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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 =head1 NAME
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20
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21 Bio::EnsEMBL::Compara::DnaFrag - Defines the DNA sequences used in the database.
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22
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23 =head1 SYNOPSIS
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24
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25 use Bio::EnsEMBL::Compara::DnaFrag;
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26 my $dnafrag = new Bio::EnsEMBL::Compara::DnaFrag(
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27 -dbID => 1,
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28 -adaptor => $dnafrag_adaptor,
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29 -length => 256,
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30 -name => "19",
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31 -genome_db => $genome_db,
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32 -coord_system_name => "chromosome"
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33 );
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34
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35
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36 SET VALUES
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37 $dnafrag->dbID(1);
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38 $dnafrag->adaptor($dnafrag_adaptor);
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39 $dnafrag->length(256);
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40 $dnafrag->genome_db($genome_db);
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41 $dnafrag->genome_db_id(123);
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42 $dnafrag->coord_system_name("chromosome");
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43 $dnafrag->name("19");
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44
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45 GET VALUES
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46 $dbID = $dnafrag->dbID;
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47 $dnafrag_adaptor = $dnafrag->adaptor;
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48 $length = $dnafrag->length;
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49 $genome_db = $dnafrag->genome_db;
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50 $genome_db_id = $dnafrag->genome_db_id;
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51 $coord_system_name = $dnafrag->coord_system_name;
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52 $name = $dnafrag->name;
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53
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54 =head1 DESCRIPTION
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55 The DnaFrag object stores information on the toplevel sequences such as the name, coordinate system, length and species.
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56
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57 =head1 OBJECT ATTRIBUTES
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58
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59 =over
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60
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61 =item dbID
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62
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63 corresponds to dnafrag.dnafrag_id
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64
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65 =item adaptor
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66
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67 Bio::EnsEMBL::Compara::DBSQL::DnaFragAdaptor object to access DB
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68
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69 =item length
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70
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71 corresponds to dnafrag.length
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72
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73 =item genome_db_id
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74
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75 corresponds to dnafrag.genome_db_id
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76
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77 =item genome_db
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78
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79 Bio::EnsEMBL::Compara::GenomeDB object corresponding to genome_db_id
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80
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81 =item coord_system_name
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82
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83 corresponds to dnafrag.coord_system_name
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84
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85 =item name
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86
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87 corresponds to dnafrag.name
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88
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89 =back
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90
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91 =head1 APPENDIX
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92
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93 The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
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94
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95 =cut
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96
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97
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98 # Let the code begin...
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99
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100
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101 package Bio::EnsEMBL::Compara::DnaFrag;
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102
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103 use strict;
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104 use Bio::EnsEMBL::Utils::Exception qw(deprecate throw);
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105 use Bio::EnsEMBL::Utils::Argument;
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106
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107 =head2 new
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108
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109 Arg [-DBID] : (opt.) int $dbID (the database internal ID for this object)
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110 Arg [-ADAPTOR]
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111 : (opt.) Bio::EnsEMBL::Compara::DBSQL::DnaFragAdaptor $adaptor
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112 (the adaptor for connecting to the database)
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113 Arg [-LENGTH]:(opt.) int $length (the length of this dnafrag)
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114 Arg [-NAME]: (opt.) string $name (the name of this dnafrag)
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115 Arg [-GENOME_DB]
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116 :(opt.) Bio::EnsEMBL::Compara::GenomeDB $genome_db (the
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117 genome_db object representing the species of this dnafrag)
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118 Arg [-GENOME_DB_ID]
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119 :(opt.) int $genome_db_id (the database internal for the
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120 genome_db)
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121 Arg [-COORD_SYSTEM_NAME]
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122 :(opt.) string $coord_system_name (the name of the toplevel
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123 coordinate system of the dnafrag eg 'chromosome', 'scaffold')
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124 Example : my $dnafrag = new Bio::EnsEMBL::Compara::DnaFrag(
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125 -length 247249719,
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126 -name "1",
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127 -genome_db $genome_db,
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128 -coord_system_name "chromosome");
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129 Example : my $dnafrag = new Bio::EnsEMBL::Compara::DnaFrag(
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130 -length 247249719,
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131 -name "1",
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132 -genome_db_id 22,
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133 -coord_system_name "chromosome");
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134 Description: Creates a new DnaFrag object
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135 Returntype : Bio::EnsEMBL::Compara::DnaFrag
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136 Exceptions : none
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137 Caller : general
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138 Status : Stable
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139
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140 =cut
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141
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142
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143 sub new {
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144 my($class,@args) = @_;
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145
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146 my $self = {};
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147
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148 bless $self,$class;
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149
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150 # my ($name,$contig,$genomedb,$type,$adaptor,$dbID) =
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151 # rearrange([qw(NAME CONTIG GENOMEDB TYPE ADAPTOR DBID)],@args);
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152 # if ( defined $contig) {
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153 # $self->contig($contig);
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154 # }
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155
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156 my ($dbID, $adaptor, $length, $name, $genome_db, $genome_db_id, $coord_system_name, $is_reference,
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157 $start, $end, $genomedb, $type
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158 ) =
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159 rearrange([qw(DBID ADAPTOR LENGTH NAME GENOME_DB GENOME_DB_ID COORD_SYSTEM_NAME IS_REFERENCE
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160 START END
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161 )],@args);
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162
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163 $self->dbID($dbID) if (defined($dbID));
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164 $self->adaptor($adaptor) if (defined($adaptor));
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165 $self->length($length) if (defined($length));
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166 $self->name($name) if (defined($name));
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167 $self->genome_db($genome_db) if (defined($genome_db));
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168 $self->genome_db_id($genome_db_id) if (defined($genome_db_id));
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169 $self->coord_system_name($coord_system_name) if (defined($coord_system_name));
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170 $self->is_reference($is_reference) if (defined($is_reference));
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171
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172 ###################################################################
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173 ## Support for backwards compatibility
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174 $self->start($start) if (defined($start));
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175 $self->end($end) if (defined($end));
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176 ##
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177 ###################################################################
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178
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179 return $self;
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180 }
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181
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182 =head2 new_fast
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183
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184 Arg [1] : hash reference $hashref
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185 Example : none
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186 Description: This is an ultra fast constructor which requires knowledge of
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187 the objects internals to be used.
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188 Returntype :
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189 Exceptions : none
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190 Caller :
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191 Status : Stable
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192
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193 =cut
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194
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195 sub new_fast {
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196 my $class = shift;
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197 my $hashref = shift;
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198
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199 return bless $hashref, $class;
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200 }
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201
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202 =head2 dbID
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203
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204 Arg [1] : int $dbID
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205 Example : $dbID = $dnafrag->dbID()
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206 Example : $dnafrag->dbID(1)
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207 Function : get/set dbID attribute.
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208 Returns : integer
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209 Exeption : none
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210 Caller : $object->dbID
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211 Status : Stable
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212
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213 =cut
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214
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215 sub dbID {
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216 my ($self, $dbID) = @_;
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217
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218 if (defined($dbID)) {
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219 $self->{'dbID'} = $dbID;
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220 }
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221
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222 return $self->{'dbID'};
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223 }
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224
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225
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226 =head2 adaptor
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227
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228 Arg [1] : Bio::EnsEMBL::Compara::DBSQL::DnaFragAdaptor $dnafrag_adaptor
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229 Example : $dnafrag_adaptor = $dnafrag->adaptor()
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230 Example : $dnafrag->adaptor($dnafrag_adaptor)
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231 Function : get/set adaptor attribute.
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232 Returns : Bio::EnsEMBL::Compara::DBSQL::DnaFragAdaptor object
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233 Exeption : thrown if argument is not a Bio::EnsEMBL::Compara::DBSQL::DnaFragAdaptor
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234 object
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235 Caller : $object->adaptor
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236 Status : Stable
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237
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238 =cut
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239
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240 sub adaptor {
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241 my ($self, $adaptor) = @_;
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242
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243 if (defined($adaptor)) {
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244 throw("[$adaptor] must be a Bio::EnsEMBL::Compara::DBSQL::DnaFragAdaptor object")
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245 unless ($adaptor->isa("Bio::EnsEMBL::Compara::DBSQL::DnaFragAdaptor"));
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246 $self->{'adaptor'} = $adaptor;
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247 }
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248
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249 return $self->{'adaptor'};
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250 }
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251
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252
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253 =head2 length
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254
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255 Arg [1] : int $length
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256 Example : $length = $dnafrag->length()
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257 Example : $dnafrag->length(256)
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258 Function : get/set length attribute. Use 0 as argument to reset this attribute.
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259 Returns : integer
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260 Exeption : none
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261 Caller : $object->length
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262 Status : Stable
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263
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264 =cut
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265
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266 sub length {
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267 my ($self, $length) = @_;
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268
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269 if (defined($length)) {
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270 $self->{'length'} = ($length or undef);
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271 }
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272
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273 return $self->{'length'};
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274 }
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275
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276
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277 =head2 name
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278
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279 Arg [1] : string $name
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280 Example : $name = $dnafrag->name()
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281 Example : $dnafrag->name("19")
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282 Function : get/set name attribute. Use "" as argument to reset this attribute.
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283 Returns : string
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284 Exeption : none
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285 Caller : $object->name
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286 Status : Stable
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287
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288 =cut
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289
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290 sub name {
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291 my ($self, $name) = @_;
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292
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293 if (defined($name)) {
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294 $self->{'name'} = ($name or undef);
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295 }
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296
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297 return $self->{'name'};
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298 }
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299
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300
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301 =head2 genome_db
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302
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303 Arg [1] : Bio::EnsEMBL::Compara::GenomeDB $genome_db
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304 Example : $genome_db = $dnafrag->genome_db()
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305 Example : $dnafrag->genome_db($genome_db)
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306 Function : get/set genome_db attribute. If no argument is given and the genome_db
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307 is not defined, it tries to get the data from other sources like the
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308 database using the genome_db_id.
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309 Returns : Bio::EnsEMBL::Compara::GenomeDB object
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310 Exeption : thrown if argument is not a Bio::EnsEMBL::Compara::GenomeDB
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311 object
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312 Caller : $object->genome_db
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313 Status : Stable
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314
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315 =cut
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316
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317 sub genome_db {
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318 my ($self, $genome_db) = @_;
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319
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320 if (defined($genome_db)) {
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321 throw("[$genome_db] must be a Bio::EnsEMBL::Compara::GenomeDB object")
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322 unless ($genome_db and $genome_db->isa("Bio::EnsEMBL::Compara::GenomeDB"));
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323 if ($genome_db->dbID and defined($self->genome_db_id)) {
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324 throw("dbID of genome_db object does not match previously defined".
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325 " genome_db_id. If you want to override this".
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326 " Bio::EnsEMBL::Compara::GenomeDB object, you can reset the ".
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327 "genome_db_id using \$dnafrag->genome_db_id(0)")
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328 unless ($genome_db->dbID == $self->genome_db_id);
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329 }
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330 $self->{'genome_db'} = $genome_db;
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331
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332 } elsif (!defined($self->{'genome_db'})) {
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333 # Try to get data from other sources
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334 if (defined($self->{'genome_db_id'}) and defined($self->{'adaptor'})) {
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335 $self->{'genome_db'} =
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336 $self->{'adaptor'}->db->get_GenomeDBAdaptor->fetch_by_dbID($self->{'genome_db_id'});
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337 }
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338 }
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339
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340 return $self->{'genome_db'};
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341 }
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342
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343
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344 =head2 genome_db_id
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345
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346 Arg [1] : int $genome_db_id
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347 Example : $genome_db_id = $dnafrag->genome_db_id()
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348 Example : $dnafrag->genome_db_id(123)
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349 Function : get/set genome_db_id attribute. If no argument is given and the genome_db_id
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350 is not defined, it tries to get the data from other sources like the
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351 corresponding Bio::EnsEMBL::Compara::GenomeDB object. Use 0 as argument to
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352 clear this attribute.
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353 Returns : integer
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354 Exeption : none
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355 Caller : $object->genome_db_id
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356 Status : Stable
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357
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358 =cut
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359
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360 sub genome_db_id {
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361 my ($self, $genome_db_id) = @_;
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362
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363 if (defined($genome_db_id)) {
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364 if (defined($self->genome_db) and $genome_db_id) {
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365 if (defined($self->genome_db->dbID)) {
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366 throw("genome_db_id does not match previously defined".
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367 " dbID of genome_db object.")
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368 unless ($genome_db_id == $self->genome_db->dbID);
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369 } else {
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370 $self->genome_db->dbID($genome_db_id);
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371 }
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372 }
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373 $self->{'genome_db_id'} = ($genome_db_id or undef);
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374
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375 } elsif (!defined($self->{'genome_db_id'})) {
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376 # Try to get data from other sources
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377 if (defined($self->{'genome_db'})) {
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378 # From the dbID of the corresponding Bio::EnsEMBL::Compara::GenomeDB object
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379 $self->{'genome_db_id'} = $self->{'genome_db'}->dbID;
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380 }
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381 }
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382
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383 return $self->{'genome_db_id'};
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384 }
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385
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386
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387 =head2 coord_system_name
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388
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389 Arg [1] : string $coord_system_name
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390 Example : $coord_system_name = $dnafrag->coord_system_name()
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391 Example : $dnafrag->coord_system_name("chromosome")
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392 Function : get/set coord_system_name attribute. Use "" or 0 as argument to
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393 clear this attribute.
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394 Returns : string
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395 Exeption : none
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396 Caller : $object->coord_system_name
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397 Status : Stable
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398
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399 =cut
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400
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401 sub coord_system_name {
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402 my ($self, $coord_system_name) = @_;
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403
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404 if (defined($coord_system_name)) {
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405 $self->{'coord_system_name'} = ($coord_system_name or undef);
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406 }
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407
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408 return $self->{'coord_system_name'};
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409 }
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410
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411
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412 =head2 is_reference
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413
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414 Arg [1] : bool $is_reference
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415 Example : $is_reference = $dnafrag->is_reference()
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416 Example : $dnafrag->is_reference(1)
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417 Function : get/set is_reference attribute. The default value
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418 is 1 (TRUE).
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419 Returns : bool
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420 Exeption : none
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421 Caller : $object->is_reference
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422 Status : Stable
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423
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424 =cut
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425
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426 sub is_reference {
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427 my ($self, $is_reference) = @_;
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428
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429 if (defined($is_reference)) {
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430 $self->{'is_reference'} = $is_reference;
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431 }
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432 if (!defined($self->{'is_reference'})) {
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433 $self->{'is_reference'} = 1;
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434 }
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435
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436 return $self->{'is_reference'};
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437 }
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438
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439
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440 =head2 slice
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441
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442 Arg 1 : -none-
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443 Example : $slice = $dnafrag->slice;
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444 Description: Returns the Bio::EnsEMBL::Slice object corresponding to this
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445 Bio::EnsEMBL::Compara::DnaFrag object.
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446 Returntype : Bio::EnsEMBL::Slice object
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447 Exceptions : warns when the corresponding Bio::EnsEMBL::Compara::GenomeDB,
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448 coord_system_name, name or Bio::EnsEMBL::DBSQL::DBAdaptor
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449 cannot be retrieved and returns undef.
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450 Caller : $object->methodname
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451 Status : Stable
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452
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453 =cut
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454
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455 sub slice {
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456 my ($self) = @_;
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457
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458 unless (defined $self->{'_slice'}) {
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459 if (!defined($self->genome_db)) {
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|
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460 warn "Cannot get the Bio::EnsEMBL::Compara::GenomeDB object corresponding to [".$self."]";
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461 return undef;
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462 }
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463 if (!defined($self->coord_system_name)) {
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464 warn "Cannot get the coord_system_name corresponding to [".$self."]";
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465 return undef;
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|
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466 }
|
|
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467 if (!defined($self->name)) {
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|
|
468 warn "Cannot get the name corresponding to [".$self."]";
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|
|
469 return undef;
|
|
|
470 }
|
|
|
471 my $dba = $self->genome_db->db_adaptor;
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|
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472 if (!defined($dba)) {
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|
|
473 warn "Cannot get the Bio::EnsEMBL::DBSQL::DBAdaptor corresponding to [".$self->genome_db->name."]";
|
|
|
474 return undef;
|
|
|
475 }
|
|
|
476 $dba->dbc->reconnect_when_lost(1);
|
|
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477
|
|
|
478 $self->{'_slice'} = $dba->get_SliceAdaptor->fetch_by_region($self->coord_system_name, $self->name);
|
|
|
479 }
|
|
|
480
|
|
|
481 return $self->{'_slice'};
|
|
|
482 }
|
|
|
483
|
|
|
484
|
|
|
485 =head2 display_id
|
|
|
486
|
|
|
487 Args : none
|
|
|
488 Example : my $id = $dnafrag->display_id;
|
|
|
489 Description: returns string describing this chunk which can be used
|
|
|
490 as display_id of a Bio::Seq object or in a fasta file.
|
|
|
491 Uses dnafrag information in addition to start and end.
|
|
|
492 Returntype : string
|
|
|
493 Exceptions : none
|
|
|
494 Caller : general
|
|
|
495 Status : Stable
|
|
|
496
|
|
|
497 =cut
|
|
|
498
|
|
|
499 sub display_id {
|
|
|
500 my $self = shift;
|
|
|
501
|
|
|
502 return "" unless($self->genome_db);
|
|
|
503 my $id = $self->genome_db->taxon_id. ".".
|
|
|
504 $self->genome_db->dbID. ":".
|
|
|
505 $self->coord_system_name.":".
|
|
|
506 $self->name;
|
|
|
507 return $id;
|
|
|
508 }
|
|
|
509
|
|
|
510
|
|
|
511 #####################################################################
|
|
|
512 #####################################################################
|
|
|
513
|
|
|
514 =head1 DEPRECATED METHODS
|
|
|
515
|
|
|
516 Bio::EnsEMBL::Compara::DnaFrag::start and Bio::EnsEMBL::Compara::DnaFrag::end
|
|
|
517 methods are no longer used. All Bio::EnsEMBL::Compara::DnaFrag objects start
|
|
|
518 in 1. Start and end coordinates have been replaced by length attribute. Please,
|
|
|
519 use Bio::EnsEMBL::Compara::DnaFrag::length method to access it.
|
|
|
520
|
|
|
521 Bio::EnsEMBL::Compara::DnaFrag::genomedb has been renamed
|
|
|
522 Bio::EnsEMBL::Compara::DnaFrag::genome_db.
|
|
|
523
|
|
|
524 Bio::EnsEMBL::Compara::DnaFrag::type has been renamed
|
|
|
525 Bio::EnsEMBL::Compara::DnaFrag::coord_system_name.
|
|
|
526
|
|
|
527 =cut
|
|
|
528
|
|
|
529 #####################################################################
|
|
|
530 #####################################################################
|
|
|
531
|
|
|
532
|
|
|
533
|
|
|
534
|
|
|
535 =head2 start [DEPRECATED]
|
|
|
536
|
|
|
537 DEPRECATED! All Bio::EnsEMBL::Compara::DnaFrag objects start in 1
|
|
|
538
|
|
|
539 Arg [1] : int
|
|
|
540 Example : $dnafrag->start(1);
|
|
|
541 Description: Getter/Setter for the start attribute
|
|
|
542 Returntype : int
|
|
|
543 Exceptions : thrown when trying to set a starting position different from 1
|
|
|
544 Caller : general
|
|
|
545
|
|
|
546 =cut
|
|
|
547
|
|
|
548 sub start {
|
|
|
549 my ($self,$value) = @_;
|
|
|
550
|
|
|
551 deprecate("All Bio::EnsEMBL::Compara::DnaFrag objects start in 1");
|
|
|
552 if (defined($value) and ($value != 1)) {
|
|
|
553 throw("Trying to set a start value different from 1!\n".
|
|
|
554 "All Bio::EnsEMBL::Compara::DnaFrag objects start in 1");
|
|
|
555 }
|
|
|
556
|
|
|
557 return 1;
|
|
|
558 }
|
|
|
559
|
|
|
560
|
|
|
561
|
|
|
562 =head2 end [DEPRECATED]
|
|
|
563
|
|
|
564 DEPRECATED! Use Bio::EnsEMBL::Compara::DnaFrag->length() method instead
|
|
|
565
|
|
|
566 Arg [1] : int $end
|
|
|
567 Example : $dnafrag->end(42);
|
|
|
568 Description: Getter/Setter for the start attribute
|
|
|
569 Returntype : int
|
|
|
570 Exceptions : none
|
|
|
571 Caller : general
|
|
|
572
|
|
|
573 =cut
|
|
|
574
|
|
|
575 sub end {
|
|
|
576 my ($self, $end) = @_;
|
|
|
577 deprecate("Use Bio::EnsEMBL::Compara::DnaFrag->length() method instead");
|
|
|
578
|
|
|
579 return $self->length($end);
|
|
|
580 }
|
|
|
581
|
|
|
582
|
|
|
583 1;
|
|
|
584
|
|
|
585
|
