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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::IdMapping::TinyTranscript - lightweight transcript object
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24
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25 =head1 SYNOPSIS
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26
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27 # fetch a transcript from the db and create a lightweight
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28 # transcript object from it
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29 my $tr = $transcript_adaptor->fetch_by_stable_id('ENST000345437');
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30 my $lightweight_tr =
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31 Bio::EnsEMBL::IdMapping::TinyTranscript->new_fast( [
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32 $tr->dbID, $tr->stable_id,
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33 $tr->version, $tr->created_date,
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34 $tr->modified_date, $tr->start,
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35 $tr->end, $tr->strand,
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36 $tr->length, md5_hex( $tr->spliced_seq ),
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37 ( $tr->is_known ? 1 : 0 ),
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38 ] );
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39
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40 =head1 DESCRIPTION
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41
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42 This is a lightweight transcript object for the stable Id mapping. See
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43 the documentation in TinyFeature for general considerations about its
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44 design.
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45
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46 =head1 METHODS
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47
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48 start
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49 end
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50 strand
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51 length
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52 seq_md5_sum
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53 is_known
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54 add_Translation
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55 translation
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56 add_Exon
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57 get_all_Exons
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58
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59 =cut
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60
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61 package Bio::EnsEMBL::IdMapping::TinyTranscript;
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62
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63 # internal data structure (array indices):
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64 #
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65 # 0-4 see TinyFeature
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66 # 5 start
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67 # 6 end
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68 # 7 strand
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69 # 8 length
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70 # 9 seq_md5_sum
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71 # 10 is_known
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72 # 11 translation
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73 # 12 [exons]
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74 # 13 biotype
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75
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76
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77 use strict;
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78 use warnings;
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79 no warnings 'uninitialized';
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80
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81 use Bio::EnsEMBL::IdMapping::TinyFeature;
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82 our @ISA = qw(Bio::EnsEMBL::IdMapping::TinyFeature);
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83
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84 use Bio::EnsEMBL::Utils::Exception qw(throw warning);
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85
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86
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87 =head2 start
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88
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89 Arg[1] : (optional) Int - the transcript's start coordinate
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90 Description : Getter/setter for the transcript's start coordinate.
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91 Return type : Int
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92 Exceptions : none
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93 Caller : general
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94 Status : At Risk
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95 : under development
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96
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97 =cut
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98
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99 sub start {
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100 my $self = shift;
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101 $self->[5] = shift if (@_);
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102 return $self->[5];
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103 }
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104
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105
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106 =head2 end
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107
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108 Arg[1] : (optional) Int - the transcript's end coordinate
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109 Description : Getter/setter for the transcript's end coordinate.
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110 Return type : Int
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111 Exceptions : none
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112 Caller : general
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113 Status : At Risk
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114 : under development
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115
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116 =cut
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117
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118 sub end {
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119 my $self = shift;
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120 $self->[6] = shift if (@_);
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121 return $self->[6];
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122 }
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123
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124
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125 =head2 strand
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126
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127 Arg[1] : (optional) Int - the transcript's strand
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128 Description : Getter/setter for the transcript's strand.
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129 Return type : Int
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130 Exceptions : none
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131 Caller : general
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132 Status : At Risk
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133 : under development
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134
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135 =cut
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136
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137 sub strand {
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138 my $self = shift;
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139 $self->[7] = shift if (@_);
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140 return $self->[7];
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141 }
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142
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143
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144 =head2 length
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145
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146 Arg[1] : (optional) Int - the transcript's length
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147 Description : Getter/setter for the transcript's length. Note that this is
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148 *not* the distance between start and end, but rather the sum of
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149 the lengths of all exons.
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150 Return type : Int
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151 Exceptions : none
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152 Caller : general
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153 Status : At Risk
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154 : under development
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155
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156 =cut
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157
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158 sub length {
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159 my $self = shift;
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160 $self->[8] = shift if (@_);
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161 return $self->[8];
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162 }
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163
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164
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165 =head2 seq_md5_sum
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166
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167 Arg[1] : (optional) String - the md5 digest of the transcript's sequence
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168 Description : Getter/setter for the md5 digest of the transcript's sequence.
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169 Note that when used as a setter, you are expected to pass a
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170 digest, not the raw sequence (i.e. the digest is not created for
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171 you).
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172 Return type : String
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173 Exceptions : none
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174 Caller : general
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175 Status : At Risk
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176 : under development
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177
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178 =cut
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179
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180 sub seq_md5_sum {
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181 my $self = shift;
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182 $self->[9] = shift if (@_);
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183 return $self->[9];
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184 }
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185
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186
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187 =head2 is_known
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188
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189 Arg[1] : (optional) Boolean - the transcript's "known" status
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190 Description : Getter/setter for the transcript's "known" status.
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191 Return type : Boolean
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192 Exceptions : none
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193 Caller : general
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194 Status : At Risk
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195 : under development
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196
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197 =cut
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198
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199 sub is_known {
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200 my $self = shift;
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201 $self->[10] = shift if (@_);
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202 return $self->[10];
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203 }
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204
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205
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206 =head2 add_Translation
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207
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208 Arg[1] : Bio::EnsEMBL::IdMapping::TinyTranslation $tl - the translation
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209 to add
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210 Example : $tiny_transcript->add_Translation($tiny_translation);
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211 Description : Adds a translation to this transcript.
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212 Return type : none
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213 Exceptions : thrown on wrong or missing argument
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214 Caller : general
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215 Status : At Risk
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216 : under development
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217
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218 =cut
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219
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220 sub add_Translation {
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221 my $self = shift;
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222 my $tl = shift;
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223
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224 unless ($tl && $tl->isa('Bio::EnsEMBL::IdMapping::TinyTranslation')) {
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225 throw('Need a Bio::EnsEMBL::IdMapping::TinyTranslation.');
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226 }
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227
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228 $self->[11] = $tl;
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229 }
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230
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231
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232 =head2 translation
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233
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234 Description : Getter for the transcript's translation.
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235 Return type : Bio::EnsEMBL::IdMapping::TinyTranslation
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236 Exceptions : none
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237 Caller : general
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238 Status : At Risk
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239 : under development
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240
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241 =cut
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242
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243 sub translation {
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244 return $_[0]->[11];
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245 }
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246
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247
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248 =head2 add_Exon
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249
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250 Arg[1] : Bio::EnsEMBL::IdMapping::TinyExon $exon - the exon to add
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251 Example : $tiny_transcript->add_Exon($tiny_exon);
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252 Description : Adds an exon to this transcript.
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253 Return type : none
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254 Exceptions : thrown on wrong or missing argument
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255 Caller : general
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256 Status : At Risk
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257 : under development
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258
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259 =cut
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260
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261 sub add_Exon {
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262 my $self = shift;
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263 my $exon = shift;
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264
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265 unless ($exon && $exon->isa('Bio::EnsEMBL::IdMapping::TinyExon')) {
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266 throw('Need a Bio::EnsEMBL::IdMapping::TinyExon.');
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267 }
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268
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269 push @{ $self->[12] }, $exon;
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270 }
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271
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272
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273 =head2 get_all_Exons
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274
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275 Example : foreach my $exon (@{ $tiny_transcript->get_all_Exons }) {
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276 # do something with exon
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277 }
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278 Description : Returns all exons attached to that transcript.
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279 Return type : Arrayref of Bio::EnsEMBL::IdMapping::TinyExon objects
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280 Exceptions : none
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281 Caller : general
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282 Status : At Risk
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283 : under development
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284
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285 =cut
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286
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287 sub get_all_Exons {
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288 return $_[0]->[12] || [];
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289 }
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290
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291 sub biotype {
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292 my $self = shift;
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293 $self->[13] = shift if (@_);
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294 return $self->[13];
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295 }
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296
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297
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298 1;
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299
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