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1 =head1 LICENSE
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2
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3 Copyright (c) 1999-2012 The European Bioinformatics Institute and
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4 Genome Research Limited. All rights reserved.
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5
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6 This software is distributed under a modified Apache license.
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7 For license details, please see
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8
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9 http://www.ensembl.org/info/about/code_licence.html
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10
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11 =head1 CONTACT
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12
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13 Please email comments or questions to the public Ensembl
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14 developers list at <dev@ensembl.org>.
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15
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16 Questions may also be sent to the Ensembl help desk at
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17 <helpdesk@ensembl.org>.
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18
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19 =cut
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20
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21 =head1 NAME
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22
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23 Bio::EnsEMBL::DBSQL::ProteinAlignFeatureAdaptor -
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24 Adaptor for ProteinAlignFeatures
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25
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26 =head1 SYNOPSIS
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27
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28 $pafa =
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29 $registry->get_adaptor( 'Human', 'Core', 'ProteinAlignFeature' );
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30
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31 my @features = @{ $pafa->fetch_all_by_Slice($slice) };
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32
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33 $pafa->store(@features);
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34
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35 =head1 METHODS
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36
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37 =cut
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38
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39
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40 package Bio::EnsEMBL::DBSQL::ProteinAlignFeatureAdaptor;
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41 use vars qw(@ISA);
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42 use strict;
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43
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44 use Bio::EnsEMBL::DBSQL::BaseAlignFeatureAdaptor;
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45 use Bio::EnsEMBL::DnaPepAlignFeature;
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46 use Bio::EnsEMBL::Utils::Exception qw(throw warning);
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47 @ISA = qw(Bio::EnsEMBL::DBSQL::BaseAlignFeatureAdaptor);
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48
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49
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50 =head2 store
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51
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52 Arg [1] : list of Bio::EnsEMBL::DnaPepAlignFeature @feats
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53 Example : $protein_align_feature_adaptor->store(@feats);
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54 Description: stores a list of ProteinAlignFeatures in the database
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55 Returntype : none
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56 Exceptions : throw if any of the provided features cannot be stored
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57 which may occur if:
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58 * The feature does not have an associated Slice
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59 * The feature does not have an associated analysis
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60 * The Slice the feature is associated with is on a seq_region
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61 unknown to this database
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62 A warning is given if:
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63 * The feature has already been stored in this db
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64 Caller : Pipeline
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65 Status : Stable
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66
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67 =cut
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68
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69
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70 sub store{
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71 my ($self, @feats) = @_;
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72
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73 throw("Must call store with features") if( scalar(@feats) == 0 );
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74
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75 my @tabs = $self->_tables;
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76 my ($tablename) = @{$tabs[0]};
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77
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78 my $db = $self->db();
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79 my $slice_adaptor = $db->get_SliceAdaptor();
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80 my $analysis_adaptor = $db->get_AnalysisAdaptor();
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81
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82 my $sth = $self->prepare(
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83 "INSERT INTO $tablename (seq_region_id, seq_region_start, seq_region_end,
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84 seq_region_strand, hit_start, hit_end,
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85 hit_name, cigar_line,
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86 analysis_id, score, evalue, perc_ident, external_db_id, hcoverage)
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87 VALUES (?,?,?,?,?,?,?,?,?,?, ?, ?, ?, ?)");
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88
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89 FEATURE: foreach my $feat ( @feats ) {
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90 if( !ref $feat || !$feat->isa("Bio::EnsEMBL::DnaPepAlignFeature") ) {
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91 throw("feature must be a Bio::EnsEMBL::DnaPepAlignFeature,"
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92 . " not a [".ref($feat)."].");
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93 }
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94
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95 if($feat->is_stored($db)) {
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96 warning("PepDnaAlignFeature [".$feat->dbID."] is already stored" .
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97 " in this database.");
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98 next FEATURE;
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99 }
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100
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101 #sanity check the hstart and hend
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102 my $hstart = $feat->hstart();
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103 my $hend = $feat->hend();
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104 $self->_check_start_end_strand($hstart,$hend,1);
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105
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106 my $cigar_string = $feat->cigar_string();
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107 if(!$cigar_string) {
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108 $cigar_string = $feat->length() . 'M';
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109 warning("DnaPepAlignFeature does not define a cigar_string.\n" .
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110 "Assuming ungapped block with cigar_string=$cigar_string\n");
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111 }
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112
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113 my $hseqname = $feat->hseqname();
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114 if(!$hseqname) {
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115 throw("DnaPepAlignFeature must define an hseqname.");
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116 }
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117
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118 if(!defined($feat->analysis)) {
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119 throw("An analysis must be attached to the features to be stored.");
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120 }
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121
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122 #store the analysis if it has not been stored yet
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123 if(!$feat->analysis->is_stored($db)) {
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124 $analysis_adaptor->store($feat->analysis());
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125 }
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126
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127 my $slice = $feat->slice();
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128 if(!defined($slice) || !($slice->isa("Bio::EnsEMBL::Slice") or $slice->isa('Bio::EnsEMBL::LRGSlice')) ) {
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129 throw("A slice must be attached to the features to be stored.");
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130 }
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131
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132 my $original = $feat;
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133 my $seq_region_id;
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134 ($feat, $seq_region_id) = $self->_pre_store($feat);
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135
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136 $sth->bind_param(1,$seq_region_id,SQL_INTEGER);
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137 $sth->bind_param(2,$feat->start,SQL_INTEGER);
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138 $sth->bind_param(3,$feat->end,SQL_INTEGER);
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139 $sth->bind_param(4,$feat->strand,SQL_TINYINT);
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140 $sth->bind_param(5,$feat->hstart,SQL_INTEGER);
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141 $sth->bind_param(6,$feat->hend,SQL_INTEGER);
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142 $sth->bind_param(7,$feat->hseqname,SQL_VARCHAR);
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143 $sth->bind_param(8,$feat->cigar_string,SQL_LONGVARCHAR);
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144 $sth->bind_param(9,$feat->analysis->dbID,SQL_INTEGER);
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145 $sth->bind_param(10,$feat->score,SQL_DOUBLE);
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146 $sth->bind_param(11,$feat->p_value,SQL_DOUBLE);
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147 $sth->bind_param(12,$feat->percent_id,SQL_REAL);
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148 $sth->bind_param(13,$feat->external_db_id,SQL_INTEGER);
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149 $sth->bind_param(14,$feat->hcoverage,SQL_DOUBLE);
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150
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151 $sth->execute();
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152 $original->dbID($sth->{'mysql_insertid'});
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153 $original->adaptor($self);
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154 }
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155
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156 $sth->finish();
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157 }
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158
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159
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160 =head2 _objs_from_sth
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161
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162 Arg [1] : DBI statement handle $sth
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163 an exectuted DBI statement handle generated by selecting
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164 the columns specified by _columns() from the table specified
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165 by _table()
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166 Example : @dna_dna_align_feats = $self->_obj_from_hashref
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167 Description: PROTECTED implementation of superclass abstract method.
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168 Creates DnaDnaAlignFeature objects from a DBI hashref
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169 Returntype : listref of Bio::EnsEMBL::ProteinAlignFeatures
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170 Exceptions : none
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171 Caller : Bio::EnsEMBL::BaseFeatureAdaptor::generic_fetch
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172 Status : Stable
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173
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174 =cut
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175
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176 sub _objs_from_sth {
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177 my ($self, $sth, $mapper, $dest_slice) = @_;
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178
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179 #
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180 # This code is ugly because an attempt has been made to remove as many
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181 # function calls as possible for speed purposes. Thus many caches and
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182 # a fair bit of gymnastics is used.
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183 #
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184
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185 my $sa = $self->db()->get_SliceAdaptor();
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186 my $aa = $self->db->get_AnalysisAdaptor();
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187
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188 my @features;
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189 my %analysis_hash;
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190 my %slice_hash;
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191 my %sr_name_hash;
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192 my %sr_cs_hash;
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193
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194 my ($protein_align_feature_id, $seq_region_id, $seq_region_start,
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195 $seq_region_end, $analysis_id, $seq_region_strand, $hit_start,
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196 $hit_end, $hit_name, $cigar_line, $evalue, $perc_ident, $score,
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197 $external_db_id, $hcoverage, $external_db_name, $external_display_db_name );
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198
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199 $sth->bind_columns(\$protein_align_feature_id, \$seq_region_id,
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200 \$seq_region_start,\$seq_region_end, \$analysis_id,
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201 \$seq_region_strand, \$hit_start,\$hit_end, \$hit_name,
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202 \$cigar_line, \$evalue, \$perc_ident, \$score,
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203 \$external_db_id, \$hcoverage, \$external_db_name, \$external_display_db_name );
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204
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205 my $asm_cs;
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206 my $cmp_cs;
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207 my $asm_cs_vers;
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208 my $asm_cs_name;
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209 my $cmp_cs_vers;
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210 my $cmp_cs_name;
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211 if($mapper) {
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212 $asm_cs = $mapper->assembled_CoordSystem();
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213 $cmp_cs = $mapper->component_CoordSystem();
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214 $asm_cs_name = $asm_cs->name();
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215 $asm_cs_vers = $asm_cs->version();
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216 $cmp_cs_name = $cmp_cs->name();
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217 $cmp_cs_vers = $cmp_cs->version();
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218 }
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219
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220 my $dest_slice_start;
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221 my $dest_slice_end;
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222 my $dest_slice_strand;
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223 my $dest_slice_length;
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224 my $dest_slice_sr_name;
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225 my $dest_slice_sr_id;
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226 if($dest_slice) {
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227 $dest_slice_start = $dest_slice->start();
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228 $dest_slice_end = $dest_slice->end();
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229 $dest_slice_strand = $dest_slice->strand();
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230 $dest_slice_length = $dest_slice->length();
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231 $dest_slice_sr_name = $dest_slice->seq_region_name();
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232 $dest_slice_sr_id = $dest_slice->get_seq_region_id();
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233 }
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234
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235 FEATURE: while($sth->fetch()) {
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236 #get the analysis object
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237 my $analysis = $analysis_hash{$analysis_id} ||=
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238 $aa->fetch_by_dbID($analysis_id);
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239
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240 #get the slice object
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241 my $slice = $slice_hash{"ID:".$seq_region_id};
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242
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243 if(!$slice) {
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244 $slice = $sa->fetch_by_seq_region_id($seq_region_id);
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245 $slice_hash{"ID:".$seq_region_id} = $slice;
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246 $sr_name_hash{$seq_region_id} = $slice->seq_region_name();
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247 $sr_cs_hash{$seq_region_id} = $slice->coord_system();
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248 }
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249
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250 my $sr_name = $sr_name_hash{$seq_region_id};
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251 my $sr_cs = $sr_cs_hash{$seq_region_id};
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252 #
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253 # remap the feature coordinates to another coord system
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254 # if a mapper was provided
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255 #
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256 if($mapper) {
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257
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258 if (defined $dest_slice && $mapper->isa('Bio::EnsEMBL::ChainedAssemblyMapper') ) {
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259 ( $seq_region_id, $seq_region_start,
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260 $seq_region_end, $seq_region_strand )
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261 =
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262 $mapper->map( $sr_name, $seq_region_start, $seq_region_end,
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263 $seq_region_strand, $sr_cs, 1, $dest_slice);
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264
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265 } else {
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266
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267 ( $seq_region_id, $seq_region_start,
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268 $seq_region_end, $seq_region_strand )
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269 =
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270 $mapper->fastmap( $sr_name, $seq_region_start, $seq_region_end,
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271 $seq_region_strand, $sr_cs );
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272 }
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273
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274 #skip features that map to gaps or coord system boundaries
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275 next FEATURE if(!defined($seq_region_id));
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276
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277 # #get a slice in the coord system we just mapped to
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278 # if($asm_cs == $sr_cs || ($cmp_cs != $sr_cs && $asm_cs->equals($sr_cs))) {
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279 $slice = $slice_hash{"ID:".$seq_region_id} ||=
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280 $sa->fetch_by_seq_region_id($seq_region_id);
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281 # } else {
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282 # $slice = $slice_hash{"ID:".$seq_region_id} ||=
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283 # $sa->fetch_by_seq_region_id($asm_cs_name, $sr_name, undef, undef, undef,
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284 # $asm_cs_vers);
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285 # }
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286 }
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287
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288 #
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289 # If a destination slice was provided convert the coords
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290 # If the dest_slice starts at 1 and is foward strand, nothing needs doing
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291 #
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292 if($dest_slice) {
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293 if($dest_slice_start != 1 || $dest_slice_strand != 1) {
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294 if($dest_slice_strand == 1) {
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295 $seq_region_start = $seq_region_start - $dest_slice_start + 1;
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296 $seq_region_end = $seq_region_end - $dest_slice_start + 1;
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297 } else {
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298 my $tmp_seq_region_start = $seq_region_start;
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299 $seq_region_start = $dest_slice_end - $seq_region_end + 1;
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300 $seq_region_end = $dest_slice_end - $tmp_seq_region_start + 1;
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301 $seq_region_strand *= -1;
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302 }
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303 }
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304
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305 #throw away features off the end of the requested slice
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306 if($seq_region_end < 1 || $seq_region_start > $dest_slice_length ||
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307 ( $dest_slice_sr_id ne $seq_region_id )) {
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308 next FEATURE;
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309 }
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310 $slice = $dest_slice;
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311 }
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312
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313 # Finally, create the new ProteinAlignFeature.
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314 push(
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315 @features,
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316 $self->_create_feature_fast(
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317 'Bio::EnsEMBL::DnaPepAlignFeature', {
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318 'slice' => $slice,
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319 'start' => $seq_region_start,
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320 'end' => $seq_region_end,
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321 'strand' => $seq_region_strand,
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322 'hseqname' => $hit_name,
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323 'hstart' => $hit_start,
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324 'hend' => $hit_end,
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325 'hstrand' => 1, # dna_pep_align features
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326 # are always hstrand 1
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327 'score' => $score,
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328 'p_value' => $evalue,
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329 'percent_id' => $perc_ident,
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330 'cigar_string' => $cigar_line,
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331 'analysis' => $analysis,
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332 'adaptor' => $self,
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333 'dbID' => $protein_align_feature_id,
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334 'external_db_id' => $external_db_id,
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335 'hcoverage' => $hcoverage,
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336 'dbname' => $external_db_name,
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337 'db_display_name' => $external_display_db_name
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338 } ) );
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339
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340 }
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341
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342 return \@features;
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343 }
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344
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345
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346
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347 sub _tables {
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348 my $self = shift;
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349
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350 return (['protein_align_feature', 'paf'], ['external_db','exdb']);
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351 }
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352
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353
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354 sub _columns {
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355 my $self = shift;
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356
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357 #warning _objs_from_hashref method depends on ordering of this list
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358 return qw( paf.protein_align_feature_id
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359 paf.seq_region_id
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360 paf.seq_region_start
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361 paf.seq_region_end
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362 paf.analysis_id
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363 paf.seq_region_strand
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364 paf.hit_start
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365 paf.hit_end
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366 paf.hit_name
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367 paf.cigar_line
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368 paf.evalue
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369 paf.perc_ident
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370 paf.score
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371 paf.external_db_id
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372 paf.hcoverage
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373 exdb.db_name
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374 exdb.db_display_name);
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375 }
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376
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377 sub _left_join{
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378 return (['external_db',"exdb.external_db_id = paf.external_db_id"]);
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379 }
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380
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381 =head2 list_dbIDs
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382
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383 Arg [1] : none
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384 Example : @feature_ids = @{$protein_align_feature_adaptor->list_dbIDs()};
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385 Description: Gets an array of internal ids for all protein align
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386 features in the current db
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387 Arg[1] : <optional> int. not 0 for the ids to be sorted by the seq_region.
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388 Returntype : listref of ints
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389 Exceptions : none
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390 Caller : ?
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391 Status : Stable
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392
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393 =cut
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394
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395 sub list_dbIDs {
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396 my ($self,$ordered) = @_;
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397
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398 return $self->_list_dbIDs("protein_align_feature", undef, $ordered);
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399 }
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400
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401
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402
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403
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404
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405
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406 1;
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