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1 # $Id: Exon.pm,v 1.10 2002/10/22 07:38:48 lapp Exp $
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2 #
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3 # BioPerl module for Bio::Tools::Prediction::Exon
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4 #
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5 # Cared for by Hilmar Lapp <hlapp@gmx.net>
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6 #
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7 # Copyright Hilmar Lapp
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8 #
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9 # You may distribute this module under the same terms as perl itself
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10
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11 # POD documentation - main docs before the code
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12
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13 =head1 NAME
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14
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15 Bio::Tools::Prediction::Exon - A predicted exon feature
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16
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17 =head1 SYNOPSIS
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18
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19 See documentation of methods.
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20
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21 =head1 DESCRIPTION
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22
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23 A feature representing a predicted exon. This class actually inherits
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24 off Bio::SeqFeature::Gene::Exon and therefore has all that
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25 functionality (also implements Bio::SeqFeatureI), plus a few methods
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26 supporting predicted features, like various scores and a
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27 significance. Even though these were inspired by GenScan results, at
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28 least a subset should be generally useable for exon prediction
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29 results.
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30
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31 =head1 FEEDBACK
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32
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33 =head2 Mailing Lists
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34
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35 User feedback is an integral part of the evolution of this
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36 and other Bioperl modules. Send your comments and suggestions preferably
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37 to one of the Bioperl mailing lists.
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38 Your participation is much appreciated.
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39
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40 bioperl-l@bioperl.org - General discussion
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41 http://bio.perl.org/MailList.html - About the mailing lists
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42
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43 =head2 Reporting Bugs
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44
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45 Report bugs to the Bioperl bug tracking system to help us keep track
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46 the bugs and their resolution.
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47 Bug reports can be submitted via email or the web:
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48
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49 bioperl-bugs@bio.perl.org
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50 http://bugzilla.bioperl.org/
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51
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52 =head1 AUTHOR - Hilmar Lapp
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53
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54 Email hlapp@gmx.net
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55
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56 Describe contact details here
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57
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58 =head1 APPENDIX
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59
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60 The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
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61
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62 =cut
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63
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64
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65 # Let the code begin...
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66
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67
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68 package Bio::Tools::Prediction::Exon;
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69 use vars qw(@ISA);
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70 use strict;
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71
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72 use Bio::SeqFeature::Gene::Exon;
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73
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74 @ISA = qw(Bio::SeqFeature::Gene::Exon);
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75
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76 sub new {
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77 my($class,@args) = @_;
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78
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79 my $self = $class->SUPER::new(@args);
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80
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81 my ($primary) = $self->_rearrange([qw(PRIMARY)],@args);
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82
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83 return $self;
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84 }
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85
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86
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87 =head2 predicted_cds
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88
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89 Title : predicted_cds
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90 Usage : $predicted_cds_dna = $exon->predicted_cds();
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91 $exon->predicted_cds($predicted_cds_dna);
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92 Function: Get/Set the CDS (coding sequence) as predicted by a program.
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93
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94 This method is independent of an attached_seq. There is no
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95 guarantee whatsoever that the returned CDS has anything to do
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96 (e.g., matches) with the sequence covered by the exons as annotated
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97 through this object.
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98
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99 Example :
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100 Returns : A Bio::PrimarySeqI implementing object holding the DNA sequence
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101 defined as coding by a prediction of a program.
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102 Args : On set, a Bio::PrimarySeqI implementing object holding the DNA
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103 sequence defined as coding by a prediction of a program.
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104
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105 =cut
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106
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107 sub predicted_cds {
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108 my ($self, $cds) = @_;
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109
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110 if(defined($cds)) {
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111 $self->{'_predicted_cds'} = $cds;
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112 }
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113 return $self->{'_predicted_cds'};
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114 }
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115
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116 =head2 predicted_protein
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117
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118 Title : predicted_protein
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119 Usage : $predicted_protein_seq = $exon->predicted_protein();
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120 $exon->predicted_protein($predicted_protein_seq);
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121 Function: Get/Set the protein translation as predicted by a program.
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122
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123 This method is independent of an attached_seq. There is no
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124 guarantee whatsoever that the returned translation has anything to
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125 do with the sequence covered by the exons as annotated
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126 through this object, or the sequence returned by predicted_cds(),
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127 although it should usually be just the standard translation.
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128
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129 Example :
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130 Returns : A Bio::PrimarySeqI implementing object holding the protein
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131 translation as predicted by a program.
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132 Args : On set, a Bio::PrimarySeqI implementing object holding the protein
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133 translation as predicted by a program.
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134
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135 =cut
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136
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137 sub predicted_protein {
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138 my ($self, $aa) = @_;
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139
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140 if(defined($aa)) {
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141 $self->{'_predicted_aa'} = $aa;
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142 }
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143 return $self->{'_predicted_aa'};
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144 }
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145
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146 =head2 significance
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147
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148 Title : significance
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149 Usage : $evalue = $obj->significance();
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150 $obj->significance($evalue);
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151 Function:
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152 Returns :
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153 Args :
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154
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155
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156 =cut
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157
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158 sub significance {
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159 my ($self, $value) = @_;
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160
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161 return $self->_tag_value('signif', $value);
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162 }
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163
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164 =head2 start_signal_score
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165
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166 Title : start_signal_score
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167 Usage : $sc = $obj->start_signal_score();
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168 $obj->start_signal_score($evalue);
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169 Function: Get/Set a score for the exon start signal (acceptor splice site
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170 or initiation signal).
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171 Returns :
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172 Args :
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173
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174
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175 =cut
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176
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177 sub start_signal_score {
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178 my ($self, $value) = @_;
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179
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180 return $self->_tag_value('AccScore', $value);
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181 }
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182
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183 =head2 end_signal_score
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184
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185 Title : end_signal_score
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186 Usage : $sc = $obj->end_signal_score();
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187 $obj->end_signal_score($evalue);
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188 Function: Get/Set a score for the exon end signal (donor splice site
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189 or termination signal).
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190 Returns :
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191 Args :
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192
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193
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194 =cut
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195
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196 sub end_signal_score {
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197 my ($self, $value) = @_;
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198
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199 return $self->_tag_value('DonScore', $value);
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200 }
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201
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202 =head2 coding_signal_score
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203
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204 Title : coding_signal_score
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205 Usage : $sc = $obj->coding_signal_score();
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206 $obj->coding_signal_score($evalue);
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207 Function: Get/Set a score for the exon coding signal (e.g., coding potential).
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208 Returns :
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209 Args :
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210
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211
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212 =cut
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213
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214 sub coding_signal_score {
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215 my ($self, $value) = @_;
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216
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217 return $self->_tag_value('CodScore', $value);
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218 }
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219
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220 #
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221 # Everything else is just inherited from SeqFeature::Generic.
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222 #
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223
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224 1;
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