMBL::Transcript',
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|
|
743 ens_variant_class => 'Bio::EnsEMBL::Variation::TranscriptVariation',
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|
|
744 },
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|
|
745 {
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|
|
746 SO_accession => 'SO:0000655',
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|
|
747 SO_term => 'ncRNA',
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|
|
748 ens_feature_class => 'Bio::EnsEMBL::Transcript',
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|
|
749 ens_variant_class => 'Bio::EnsEMBL::Variation::TranscriptVariation',
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|
|
750 },
|
|
|
751 {
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|
|
752 SO_accession => 'SO:0000276',
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|
|
753 SO_term => 'miRNA',
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|
|
754 ens_feature_class => 'Bio::EnsEMBL::Transcript',
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|
|
755 ens_variant_class => 'Bio::EnsEMBL::Variation::TranscriptVariation',
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|
|
756 },
|
|
|
757 {
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|
|
758 SO_accession => 'SO:0005836',
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|
|
759 SO_term => 'regulatory_region',
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|
|
760 ens_feature_class => 'Bio::EnsEMBL::Funcgen::RegulatoryFeature',
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|
|
761 ens_variant_class => 'Bio::EnsEMBL::Variation::RegulatoryFeatureVariation',
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|
|
762 },
|
|
|
763 {
|
|
|
764 SO_accession => 'SO:0000409',
|
|
|
765 SO_term => 'binding_site',
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|
|
766 ens_feature_class => 'Bio::EnsEMBL::Funcgen::MotifFeature',
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|
|
767 ens_variant_class => 'Bio::EnsEMBL::Variation::MotifFeatureVariation',
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|
|
768 },
|
|
|
769 {
|
|
|
770 SO_accession => 'SO:0005836',
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|
|
771 SO_term => 'regulatory_region',
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|
|
772 ens_feature_class => 'Bio::EnsEMBL::Funcgen::ExternalFeature',
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|
|
773 ens_variant_class => 'Bio::EnsEMBL::Variation::ExternalFeatureVariation',
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|
|
774 ens_feature_subtype => 'VISTA enhancer set',
|
|
|
775 },
|
|
|
776 {
|
|
|
777 SO_accession => 'SO:0000409',
|
|
|
778 SO_term => 'binding_site',
|
|
|
779 ens_feature_class => 'Bio::EnsEMBL::Funcgen::ExternalFeature',
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|
|
780 ens_variant_class => 'Bio::EnsEMBL::Variation::ExternalFeatureVariation',
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|
|
781 ens_feature_subtype => 'cisRED motif',
|
|
|
782 },
|
|
|
783 {
|
|
|
784 SO_accession => 'SO:0005836',
|
|
|
785 SO_term => 'regulatory_region',
|
|
|
786 ens_feature_class => 'Bio::EnsEMBL::Funcgen::ExternalFeature',
|
|
|
787 ens_variant_class => 'Bio::EnsEMBL::Variation::ExternalFeatureVariation',
|
|
|
788 ens_feature_subtype => 'miRanda miRNA target',
|
|
|
789 },
|
|
|
790 {
|
|
|
791 SO_accession => 'SO:0000110',
|
|
|
792 SO_term => 'sequence_feature',
|
|
|
793 ens_feature_class => 'Bio::EnsEMBL::Feature',
|
|
|
794 ens_variant_class => 'Bio::EnsEMBL::Variation::StructuralVariationFeatureOverlap',
|
|
|
795 },
|
|
|
796 );
|
|
|
797
|
|
|
798 # attrib_types are specified as hashrefs in the @ATTRIB_TYPES array. Each hashref should have a value for the key 'code' and optionally values for the keys 'name' and 'description'
|
|
|
799 our @ATTRIB_TYPES = (
|
|
|
800 {
|
|
|
801 code => 'SO_accession',
|
|
|
802 description => 'Sequence Ontology accession',
|
|
|
803 },
|
|
|
804 {
|
|
|
805 code => 'SO_term',
|
|
|
806 description => 'Sequence Ontology term',
|
|
|
807 },
|
|
|
808 {
|
|
|
809 code => 'display_term',
|
|
|
810 description => 'Ensembl display term',
|
|
|
811 },
|
|
|
812 {
|
|
|
813 code => 'NCBI_term',
|
|
|
814 description => 'NCBI term',
|
|
|
815 },
|
|
|
816 {
|
|
|
817 code => 'feature_SO_term',
|
|
|
818 description => 'Sequence Ontology term for the associated feature',
|
|
|
819 },
|
|
|
820 {
|
|
|
821 code => 'rank',
|
|
|
822 description => 'Relative severity of this variation consequence',
|
|
|
823 },
|
|
|
824 {
|
|
|
825 code => 'polyphen_prediction',
|
|
|
826 description => 'PolyPhen-2 prediction',
|
|
|
827 },
|
|
|
828 {
|
|
|
829 code => 'sift_prediction',
|
|
|
830 description => 'SIFT prediction',
|
|
|
831 },
|
|
|
832 {
|
|
|
833 code => 'short_name',
|
|
|
834 name => 'Short name',
|
|
|
835 description => 'A shorter name for an instance, e.g. a VariationSet',
|
|
|
836 },
|
|
|
837 {
|
|
|
838 code => 'dbsnp_clin_sig',
|
|
|
839 name => 'dbSNP clinical significance',
|
|
|
840 description => 'The clinical significance of a variant as reported by dbSNP',
|
|
|
841 },
|
|
|
842 {
|
|
|
843 code => 'dgva_clin_sig',
|
|
|
844 name => 'DGVa clinical significance',
|
|
|
845 description => 'The clinical significance of a structural variant as reported by DGVa',
|
|
|
846 },
|
|
|
847 {
|
|
|
848 code => 'prot_func_analysis',
|
|
|
849 name => 'Protein function analysis ',
|
|
|
850 description => 'The program used to make protein function predictions',
|
|
|
851 },
|
|
|
852
|
|
|
853 );
|
|
|
854
|
|
|
855 # attribs are specified in the %ATTRIBS hash, having the attrib_type code as hash key and a listref containing the attribs that will be loaded as value
|
|
|
856 our %ATTRIBS = (
|
|
|
857 'short_name' => \@short_names,
|
|
|
858 'dbsnp_clin_sig' => \@dbsnp_clinical_significance_types,
|
|
|
859 'dgva_clin_sig' => \@dgva_clinical_significance_types,
|
|
|
860 'polyphen_prediction' => ['probably damaging', 'possibly damaging', 'benign', 'unknown'],
|
|
|
861 'sift_prediction' => [qw(tolerated deleterious)],
|
|
|
862 'prot_func_analysis' => [qw(sift polyphen_humvar polyphen_humdiv)],
|
|
|
863 );
|
|
|
864
|
|
|
865 # attrib sets are specified by putting a hashref in the @ATTRIB_SETS array having the attrib_type code as key and the attrib as value. new attrib entries will be inserted as necessary
|
|
|
866 our @ATTRIB_SETS = (
|
|
|
867 @VARIATION_CLASSES,
|
|
|
868 @OVERLAP_CONSEQUENCES,
|
|
|
869 @FEATURE_TYPES
|
|
|
870 );
|
|
|
871
|
|
|
872 1;
|
