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1 package Bio::EnsEMBL::Variation::Pipeline::SetVariationClass;
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2
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3 use strict;
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4 use warnings;
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5
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6 use base qw(Bio::EnsEMBL::Variation::Pipeline::BaseVariationProcess);
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7
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8 use Bio::EnsEMBL::Variation::Utils::Sequence qw(SO_variation_class);
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9
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10
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11 sub run {
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12
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13 my $self = shift;
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14
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15 my $var_id_start = $self->required_param('variation_id_start');
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16
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17 my $var_id_stop = $self->required_param('variation_id_stop');
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18
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19 my $temp_var_table = $self->param('temp_var_table');
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20
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21 my $temp_var_feat_table = $self->param('temp_var_feat_table');
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22
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23 my $var_dba = $self->get_species_adaptor('variation');
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24
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25 my $aa = $var_dba->get_AttributeAdaptor;
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26
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27 my $dbc = $var_dba->dbc;
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28
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29 # fetch the failed_descriptions to avoid a join
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30
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31 my $fds_sth = $dbc->prepare(qq{
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32 SELECT failed_description_id, description
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33 FROM failed_description
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34 });
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35
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36 $fds_sth->execute;
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37
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38 my %fds;
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39
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40 while (my ($fd_id, $desc) = $fds_sth->fetchrow_array) {
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41 $fds{$fd_id} = $desc;
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42 }
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43
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44 $fds_sth->finish();
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45
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46 my $all_sth = $dbc->prepare(qq{
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47 SELECT v.variation_id, vf.variation_feature_id, vf.allele_string, fv.failed_description_id
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48 FROM (variation v LEFT JOIN variation_feature vf ON v.variation_id = vf.variation_id)
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49 LEFT JOIN failed_variation fv ON v.variation_id = fv.variation_id, source s
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50 WHERE v.variation_id >= ?
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51 AND v.variation_id <= ?
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52 AND v.source_id = s.source_id
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53 AND s.name != 'HGMD-PUBLIC'
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54 });
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55
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56 my $vf_insert_sth;
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57 my $v_insert_sth;
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58
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59 if (defined $temp_var_feat_table) {
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60 $vf_insert_sth = $dbc->prepare(qq{
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61 INSERT IGNORE INTO $temp_var_feat_table (class_attrib_id, variation_feature_id)
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62 VALUES (?,?)
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63 });
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64 }
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65 else {
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66 $vf_insert_sth = $dbc->prepare(qq{
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67 UPDATE variation_feature SET class_attrib_id = ? WHERE variation_feature_id = ?
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68 });
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69 }
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70
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71 if (defined $temp_var_table) {
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72 $v_insert_sth = $dbc->prepare(qq{
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73 INSERT IGNORE INTO $temp_var_table (class_attrib_id, variation_id)
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74 VALUES (?,?)
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75 });
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76 }
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77 else {
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78 $v_insert_sth = $dbc->prepare(qq{
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79 UPDATE variation SET class_attrib_id = ? WHERE variation_id = ?
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80 });
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81 }
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82
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83 $all_sth->execute($var_id_start, $var_id_stop);
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84
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85 my @unmapped_v_ids;
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86
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87 while (my ($v_id, $vf_id, $allele_string, $fd_id) = $all_sth->fetchrow_array) {
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88
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89 unless ($vf_id) {
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90 # this variation doesn't have a corresponding variation_feature
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91 push @unmapped_v_ids, $v_id;
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92 next;
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93 }
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94
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95 my $ref_correct = 1;
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96
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97 # check to see if this variation_feature is known not to match the reference allele,
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98 # as this tells us if we can call insertions or deletions, or have to resort to indel
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99
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100 if (defined $fd_id) {
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101 my $fail_reason = $fds{$fd_id};
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102
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103 if ($fail_reason eq 'None of the variant alleles match the reference allele') {
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104 $ref_correct = 0;
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105 }
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106 }
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107
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108 my $so_term = SO_variation_class($allele_string, $ref_correct);
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109
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110 my $attrib_id = $aa->attrib_id_for_type_value('SO_term', $so_term);
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111
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112 die "No attrib_id for $so_term" unless defined $attrib_id;
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113
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114 $vf_insert_sth->execute($attrib_id, $vf_id);
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115
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116 $v_insert_sth->execute($attrib_id, $v_id);
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117 }
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118
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119 $all_sth->finish();
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120
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121 # now we need to fetch the alleles for any variations that are not mapped
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122 # and work out their class
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123
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124 if (@unmapped_v_ids) {
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125
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126 my $id_str = join ',', @unmapped_v_ids;
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127
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128 my $unmapped_sth = $dbc->prepare(qq{
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129 SELECT a.variation_id, ac.allele
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130 FROM allele a, allele_code ac
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131 WHERE a.variation_id IN ($id_str)
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132 AND a.allele_code_id = ac.allele_code_id
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133 GROUP BY ac.allele
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134 });
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135
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136 $unmapped_sth->execute or die "Failed to fetch unmapped variation alleles for variation ids: $id_str";
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137
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138 my $unmapped_alleles;
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139
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140 while (my ($v_id, $allele) = $unmapped_sth->fetchrow_array) {
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141 push @{ $unmapped_alleles->{$v_id} ||= [] }, $allele;
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142 }
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143
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144 $unmapped_sth->finish();
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145
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146 for my $v_id (keys %$unmapped_alleles) {
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147
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148 my $allele_string = join '/', @{ $unmapped_alleles->{$v_id} };
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149
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150 # we don't know what the reference is here
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151
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152 my $ref_correct = 0;
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153
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154 my $so_term = SO_variation_class($allele_string, $ref_correct);
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155
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156 my $attrib_id = $aa->attrib_id_for_type_value('SO_term', $so_term);
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157
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158 die "No attrib_id for $so_term" unless defined $attrib_id;
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159
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160 $v_insert_sth->execute($attrib_id, $v_id);
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161 }
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162 }
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163
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164 $vf_insert_sth->finish();
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165 $v_insert_sth->finish();
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166 }
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167
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168 1;
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169
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