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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::CompressedSequenceAdaptor - Facilitates DB storage and retrieval of compressed sequence
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24
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25 =head1 SYNOPSIS
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26
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27 $seq_adptr = $database_adaptor->get_SequenceAdaptor();
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28
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29 $dna =
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30 ${ $seq_adptr->fetch_by_Slice_start_end_strand( $slice, 1, 1000,
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31 -1 ) };
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32
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33 =head1 DESCRIPTION
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34
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35 An adaptor for the retrieval of compressed DNA sequence from the EnsEMBL
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36 database
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37
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38 =head1 METHODS
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39
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40 =cut
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41
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42 package Bio::EnsEMBL::DBSQL::CompressedSequenceAdaptor;
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43
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44 use vars qw(@ISA);
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45 use strict;
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46
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47 use Bio::EnsEMBL::DBSQL::SequenceAdaptor;
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48
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49 @ISA = qw(Bio::EnsEMBL::DBSQL::SequenceAdaptor);
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50
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51
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52 sub _fetch_seq {
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53 my $self = shift;
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54 my $seq_region_id = shift;
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55 my $start = shift;
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56 my $len = shift;
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57
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58 #calculate the offset and start in the compressed sequence
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59 my $comp_start = ($start-1 >> 2) + 1;
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60 my $comp_len = ($len >> 2) + 2;
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61
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62 my ($bvector, $nline);
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63
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64 my $sth = $self->prepare(
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65 "SELECT SUBSTRING( d.sequence, ?, ?), n_line
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66 FROM dnac d
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67 WHERE d.seq_region_id = ?");
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68 $sth->bind_param(1,$comp_start,SQL_INTEGER);
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69 $sth->bind_param(2,$comp_len ,SQL_INTEGER);
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70 $sth->bind_param(3,$seq_region_id,SQL_INTEGER);
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71 $sth->execute();
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72 $sth->bind_columns(\$bvector, \$nline);
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73 $sth->fetch();
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74 $sth->finish();
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75
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76 #convert sequence from binary string to 0123 string
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77 my $bitlen = length($bvector) << 2;
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78 my $str = '';
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79 for(my $i=0; $i < $bitlen; $i++) {
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80 $str .= vec($bvector, $i, 2);
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81 }
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82
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83 #convert from 0123 to ACTG
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84 $str =~ tr/0123/ACTG/;
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85
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86 $str = substr($str, ($start-1)%4, $len);
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87
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88 #expand the nlines and place them back in the sequence
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89 my @nlines = split(/:/, $nline);
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90 foreach my $nl (@nlines) {
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91 my ($offset,$char,$nlen) = $nl =~ /(\d+)(\D)(\d+)/;
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92
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93 #skip nlines entirely out of range
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94 next if(($offset+$nlen-1) < $start || $offset > ($start+$len-1));
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95
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96 #obtain relative offset into requested region
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97 $offset = $offset - $start + 1;
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98
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99 #nlines that partially overlap requested region have to be shrunk
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100 if($offset < 1) {
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101 $nlen = $nlen - (1-$offset);
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102 $offset = 1;
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103 }
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104 if($offset + $nlen > $start+$len) {
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105 $nlen = $len - $offset + 1;
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106 }
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107
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108 substr($str,$offset-1,$nlen) = $char x $nlen;
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109 }
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110
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111 return \$str;
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112 }
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113
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114
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115 =head2 store
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116
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117 Arg [1] : string $seq_region_id the id of the sequence region this dna
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118 will be associated with.
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119 Arg [2] : string reference $sequence the dna sequence to be stored in
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120 the database
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121 Example : $dbID = $seq_adaptor->store(12,\'ACTGGGTACCAAACAAACACAACA');
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122 Description: stores a dna sequence in the databases dna table and returns the
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123 database identifier for the new record.
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124 Returntype : int
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125 Exceptions : none
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126 Caller : Bio::EnsEMBL::DBSQL::RawContigAdaptor::store
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127 Status : Stable
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128
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129 =cut
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130
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131 sub store {
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132 my ($self, $seq_region_id, $sequence) = @_;
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133
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134 if(!$seq_region_id) {
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135 throw('seq_region_id is required');
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136 }
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137
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138 $sequence = uc($sequence);
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139
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140 my $bvector = '';
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141
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142 #convert sequence to 0s,1s,2s and 3s
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143 $sequence =~ tr/ACTG/0123/;
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144
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145 #nlines cover sequence which is not ACTG such as N
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146 #nline format is a set of colon delimited int, char, int triplets:
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147 #<offset><code><length>
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148 my($nline_char,$nline_len,$nline_off);
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149 my @nlines;
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150
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151 my $len = length($sequence);
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152 for(my $i=0; $i < $len; $i++) {
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153 my $char = substr($sequence,$i,1);
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154
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155 #quickly check if this character was an A,C,T or G (and was converted to
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156 # a 0,1,2,3)
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157 if($char =~ /[0-3]/) {
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158 vec($bvector, $i,2) = $char;
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159 if($nline_char) {
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160 #end of an nline
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161 push @nlines, "$nline_off$nline_char$nline_len";
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162 $nline_char = undef;
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163 $nline_len = 0;
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164 $nline_off = 0;
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165 }
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166 } else {
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167 #this was not an ACTG
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168 if($nline_char) {
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169 if($nline_char eq $char) {
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170 #continuation of an nline
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171 $nline_len++;
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172 } else {
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173 #end of a previous nline and start of a new one
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174 push @nlines, "$nline_off$nline_char$nline_len";
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175 $nline_char = $char;
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176 $nline_len = 1;
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177 $nline_off = $i+1;
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178 }
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179 } else {
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180 #start of a new nline
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181 $nline_char = $char;
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182 $nline_len = 1;
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183 $nline_off = $i+1;
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184 }
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185 $char = 0; #need to put numeric val into bitvector despite nline
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186 }
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187
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188 vec($bvector, $i,2) = $char;
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189 }
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190
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191 my $nline = join(':', @nlines);
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192 my $statement = $self->prepare(
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193 "INSERT INTO dnac(seq_region_id, sequence, n_line) VALUES(?,?,?)");
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194
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195 $statement->bind_param(1,$seq_region_id,SQL_INTEGER);
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196 $statement->bind_param(2,$bvector,SQL_BLOB);
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197 $statement->bind_param(3,$nline,SQL_LONGVARCHAR);
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198 $statement->execute();
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199
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200 $statement->finish();
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201 return;
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202 }
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203
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204
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205 1;
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