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1 package Bio::EnsEMBL::Variation::Utils::Constants;
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2
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3 #####################################################################
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4 # NB: THIS FILE HAS BEEN AUTOMATICALLY GENERATED, EDIT WITH CAUTION #
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5 #####################################################################
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6
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7 use strict;
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8 use warnings;
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9
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10 use base qw(Exporter);
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11
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12 our @EXPORT_OK = qw(%OVERLAP_CONSEQUENCES %VARIATION_CLASSES $DEFAULT_OVERLAP_CONSEQUENCE SO_TERM_INDEL SO_TERM_CODING_SEQUENCE_VARIANT SO_TERM_STOP_RETAINED_VARIANT SO_TERM_COMPLEX_STRUCTURAL_ALTERATION SO_TERM_SPLICE_ACCEPTOR_VARIANT SO_TERM_TANDEM_REPEAT SO_TERM_INTERCHROMOSOMAL_BREAKPOINT SO_TERM_FEATURE_ELONGATION SO_TERM_TRANSCRIPT_ABLATION SO_TERM_TF_BINDING_SITE_VARIANT ATTRIB_TYPE_DISPLAY_TERM SO_TERM_INTRON_VARIANT SO_TERM_STOP_GAINED SO_TERM_SPLICE_DONOR_VARIANT ATTRIB_TYPE_SIFT_PREDICTION SO_TERM_FEATURE_TRUNCATION SO_TERM_INTRACHROMOSOMAL_BREAKPOINT SO_TERM_SPLICE_REGION_VARIANT SO_TERM_TFBS_ABLATION SO_TERM_REGULATORY_REGION_AMPLIFICATION SO_TERM_MISSENSE_VARIANT SO_TERM_SNV SO_TERM_STRUCTURAL_VARIANT SO_TERM_PROBE ATTRIB_TYPE_DBSNP_CLIN_SIG SO_TERM_SEQUENCE_ALTERATION SO_TERM_REGULATORY_REGION_VARIANT SO_TERM_SUBSTITUTION ATTRIB_TYPE_DGVA_CLIN_SIG SO_TERM_INCOMPLETE_TERMINAL_CODON_VARIANT SO_TERM_DUPLICATION SO_TERM_TFBS_AMPLIFICATION SO_TERM_5_PRIME_UTR_VARIANT ATTRIB_TYPE_PROT_FUNC_ANALYSIS SO_TERM_TANDEM_DUPLICATION SO_TERM_MOBILE_ELEMENT_INSERTION SO_TERM_MATURE_MIRNA_VARIANT SO_TERM_NC_TRANSCRIPT_VARIANT SO_TERM_DOWNSTREAM_GENE_VARIANT SO_TERM_INFRAME_INSERTION SO_TERM_INSERTION SO_TERM_NMD_TRANSCRIPT_VARIANT ATTRIB_TYPE_SO_TERM SO_TERM_INTERGENIC_VARIANT SO_TERM_NON_CODING_EXON_VARIANT SO_TERM_SYNONYMOUS_VARIANT ATTRIB_TYPE_SHORT_NAME SO_TERM_TRANSLOCATION SO_TERM_COPY_NUMBER_VARIATION ATTRIB_TYPE_POLYPHEN_PREDICTION SO_TERM_REGULATORY_REGION_ABLATION SO_TERM_INVERSION SO_TERM_STOP_LOST ATTRIB_TYPE_RANK SO_TERM_INITIATOR_CODON_VARIANT SO_TERM_3_PRIME_UTR_VARIANT SO_TERM_UPSTREAM_GENE_VARIANT ATTRIB_TYPE_SO_ACCESSION SO_TERM_COPY_NUMBER_LOSS ATTRIB_TYPE_NCBI_TERM SO_TERM_DELETION ATTRIB_TYPE_FEATURE_SO_TERM SO_TERM_FRAMESHIFT_VARIANT SO_TERM_COPY_NUMBER_GAIN SO_TERM_INFRAME_DELETION SO_TERM_TRANSCRIPT_AMPLIFICATION);
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13
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14 our %EXPORT_TAGS = ( attrib_types => [qw(ATTRIB_TYPE_RANK ATTRIB_TYPE_NCBI_TERM ATTRIB_TYPE_SHORT_NAME ATTRIB_TYPE_FEATURE_SO_TERM ATTRIB_TYPE_DISPLAY_TERM ATTRIB_TYPE_SO_ACCESSION ATTRIB_TYPE_DBSNP_CLIN_SIG ATTRIB_TYPE_PROT_FUNC_ANALYSIS ATTRIB_TYPE_SO_TERM ATTRIB_TYPE_SIFT_PREDICTION ATTRIB_TYPE_POLYPHEN_PREDICTION ATTRIB_TYPE_DGVA_CLIN_SIG)], SO_consequence_terms => [qw(SO_TERM_NC_TRANSCRIPT_VARIANT SO_TERM_DOWNSTREAM_GENE_VARIANT SO_TERM_CODING_SEQUENCE_VARIANT SO_TERM_STOP_RETAINED_VARIANT SO_TERM_INFRAME_INSERTION SO_TERM_NMD_TRANSCRIPT_VARIANT SO_TERM_SPLICE_ACCEPTOR_VARIANT SO_TERM_INTERGENIC_VARIANT SO_TERM_FEATURE_ELONGATION SO_TERM_NON_CODING_EXON_VARIANT SO_TERM_TRANSCRIPT_ABLATION SO_TERM_SYNONYMOUS_VARIANT SO_TERM_TF_BINDING_SITE_VARIANT SO_TERM_INTRON_VARIANT SO_TERM_STOP_GAINED SO_TERM_SPLICE_DONOR_VARIANT SO_TERM_FEATURE_TRUNCATION SO_TERM_REGULATORY_REGION_ABLATION SO_TERM_TFBS_ABLATION SO_TERM_SPLICE_REGION_VARIANT SO_TERM_STOP_LOST SO_TERM_INITIATOR_CODON_VARIANT SO_TERM_3_PRIME_UTR_VARIANT SO_TERM_REGULATORY_REGION_AMPLIFICATION SO_TERM_UPSTREAM_GENE_VARIANT SO_TERM_MISSENSE_VARIANT SO_TERM_REGULATORY_REGION_VARIANT SO_TERM_INCOMPLETE_TERMINAL_CODON_VARIANT SO_TERM_FRAMESHIFT_VARIANT SO_TERM_TFBS_AMPLIFICATION SO_TERM_5_PRIME_UTR_VARIANT SO_TERM_INFRAME_DELETION SO_TERM_TRANSCRIPT_AMPLIFICATION SO_TERM_MATURE_MIRNA_VARIANT)], SO_class_terms => [qw(SO_TERM_INDEL SO_TERM_SNV SO_TERM_STRUCTURAL_VARIANT SO_TERM_COMPLEX_STRUCTURAL_ALTERATION SO_TERM_INSERTION SO_TERM_PROBE SO_TERM_COPY_NUMBER_LOSS SO_TERM_SEQUENCE_ALTERATION SO_TERM_TANDEM_REPEAT SO_TERM_INTERCHROMOSOMAL_BREAKPOINT SO_TERM_SUBSTITUTION SO_TERM_DELETION SO_TERM_COPY_NUMBER_GAIN SO_TERM_DUPLICATION SO_TERM_TRANSLOCATION SO_TERM_COPY_NUMBER_VARIATION SO_TERM_TANDEM_DUPLICATION SO_TERM_INVERSION SO_TERM_INTRACHROMOSOMAL_BREAKPOINT SO_TERM_MOBILE_ELEMENT_INSERTION)], );
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15
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16 use Bio::EnsEMBL::Variation::OverlapConsequence;
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17
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18 use constant ATTRIB_TYPE_SO_ACCESSION => 'SO_accession';
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19 use constant ATTRIB_TYPE_SO_TERM => 'SO_term';
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20 use constant ATTRIB_TYPE_DISPLAY_TERM => 'display_term';
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21 use constant ATTRIB_TYPE_NCBI_TERM => 'NCBI_term';
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22 use constant ATTRIB_TYPE_FEATURE_SO_TERM => 'feature_SO_term';
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23 use constant ATTRIB_TYPE_RANK => 'rank';
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24 use constant ATTRIB_TYPE_POLYPHEN_PREDICTION => 'polyphen_prediction';
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25 use constant ATTRIB_TYPE_SIFT_PREDICTION => 'sift_prediction';
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26 use constant ATTRIB_TYPE_SHORT_NAME => 'short_name';
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27 use constant ATTRIB_TYPE_DBSNP_CLIN_SIG => 'dbsnp_clin_sig';
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28 use constant ATTRIB_TYPE_DGVA_CLIN_SIG => 'dgva_clin_sig';
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29 use constant ATTRIB_TYPE_PROT_FUNC_ANALYSIS => 'prot_func_analysis';
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30
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31 use constant SO_TERM_SNV => 'SNV';
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32 use constant SO_TERM_SUBSTITUTION => 'substitution';
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33 use constant SO_TERM_COPY_NUMBER_VARIATION => 'copy_number_variation';
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34 use constant SO_TERM_INSERTION => 'insertion';
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35 use constant SO_TERM_DELETION => 'deletion';
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36 use constant SO_TERM_INDEL => 'indel';
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37 use constant SO_TERM_TANDEM_REPEAT => 'tandem_repeat';
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38 use constant SO_TERM_SEQUENCE_ALTERATION => 'sequence_alteration';
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39 use constant SO_TERM_STRUCTURAL_VARIANT => 'structural_variant';
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40 use constant SO_TERM_PROBE => 'probe';
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41 use constant SO_TERM_COPY_NUMBER_GAIN => 'copy_number_gain';
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42 use constant SO_TERM_COPY_NUMBER_LOSS => 'copy_number_loss';
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43 use constant SO_TERM_INVERSION => 'inversion';
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44 use constant SO_TERM_COMPLEX_STRUCTURAL_ALTERATION => 'complex_structural_alteration';
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45 use constant SO_TERM_TANDEM_DUPLICATION => 'tandem_duplication';
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46 use constant SO_TERM_MOBILE_ELEMENT_INSERTION => 'mobile_element_insertion';
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47 use constant SO_TERM_INTERCHROMOSOMAL_BREAKPOINT => 'interchromosomal_breakpoint';
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48 use constant SO_TERM_INTRACHROMOSOMAL_BREAKPOINT => 'intrachromosomal_breakpoint';
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49 use constant SO_TERM_TRANSLOCATION => 'translocation';
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50 use constant SO_TERM_DUPLICATION => 'duplication';
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51 use constant SO_TERM_INTERGENIC_VARIANT => 'intergenic_variant';
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52 use constant SO_TERM_UPSTREAM_GENE_VARIANT => 'upstream_gene_variant';
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53 use constant SO_TERM_DOWNSTREAM_GENE_VARIANT => 'downstream_gene_variant';
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54 use constant SO_TERM_SPLICE_DONOR_VARIANT => 'splice_donor_variant';
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55 use constant SO_TERM_SPLICE_ACCEPTOR_VARIANT => 'splice_acceptor_variant';
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56 use constant SO_TERM_SPLICE_REGION_VARIANT => 'splice_region_variant';
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57 use constant SO_TERM_INTRON_VARIANT => 'intron_variant';
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58 use constant SO_TERM_5_PRIME_UTR_VARIANT => '5_prime_UTR_variant';
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59 use constant SO_TERM_3_PRIME_UTR_VARIANT => '3_prime_UTR_variant';
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60 use constant SO_TERM_SYNONYMOUS_VARIANT => 'synonymous_variant';
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61 use constant SO_TERM_MISSENSE_VARIANT => 'missense_variant';
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62 use constant SO_TERM_INFRAME_INSERTION => 'inframe_insertion';
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63 use constant SO_TERM_INFRAME_DELETION => 'inframe_deletion';
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64 use constant SO_TERM_STOP_GAINED => 'stop_gained';
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65 use constant SO_TERM_STOP_LOST => 'stop_lost';
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66 use constant SO_TERM_STOP_RETAINED_VARIANT => 'stop_retained_variant';
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67 use constant SO_TERM_INITIATOR_CODON_VARIANT => 'initiator_codon_variant';
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68 use constant SO_TERM_FRAMESHIFT_VARIANT => 'frameshift_variant';
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69 use constant SO_TERM_INCOMPLETE_TERMINAL_CODON_VARIANT => 'incomplete_terminal_codon_variant';
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70 use constant SO_TERM_NMD_TRANSCRIPT_VARIANT => 'NMD_transcript_variant';
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71 use constant SO_TERM_NC_TRANSCRIPT_VARIANT => 'nc_transcript_variant';
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72 use constant SO_TERM_NON_CODING_EXON_VARIANT => 'non_coding_exon_variant';
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73 use constant SO_TERM_MATURE_MIRNA_VARIANT => 'mature_miRNA_variant';
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74 use constant SO_TERM_CODING_SEQUENCE_VARIANT => 'coding_sequence_variant';
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75 use constant SO_TERM_REGULATORY_REGION_VARIANT => 'regulatory_region_variant';
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76 use constant SO_TERM_TF_BINDING_SITE_VARIANT => 'TF_binding_site_variant';
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77 use constant SO_TERM_TRANSCRIPT_ABLATION => 'transcript_ablation';
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78 use constant SO_TERM_TRANSCRIPT_AMPLIFICATION => 'transcript_amplification';
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79 use constant SO_TERM_TFBS_ABLATION => 'TFBS_ablation';
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80 use constant SO_TERM_TFBS_AMPLIFICATION => 'TFBS_amplification';
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81 use constant SO_TERM_REGULATORY_REGION_ABLATION => 'regulatory_region_ablation';
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82 use constant SO_TERM_REGULATORY_REGION_AMPLIFICATION => 'regulatory_region_amplification';
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83 use constant SO_TERM_FEATURE_ELONGATION => 'feature_elongation';
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84 use constant SO_TERM_FEATURE_TRUNCATION => 'feature_truncation';
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85
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86 our %VARIATION_CLASSES = (
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87 'SNV' => {
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88 'somatic_display_term' => 'somatic_SNV',
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89 'SO_accession' => 'SO:0001483',
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90 'display_term' => 'SNP'
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91 }
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92 ,
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93 'substitution' => {
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94 'somatic_display_term' => 'somatic_substitution',
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95 'SO_accession' => 'SO:1000002',
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96 'display_term' => 'substitution'
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97 }
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98 ,
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99 'copy_number_variation' => {
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100 'somatic_display_term' => 'somatic_CNV',
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101 'SO_accession' => 'SO:0001019',
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102 'display_term' => 'CNV'
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103 }
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104 ,
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105 'insertion' => {
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106 'somatic_display_term' => 'somatic_insertion',
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107 'SO_accession' => 'SO:0000667',
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108 'display_term' => 'insertion'
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109 }
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110 ,
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111 'deletion' => {
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112 'somatic_display_term' => 'somatic_deletion',
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113 'SO_accession' => 'SO:0000159',
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114 'display_term' => 'deletion'
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115 }
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116 ,
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117 'indel' => {
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118 'somatic_display_term' => 'somatic_indel',
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119 'SO_accession' => 'SO:1000032',
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120 'display_term' => 'indel'
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121 }
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122 ,
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123 'tandem_repeat' => {
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124 'somatic_display_term' => 'somatic_tandem_repeat',
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125 'SO_accession' => 'SO:0000705',
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126 'display_term' => 'tandem_repeat'
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127 }
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128 ,
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129 'sequence_alteration' => {
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130 'somatic_display_term' => 'somatic_sequence_alteration',
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131 'SO_accession' => 'SO:0001059',
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132 'display_term' => 'sequence_alteration'
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133 }
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134 ,
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135 'structural_variant' => {
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136 'somatic_display_term' => 'somatic_SV',
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137 'SO_accession' => 'SO:0001537',
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138 'display_term' => 'SV'
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139 }
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140 ,
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141 'probe' => {
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142 'somatic_display_term' => 'somatic_CNV_PROBE',
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143 'SO_accession' => 'SO:0000051',
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144 'display_term' => 'CNV_PROBE'
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145 }
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146 ,
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147 'copy_number_gain' => {
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148 'somatic_display_term' => 'somatic_Gain',
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149 'SO_accession' => 'SO:0001742',
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150 'display_term' => 'Gain'
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151 }
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152 ,
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153 'copy_number_loss' => {
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154 'somatic_display_term' => 'somatic_Loss',
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155 'SO_accession' => 'SO:0001743',
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156 'display_term' => 'Loss'
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157 }
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158 ,
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159 'inversion' => {
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160 'somatic_display_term' => 'somatic_inversion',
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161 'SO_accession' => 'SO:1000036',
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162 'display_term' => 'inversion'
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163 }
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164 ,
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165 'complex_structural_alteration' => {
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166 'somatic_display_term' => 'somatic_Complex',
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167 'SO_accession' => 'SO:0001784',
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168 'display_term' => 'Complex'
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169 }
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170 ,
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171 'tandem_duplication' => {
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172 'somatic_display_term' => 'somatic_Tandem duplication',
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173 'SO_accession' => 'SO:1000173',
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174 'display_term' => 'Tandem duplication'
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175 }
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176 ,
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177 'mobile_element_insertion' => {
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178 'somatic_display_term' => 'somatic_Mobile element insertion',
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179 'SO_accession' => 'SO:0001837',
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180 'display_term' => 'Mobile element insertion'
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181 }
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182 ,
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183 'interchromosomal_breakpoint' => {
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184 'somatic_display_term' => 'somatic_Interchromosomal breakpoint',
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185 'SO_accession' => 'SO:0001873',
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186 'display_term' => 'Interchromosomal breakpoint'
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187 }
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188 ,
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189 'intrachromosomal_breakpoint' => {
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190 'somatic_display_term' => 'somatic_Intrachromosomal breakpoint',
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191 'SO_accession' => 'SO:0001874',
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192 'display_term' => 'Intrachromosomal breakpoint'
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193 }
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194 ,
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195 'translocation' => {
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196 'somatic_display_term' => 'somatic_translocation',
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197 'SO_accession' => 'SO:0000199',
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198 'display_term' => 'translocation'
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199 }
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200 ,
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201 'duplication' => {
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202 'somatic_display_term' => 'somatic_Duplication',
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203 'SO_accession' => 'SO:1000035',
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204 'display_term' => 'Duplication'
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205 }
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206 ,
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207 );
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208
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209 our $DEFAULT_OVERLAP_CONSEQUENCE = Bio::EnsEMBL::Variation::OverlapConsequence->new_fast({
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210 'tier' => '4',
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211 'SO_term' => 'intergenic_variant',
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212 'is_default' => 1,
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213 'label' => 'Intergenic variant',
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214 'description' => 'A sequence variant located in the intergenic region, between genes',
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215 'rank' => '38',
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216 'SO_accession' => 'SO:0001628',
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217 'display_term' => 'INTERGENIC'
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218 }
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219 );
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220
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221
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222 our %OVERLAP_CONSEQUENCES = (
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223 'intergenic_variant' => $DEFAULT_OVERLAP_CONSEQUENCE,
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224 'upstream_gene_variant' => Bio::EnsEMBL::Variation::OverlapConsequence->new_fast({
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225 'variant_feature_class' => 'Bio::EnsEMBL::Variation::BaseVariationFeature',
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226 'feature_SO_term' => 'transcript',
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227 'description' => 'A sequence variant located 5\' of a gene',
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228 'SO_accession' => 'SO:0001631',
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229 'SO_term' => 'upstream_gene_variant',
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230 'tier' => '3',
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231 'predicate' => 'Bio::EnsEMBL::Variation::Utils::VariationEffect::upstream',
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232 'label' => 'Upstream gene variant',
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233 'rank' => '24',
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234 'display_term' => 'UPSTREAM',
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235 'feature_class' => 'Bio::EnsEMBL::Transcript'
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236 }
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237 ),
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238 'downstream_gene_variant' => Bio::EnsEMBL::Variation::OverlapConsequence->new_fast({
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239 'variant_feature_class' => 'Bio::EnsEMBL::Variation::BaseVariationFeature',
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240 'feature_SO_term' => 'transcript',
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241 'description' => 'A sequence variant located 3\' of a gene',
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242 'SO_accession' => 'SO:0001632',
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243 'SO_term' => 'downstream_gene_variant',
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244 'tier' => '3',
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245 'predicate' => 'Bio::EnsEMBL::Variation::Utils::VariationEffect::downstream',
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246 'label' => 'Downstream gene variant',
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247 'rank' => '25',
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248 'display_term' => 'DOWNSTREAM',
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249 'feature_class' => 'Bio::EnsEMBL::Transcript'
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250 }
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251 ),
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252 'splice_donor_variant' => Bio::EnsEMBL::Variation::OverlapConsequence->new_fast({
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253 'variant_feature_class' => 'Bio::EnsEMBL::Variation::VariationFeature',
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254 'NCBI_term' => 'splice-5',
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255 'feature_SO_term' => 'primary_transcript',
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256 'description' => 'A splice variant that changes the 2 base region at the 5\' end of an intron',
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257 'SO_accession' => 'SO:0001575',
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258 'tier' => '3',
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259 'SO_term' => 'splice_donor_variant',
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260 'predicate' => 'Bio::EnsEMBL::Variation::Utils::VariationEffect::donor_splice_site',
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261 'label' => 'Splice donor variant',
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262 'rank' => '3',
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263 'display_term' => 'ESSENTIAL_SPLICE_SITE',
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264 'feature_class' => 'Bio::EnsEMBL::Transcript'
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265 }
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266 ),
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|
267 'splice_acceptor_variant' => Bio::EnsEMBL::Variation::OverlapConsequence->new_fast({
|
|
|
268 'variant_feature_class' => 'Bio::EnsEMBL::Variation::VariationFeature',
|
|
|
269 'NCBI_term' => 'splice-3',
|
|
|
270 'feature_SO_term' => 'primary_transcript',
|
|
|
271 'description' => 'A splice variant that changes the 2 base region at the 3\' end of an intron',
|
|
|
272 'SO_accession' => 'SO:0001574',
|
|
|
273 'tier' => '3',
|
|
|
274 'SO_term' => 'splice_acceptor_variant',
|
|
|
275 'predicate' => 'Bio::EnsEMBL::Variation::Utils::VariationEffect::acceptor_splice_site',
|
|
|
276 'label' => 'Splice acceptor variant',
|
|
|
277 'rank' => '3',
|
|
|
278 'display_term' => 'ESSENTIAL_SPLICE_SITE',
|
|
|
279 'feature_class' => 'Bio::EnsEMBL::Transcript'
|
|
|
280 }
|
|
|
281 ),
|
|
|
282 'splice_region_variant' => Bio::EnsEMBL::Variation::OverlapConsequence->new_fast({
|
|
|
283 'variant_feature_class' => 'Bio::EnsEMBL::Variation::VariationFeature',
|
|
|
284 'feature_SO_term' => 'primary_transcript',
|
|
|
285 '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',
|
|
|
286 'SO_accession' => 'SO:0001630',
|
|
|
287 'SO_term' => 'splice_region_variant',
|
|
|
288 'tier' => '3',
|
|
|
289 'predicate' => 'Bio::EnsEMBL::Variation::Utils::VariationEffect::splice_region',
|
|
|
290 'label' => 'Splice region variant',
|
|
|
291 'rank' => '13',
|
|
|
292 'display_term' => 'SPLICE_SITE',
|
|
|
293 'feature_class' => 'Bio::EnsEMBL::Transcript'
|
|
|
294 }
|
|
|
295 ),
|
|
|
296 'intron_variant' => Bio::EnsEMBL::Variation::OverlapConsequence->new_fast({
|
|
|
297 'variant_feature_class' => 'Bio::EnsEMBL::Variation::BaseVariationFeature',
|
|
|
298 'NCBI_term' => 'intron',
|
|
|
299 'feature_SO_term' => 'primary_transcript',
|
|
|
300 'description' => 'A transcript variant occurring within an intron',
|
|
|
301 'SO_accession' => 'SO:0001627',
|
|
|
302 'tier' => '3',
|
|
|
303 'SO_term' => 'intron_variant',
|
|
|
304 'predicate' => 'Bio::EnsEMBL::Variation::Utils::VariationEffect::within_intron',
|
|
|
305 'label' => 'Intron variant',
|
|
|
306 'rank' => '20',
|
|
|
307 'display_term' => 'INTRONIC',
|
|
|
308 'feature_class' => 'Bio::EnsEMBL::Transcript'
|
|
|
309 }
|
|
|
310 ),
|
|
|
311 '5_prime_UTR_variant' => Bio::EnsEMBL::Variation::OverlapConsequence->new_fast({
|
|
|
312 'variant_feature_class' => 'Bio::EnsEMBL::Variation::BaseVariationFeature',
|
|
|
313 'NCBI_term' => 'untranslated_5',
|
|
|
314 'feature_SO_term' => 'mRNA',
|
|
|
315 'description' => 'A UTR variant of the 5\' UTR',
|
|
|
316 'SO_accession' => 'SO:0001623',
|
|
|
317 'tier' => '3',
|
|
|
318 'SO_term' => '5_prime_UTR_variant',
|
|
|
319 'predicate' => 'Bio::EnsEMBL::Variation::Utils::VariationEffect::within_5_prime_utr',
|
|
|
320 'label' => '5 prime UTR variant',
|
|
|
321 'rank' => '18',
|
|
|
322 'display_term' => '5PRIME_UTR',
|
|
|
323 'feature_class' => 'Bio::EnsEMBL::Transcript'
|
|
|
324 }
|
|
|
325 ),
|
|
|
326 '3_prime_UTR_variant' => Bio::EnsEMBL::Variation::OverlapConsequence->new_fast({
|
|
|
327 'variant_feature_class' => 'Bio::EnsEMBL::Variation::BaseVariationFeature',
|
|
|
328 'NCBI_term' => 'untranslated_3',
|
|
|
329 'feature_SO_term' => 'mRNA',
|
|
|
330 'description' => 'A UTR variant of the 3\' UTR',
|
|
|
331 'SO_accession' => 'SO:0001624',
|
|
|
332 'tier' => '3',
|
|
|
333 'SO_term' => '3_prime_UTR_variant',
|
|
|
334 'predicate' => 'Bio::EnsEMBL::Variation::Utils::VariationEffect::within_3_prime_utr',
|
|
|
335 'label' => '3 prime UTR variant',
|
|
|
336 'rank' => '19',
|
|
|
337 'display_term' => '3PRIME_UTR',
|
|
|
338 'feature_class' => 'Bio::EnsEMBL::Transcript'
|
|
|
339 }
|
|
|
340 ),
|
|
|
341 'synonymous_variant' => Bio::EnsEMBL::Variation::OverlapConsequence->new_fast({
|
|
|
342 'variant_feature_class' => 'Bio::EnsEMBL::Variation::VariationFeature',
|
|
|
343 'NCBI_term' => 'cds-synon',
|
|
|
344 'feature_SO_term' => 'mRNA',
|
|
|
345 'description' => 'A sequence variant where there is no resulting change to the encoded amino acid',
|
|
|
346 'SO_accession' => 'SO:0001819',
|
|
|
347 'tier' => '3',
|
|
|
348 'SO_term' => 'synonymous_variant',
|
|
|
349 'predicate' => 'Bio::EnsEMBL::Variation::Utils::VariationEffect::synonymous_variant',
|
|
|
350 'label' => 'Synonymous variant',
|
|
|
351 'rank' => '15',
|
|
|
352 'display_term' => 'SYNONYMOUS_CODING',
|
|
|
353 'feature_class' => 'Bio::EnsEMBL::Transcript'
|
|
|
354 }
|
|
|
355 ),
|
|
|
356 'missense_variant' => Bio::EnsEMBL::Variation::OverlapConsequence->new_fast({
|
|
|
357 'variant_feature_class' => 'Bio::EnsEMBL::Variation::VariationFeature',
|
|
|
358 'NCBI_term' => 'missense',
|
|
|
359 'feature_SO_term' => 'mRNA',
|
|
|
360 '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',
|
|
|
361 'SO_accession' => 'SO:0001583',
|
|
|
362 'tier' => '3',
|
|
|
363 'SO_term' => 'missense_variant',
|
|
|
364 'predicate' => 'Bio::EnsEMBL::Variation::Utils::VariationEffect::missense_variant',
|
|
|
365 'label' => 'Missense variant',
|
|
|
366 'rank' => '12',
|
|
|
367 'display_term' => 'NON_SYNONYMOUS_CODING',
|
|
|
368 'feature_class' => 'Bio::EnsEMBL::Transcript'
|
|
|
369 }
|
|
|
370 ),
|
|
|
371 'inframe_insertion' => Bio::EnsEMBL::Variation::OverlapConsequence->new_fast({
|
|
|
372 'variant_feature_class' => 'Bio::EnsEMBL::Variation::BaseVariationFeature',
|
|
|
373 'feature_SO_term' => 'mRNA',
|
|
|
374 'description' => 'An inframe non synonymous variant that inserts bases into in the coding sequence',
|
|
|
375 'SO_accession' => 'SO:0001821',
|
|
|
376 'SO_term' => 'inframe_insertion',
|
|
|
377 'tier' => '3',
|
|
|
378 'predicate' => 'Bio::EnsEMBL::Variation::Utils::VariationEffect::inframe_insertion',
|
|
|
379 'label' => 'Inframe insertion',
|
|
|
380 'rank' => '10',
|
|
|
381 'display_term' => 'NON_SYNONYMOUS_CODING',
|
|
|
382 'feature_class' => 'Bio::EnsEMBL::Transcript'
|
|
|
383 }
|
|
|
384 ),
|
|
|
385 'inframe_deletion' => Bio::EnsEMBL::Variation::OverlapConsequence->new_fast({
|
|
|
386 'variant_feature_class' => 'Bio::EnsEMBL::Variation::BaseVariationFeature',
|
|
|
387 'feature_SO_term' => 'mRNA',
|
|
|
388 'description' => 'An inframe non synonymous variant that deletes bases from the coding sequence',
|
|
|
389 'SO_accession' => 'SO:0001822',
|
|
|
390 'SO_term' => 'inframe_deletion',
|
|
|
391 'tier' => '3',
|
|
|
392 'predicate' => 'Bio::EnsEMBL::Variation::Utils::VariationEffect::inframe_deletion',
|
|
|
393 'label' => 'Inframe deletion',
|
|
|
394 'rank' => '11',
|
|
|
395 'display_term' => 'NON_SYNONYMOUS_CODING',
|
|
|
396 'feature_class' => 'Bio::EnsEMBL::Transcript'
|
|
|
397 }
|
|
|
398 ),
|
|
|
399 'stop_gained' => Bio::EnsEMBL::Variation::OverlapConsequence->new_fast({
|
|
|
400 'variant_feature_class' => 'Bio::EnsEMBL::Variation::VariationFeature',
|
|
|
401 'NCBI_term' => 'nonsense',
|
|
|
402 'feature_SO_term' => 'mRNA',
|
|
|
403 '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',
|
|
|
404 'SO_accession' => 'SO:0001587',
|
|
|
405 'tier' => '3',
|
|
|
406 'SO_term' => 'stop_gained',
|
|
|
407 'predicate' => 'Bio::EnsEMBL::Variation::Utils::VariationEffect::stop_gained',
|
|
|
408 'label' => 'Stop gained',
|
|
|
409 'rank' => '4',
|
|
|
410 'display_term' => 'STOP_GAINED',
|
|
|
411 'feature_class' => 'Bio::EnsEMBL::Transcript'
|
|
|
412 }
|
|
|
413 ),
|
|
|
414 'stop_lost' => Bio::EnsEMBL::Variation::OverlapConsequence->new_fast({
|
|
|
415 'variant_feature_class' => 'Bio::EnsEMBL::Variation::BaseVariationFeature',
|
|
|
416 'feature_SO_term' => 'mRNA',
|
|
|
417 'description' => 'A sequence variant where at least one base of the terminator codon (stop) is changed, resulting in an elongated transcript',
|
|
|
418 'SO_accession' => 'SO:0001578',
|
|
|
419 'SO_term' => 'stop_lost',
|
|
|
420 'tier' => '3',
|
|
|
421 'predicate' => 'Bio::EnsEMBL::Variation::Utils::VariationEffect::stop_lost',
|
|
|
422 'label' => 'Stop lost',
|
|
|
423 'rank' => '6',
|
|
|
424 'display_term' => 'STOP_LOST',
|
|
|
425 'feature_class' => 'Bio::EnsEMBL::Transcript'
|
|
|
426 }
|
|
|
427 ),
|
|
|
428 'stop_retained_variant' => Bio::EnsEMBL::Variation::OverlapConsequence->new_fast({
|
|
|
429 'variant_feature_class' => 'Bio::EnsEMBL::Variation::VariationFeature',
|
|
|
430 'feature_SO_term' => 'mRNA',
|
|
|
431 'description' => 'A sequence variant where at least one base in the terminator codon is changed, but the terminator remains',
|
|
|
432 'SO_accession' => 'SO:0001567',
|
|
|
433 'SO_term' => 'stop_retained_variant',
|
|
|
434 'tier' => '3',
|
|
|
435 'predicate' => 'Bio::EnsEMBL::Variation::Utils::VariationEffect::stop_retained',
|
|
|
436 'label' => 'Stop retained variant',
|
|
|
437 'rank' => '15',
|
|
|
438 'display_term' => 'SYNONYMOUS_CODING',
|
|
|
439 'feature_class' => 'Bio::EnsEMBL::Transcript'
|
|
|
440 }
|
|
|
441 ),
|
|
|
442 'initiator_codon_variant' => Bio::EnsEMBL::Variation::OverlapConsequence->new_fast({
|
|
|
443 'variant_feature_class' => 'Bio::EnsEMBL::Variation::BaseVariationFeature',
|
|
|
444 'feature_SO_term' => 'mRNA',
|
|
|
445 'description' => 'A codon variant that changes at least one base of the first codon of a transcript',
|
|
|
446 'SO_accession' => 'SO:0001582',
|
|
|
447 'SO_term' => 'initiator_codon_variant',
|
|
|
448 'tier' => '3',
|
|
|
449 'predicate' => 'Bio::EnsEMBL::Variation::Utils::VariationEffect::affects_start_codon',
|
|
|
450 'label' => 'Initiator codon variant',
|
|
|
451 'rank' => '7',
|
|
|
452 'display_term' => 'NON_SYNONYMOUS_CODING',
|
|
|
453 'feature_class' => 'Bio::EnsEMBL::Transcript'
|
|
|
454 }
|
|
|
455 ),
|
|
|
456 'frameshift_variant' => Bio::EnsEMBL::Variation::OverlapConsequence->new_fast({
|
|
|
457 'variant_feature_class' => 'Bio::EnsEMBL::Variation::BaseVariationFeature',
|
|
|
458 'NCBI_term' => 'frameshift',
|
|
|
459 'feature_SO_term' => 'mRNA',
|
|
|
460 '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',
|
|
|
461 'SO_accession' => 'SO:0001589',
|
|
|
462 'tier' => '3',
|
|
|
463 'SO_term' => 'frameshift_variant',
|
|
|
464 'predicate' => 'Bio::EnsEMBL::Variation::Utils::VariationEffect::frameshift',
|
|
|
465 'label' => 'Frameshift variant',
|
|
|
466 'rank' => '5',
|
|
|
467 'display_term' => 'FRAMESHIFT_CODING',
|
|
|
468 'feature_class' => 'Bio::EnsEMBL::Transcript'
|
|
|
469 }
|
|
|
470 ),
|
|
|
471 'incomplete_terminal_codon_variant' => Bio::EnsEMBL::Variation::OverlapConsequence->new_fast({
|
|
|
472 'variant_feature_class' => 'Bio::EnsEMBL::Variation::VariationFeature',
|
|
|
473 'feature_SO_term' => 'mRNA',
|
|
|
474 'description' => 'A sequence variant where at least one base of the final codon of an incompletely annotated transcript is changed',
|
|
|
475 'SO_accession' => 'SO:0001626',
|
|
|
476 'SO_term' => 'incomplete_terminal_codon_variant',
|
|
|
477 'tier' => '3',
|
|
|
478 'predicate' => 'Bio::EnsEMBL::Variation::Utils::VariationEffect::partial_codon',
|
|
|
479 'label' => 'Incomplete terminal codon variant',
|
|
|
480 'rank' => '14',
|
|
|
481 'display_term' => 'PARTIAL_CODON',
|
|
|
482 'feature_class' => 'Bio::EnsEMBL::Transcript'
|
|
|
483 }
|
|
|
484 ),
|
|
|
485 'NMD_transcript_variant' => Bio::EnsEMBL::Variation::OverlapConsequence->new_fast({
|
|
|
486 'variant_feature_class' => 'Bio::EnsEMBL::Variation::BaseVariationFeature',
|
|
|
487 'feature_SO_term' => 'mRNA',
|
|
|
488 'description' => 'A variant in a transcript that is the target of NMD',
|
|
|
489 'SO_accession' => 'SO:0001621',
|
|
|
490 'SO_term' => 'NMD_transcript_variant',
|
|
|
491 'tier' => '3',
|
|
|
492 'predicate' => 'Bio::EnsEMBL::Variation::Utils::VariationEffect::within_nmd_transcript',
|
|
|
493 'label' => 'NMD transcript variant',
|
|
|
494 'rank' => '21',
|
|
|
495 'display_term' => 'NMD_TRANSCRIPT',
|
|
|
496 'feature_class' => 'Bio::EnsEMBL::Transcript'
|
|
|
497 }
|
|
|
498 ),
|
|
|
499 'nc_transcript_variant' => Bio::EnsEMBL::Variation::OverlapConsequence->new_fast({
|
|
|
500 'variant_feature_class' => 'Bio::EnsEMBL::Variation::BaseVariationFeature',
|
|
|
501 'feature_SO_term' => 'ncRNA',
|
|
|
502 'description' => 'A transcript variant of a non coding RNA',
|
|
|
503 'SO_accession' => 'SO:0001619',
|
|
|
504 'SO_term' => 'nc_transcript_variant',
|
|
|
505 'tier' => '3',
|
|
|
506 'predicate' => 'Bio::EnsEMBL::Variation::Utils::VariationEffect::within_non_coding_gene',
|
|
|
507 'label' => 'NC transcript variant',
|
|
|
508 'rank' => '23',
|
|
|
509 'display_term' => 'WITHIN_NON_CODING_GENE',
|
|
|
510 'feature_class' => 'Bio::EnsEMBL::Transcript'
|
|
|
511 }
|
|
|
512 ),
|
|
|
513 'non_coding_exon_variant' => Bio::EnsEMBL::Variation::OverlapConsequence->new_fast({
|
|
|
514 'variant_feature_class' => 'Bio::EnsEMBL::Variation::BaseVariationFeature',
|
|
|
515 'feature_SO_term' => 'ncRNA',
|
|
|
516 'description' => 'A sequence variant that changes non-coding exon sequence',
|
|
|
517 'SO_accession' => 'SO:0001792',
|
|
|
518 'SO_term' => 'non_coding_exon_variant',
|
|
|
519 'tier' => '3',
|
|
|
520 'predicate' => 'Bio::EnsEMBL::Variation::Utils::VariationEffect::non_coding_exon_variant',
|
|
|
521 'label' => 'Non coding exon variant',
|
|
|
522 'rank' => '22',
|
|
|
523 'display_term' => 'WITHIN_NON_CODING_GENE',
|
|
|
524 'feature_class' => 'Bio::EnsEMBL::Transcript'
|
|
|
525 }
|
|
|
526 ),
|
|
|
527 'mature_miRNA_variant' => Bio::EnsEMBL::Variation::OverlapConsequence->new_fast({
|
|
|
528 'variant_feature_class' => 'Bio::EnsEMBL::Variation::BaseVariationFeature',
|
|
|
529 'feature_SO_term' => 'miRNA',
|
|
|
530 'description' => 'A transcript variant located with the sequence of the mature miRNA',
|
|
|
531 'SO_accession' => 'SO:0001620',
|
|
|
532 'SO_term' => 'mature_miRNA_variant',
|
|
|
533 'tier' => '2',
|
|
|
534 'predicate' => 'Bio::EnsEMBL::Variation::Utils::VariationEffect::within_mature_miRNA',
|
|
|
535 'label' => 'Mature miRNA variant',
|
|
|
536 'rank' => '17',
|
|
|
537 'display_term' => 'WITHIN_MATURE_miRNA',
|
|
|
538 'feature_class' => 'Bio::EnsEMBL::Transcript'
|
|
|
539 }
|
|
|
540 ),
|
|
|
541 'coding_sequence_variant' => Bio::EnsEMBL::Variation::OverlapConsequence->new_fast({
|
|
|
542 'variant_feature_class' => 'Bio::EnsEMBL::Variation::BaseVariationFeature',
|
|
|
543 'feature_SO_term' => 'mRNA',
|
|
|
544 'description' => 'A sequence variant that changes the coding sequence',
|
|
|
545 'SO_accession' => 'SO:0001580',
|
|
|
546 'SO_term' => 'coding_sequence_variant',
|
|
|
547 'tier' => '3',
|
|
|
548 'predicate' => 'Bio::EnsEMBL::Variation::Utils::VariationEffect::coding_unknown',
|
|
|
549 'label' => 'Coding sequence variant',
|
|
|
550 'rank' => '16',
|
|
|
551 'display_term' => 'CODING_UNKNOWN',
|
|
|
552 'feature_class' => 'Bio::EnsEMBL::Transcript'
|
|
|
553 }
|
|
|
554 ),
|
|
|
555 'regulatory_region_variant' => Bio::EnsEMBL::Variation::OverlapConsequence->new_fast({
|
|
|
556 'variant_feature_class' => 'Bio::EnsEMBL::Variation::BaseVariationFeature',
|
|
|
557 'feature_SO_term' => 'regulatory_region',
|
|
|
558 'description' => 'A sequence variant located within a regulatory region',
|
|
|
559 'SO_accession' => 'SO:0001566',
|
|
|
560 'SO_term' => 'regulatory_region_variant',
|
|
|
561 'tier' => '2',
|
|
|
562 'predicate' => 'Bio::EnsEMBL::Variation::Utils::VariationEffect::within_regulatory_feature',
|
|
|
563 'label' => 'Regulatory region variant',
|
|
|
564 'rank' => '36',
|
|
|
565 'display_term' => 'REGULATORY_REGION',
|
|
|
566 'feature_class' => 'Bio::EnsEMBL::Funcgen::RegulatoryFeature'
|
|
|
567 }
|
|
|
568 ),
|
|
|
569 'TF_binding_site_variant' => Bio::EnsEMBL::Variation::OverlapConsequence->new_fast({
|
|
|
570 'variant_feature_class' => 'Bio::EnsEMBL::Variation::BaseVariationFeature',
|
|
|
571 'feature_SO_term' => 'TF_binding_site',
|
|
|
572 'description' => 'In regulatory region annotated by Ensembl',
|
|
|
573 'SO_accession' => 'SO:0001782',
|
|
|
574 'SO_term' => 'TF_binding_site_variant',
|
|
|
575 'tier' => '2',
|
|
|
576 'predicate' => 'Bio::EnsEMBL::Variation::Utils::VariationEffect::within_motif_feature',
|
|
|
577 'label' => 'A sequence variant located within a transcription factor binding site',
|
|
|
578 'rank' => '30',
|
|
|
579 'display_term' => 'REGULATORY_REGION',
|
|
|
580 'feature_class' => 'Bio::EnsEMBL::Funcgen::MotifFeature'
|
|
|
581 }
|
|
|
582 ),
|
|
|
583 'transcript_ablation' => Bio::EnsEMBL::Variation::OverlapConsequence->new_fast({
|
|
|
584 'variant_feature_class' => 'Bio::EnsEMBL::Variation::BaseVariationFeature',
|
|
|
585 'feature_SO_term' => 'mRNA',
|
|
|
586 'description' => 'A feature ablation whereby the deleted region includes a transcript feature',
|
|
|
587 'SO_accession' => 'SO:0001893',
|
|
|
588 'SO_term' => 'transcript_ablation',
|
|
|
589 'tier' => '1',
|
|
|
590 'predicate' => 'Bio::EnsEMBL::Variation::Utils::VariationEffect::feature_ablation',
|
|
|
591 'label' => 'Transcript ablation',
|
|
|
592 'rank' => '1',
|
|
|
593 'feature_class' => 'Bio::EnsEMBL::Transcript'
|
|
|
594 }
|
|
|
595 ),
|
|
|
596 'transcript_amplification' => Bio::EnsEMBL::Variation::OverlapConsequence->new_fast({
|
|
|
597 'variant_feature_class' => 'Bio::EnsEMBL::Variation::BaseVariationFeature',
|
|
|
598 'feature_SO_term' => 'mRNA',
|
|
|
599 'description' => 'A feature amplification of a region containing a transcript',
|
|
|
600 'SO_accession' => 'SO:0001889',
|
|
|
601 'SO_term' => 'transcript_amplification',
|
|
|
602 'tier' => '1',
|
|
|
603 'predicate' => 'Bio::EnsEMBL::Variation::Utils::VariationEffect::feature_amplification',
|
|
|
604 'label' => 'Transcript amplification',
|
|
|
605 'rank' => '8',
|
|
|
606 'feature_class' => 'Bio::EnsEMBL::Transcript'
|
|
|
607 }
|
|
|
608 ),
|
|
|
609 'TFBS_ablation' => Bio::EnsEMBL::Variation::OverlapConsequence->new_fast({
|
|
|
610 'variant_feature_class' => 'Bio::EnsEMBL::Variation::BaseVariationFeature',
|
|
|
611 'feature_SO_term' => 'TF_binding_site',
|
|
|
612 'description' => 'A feature ablation whereby the deleted region includes a transcription factor binding site',
|
|
|
613 'SO_accession' => 'SO:0001895',
|
|
|
614 'SO_term' => 'TFBS_ablation',
|
|
|
615 'tier' => '2',
|
|
|
616 'predicate' => 'Bio::EnsEMBL::Variation::Utils::VariationEffect::feature_ablation',
|
|
|
617 'label' => 'TFBS ablation',
|
|
|
618 'rank' => '26',
|
|
|
619 'feature_class' => 'Bio::EnsEMBL::Funcgen::MotifFeature'
|
|
|
620 }
|
|
|
621 ),
|
|
|
622 'TFBS_amplification' => Bio::EnsEMBL::Variation::OverlapConsequence->new_fast({
|
|
|
623 'variant_feature_class' => 'Bio::EnsEMBL::Variation::BaseVariationFeature',
|
|
|
624 'feature_SO_term' => 'TF_binding_site',
|
|
|
625 'description' => 'A feature amplification of a region containing a transcription factor binding site',
|
|
|
626 'SO_accession' => 'SO:0001892',
|
|
|
627 'SO_term' => 'TFBS_amplification',
|
|
|
628 'tier' => '2',
|
|
|
629 'predicate' => 'Bio::EnsEMBL::Variation::Utils::VariationEffect::feature_amplification',
|
|
|
630 'label' => 'TFBS amplification',
|
|
|
631 'rank' => '28',
|
|
|
632 'feature_class' => 'Bio::EnsEMBL::Funcgen::MotifFeature'
|
|
|
633 }
|
|
|
634 ),
|
|
|
635 'regulatory_region_ablation' => Bio::EnsEMBL::Variation::OverlapConsequence->new_fast({
|
|
|
636 'variant_feature_class' => 'Bio::EnsEMBL::Variation::BaseVariationFeature',
|
|
|
637 'feature_SO_term' => 'TF_binding_site',
|
|
|
638 'description' => 'A feature ablation whereby the deleted region includes a regulatory region',
|
|
|
639 'SO_accession' => 'SO:0001894',
|
|
|
640 'SO_term' => 'regulatory_region_ablation',
|
|
|
641 'tier' => '2',
|
|
|
642 'predicate' => 'Bio::EnsEMBL::Variation::Utils::VariationEffect::feature_ablation',
|
|
|
643 'label' => 'Regulatory region ablation',
|
|
|
644 'rank' => '31',
|
|
|
645 'feature_class' => 'Bio::EnsEMBL::Funcgen::RegulatoryFeature'
|
|
|
646 }
|
|
|
647 ),
|
|
|
648 'regulatory_region_amplification' => Bio::EnsEMBL::Variation::OverlapConsequence->new_fast({
|
|
|
649 'variant_feature_class' => 'Bio::EnsEMBL::Variation::BaseVariationFeature',
|
|
|
650 'feature_SO_term' => 'TF_binding_site',
|
|
|
651 'description' => 'A feature amplification of a region containing a regulatory region',
|
|
|
652 'SO_accession' => 'SO:0001891',
|
|
|
653 'SO_term' => 'regulatory_region_amplification',
|
|
|
654 'tier' => '2',
|
|
|
655 'predicate' => 'Bio::EnsEMBL::Variation::Utils::VariationEffect::feature_amplification',
|
|
|
656 'label' => 'Regulatory region amplification',
|
|
|
657 'rank' => '33',
|
|
|
658 'feature_class' => 'Bio::EnsEMBL::Funcgen::RegulatoryFeature'
|
|
|
659 }
|
|
|
660 ),
|
|
|
661 'feature_elongation' => Bio::EnsEMBL::Variation::OverlapConsequence->new_fast({
|
|
|
662 'variant_feature_class' => 'Bio::EnsEMBL::Variation::BaseVariationFeature',
|
|
|
663 'description' => 'A sequence variant that causes the extension of a genomic feature, with regard to the reference sequence',
|
|
|
664 'SO_accession' => 'SO:0001907',
|
|
|
665 'SO_term' => 'feature_elongation',
|
|
|
666 'tier' => '3',
|
|
|
667 'predicate' => 'Bio::EnsEMBL::Variation::Utils::VariationEffect::feature_elongation',
|
|
|
668 'label' => 'Feature elongation',
|
|
|
669 'rank' => '36',
|
|
|
670 'feature_class' => 'Bio::EnsEMBL::Feature'
|
|
|
671 }
|
|
|
672 ),
|
|
|
673 'feature_truncation' => Bio::EnsEMBL::Variation::OverlapConsequence->new_fast({
|
|
|
674 'variant_feature_class' => 'Bio::EnsEMBL::Variation::BaseVariationFeature',
|
|
|
675 'description' => 'A sequence variant that causes the reduction of a genomic feature, with regard to the reference sequence',
|
|
|
676 'SO_accession' => 'SO:0001906',
|
|
|
677 'SO_term' => 'feature_truncation',
|
|
|
678 'tier' => '3',
|
|
|
679 'predicate' => 'Bio::EnsEMBL::Variation::Utils::VariationEffect::feature_truncation',
|
|
|
680 'label' => 'Feature truncation',
|
|
|
681 'rank' => '37',
|
|
|
682 'feature_class' => 'Bio::EnsEMBL::Feature'
|
|
|
683 }
|
|
|
684 ),
|
|
|
685 );
|
|
|
686
|
|
|
687 1;
|
