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1 # $Id: RichSeq.pm,v 1.9 2002/11/11 18:16:31 lapp Exp $
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2 #
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3 # BioPerl module for Bio::Seq::RichSeq
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4 #
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5 # Cared for by Ewan Birney <birney@ebi.ac.uk>
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6 #
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7 # Copyright Ewan Birney
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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::Seq::RichSeq - Module implementing a sequence created from a rich
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16 sequence database entry
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17
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18 =head1 SYNOPSIS
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19
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20 See Bio::Seq::RichSeqI and documentation of methods.
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21
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22 =head1 DESCRIPTION
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23
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24 This module implements Bio::Seq::RichSeqI, an interface for sequences
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25 created from or created for entries from/of rich sequence databanks,
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26 like EMBL, GenBank, and SwissProt. Methods added to the Bio::SeqI
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27 interface therefore focus on databank-specific information. Note that
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28 not every rich databank format may use all of the properties provided.
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29
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30 =head1 Implemented Interfaces
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31
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32 This class implementes the following interfaces.
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33
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34 =over 4
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35
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36 =item Bio::Seq::RichSeqI
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37
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38 Note that this includes implementing Bio::PrimarySeqI and Bio::SeqI.
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39
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40 =item Bio::IdentifiableI
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41
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42 =item Bio::DescribableI
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43
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44 =item Bio::AnnotatableI
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45
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46 =back
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47
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48 =head1 FEEDBACK
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49
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50 =head2 Mailing Lists
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51
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52 User feedback is an integral part of the evolution of this
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53 and other Bioperl modules. Send your comments and suggestions preferably
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54 to one of the Bioperl mailing lists.
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55 Your participation is much appreciated.
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56
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57 bioperl-l@bioperl.org - General discussion
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58 http://bio.perl.org/MailList.html - About the mailing lists
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59
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60 =head2 Reporting Bugs
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61
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62 Report bugs to the Bioperl bug tracking system to help us keep track
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63 the bugs and their resolution.
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64 Bug reports can be submitted via email or the web:
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65
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66 bioperl-bugs@bio.perl.org
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67 http://bugzilla.bioperl.org/
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68
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69 =head1 AUTHOR - Ewan Birney
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70
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71 Email birney@ebi.ac.uk
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72
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73 Describe contact details here
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74
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75 =head1 APPENDIX
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76
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77 The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
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78
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79 =cut
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80
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81
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82 # Let the code begin...
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83
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84
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85 package Bio::Seq::RichSeq;
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86 use vars qw($AUTOLOAD @ISA);
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87 use strict;
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88
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89 # Object preamble - inherits from Bio::Root::Object
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90
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91 use Bio::Seq;
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92 use Bio::Seq::RichSeqI;
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93
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94 @ISA = qw(Bio::Seq Bio::Seq::RichSeqI);
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95
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96
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97 =head2 new
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98
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99 Title : new
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100 Usage : $seq = Bio::Seq::RichSeq->new( -seq => 'ATGGGGGTGGTGGTACCCT',
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101 -id => 'human_id',
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102 -accession_number => 'AL000012',
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103 );
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104
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105 Function: Returns a new seq object from
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106 basic constructors, being a string for the sequence
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107 and strings for id and accession_number
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108 Returns : a new Bio::Seq::RichSeq object
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109
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110 =cut
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111
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112 sub new {
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113 # standard new call..
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114 my($caller,@args) = @_;
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115 my $self = $caller->SUPER::new(@args);
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116
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117 $self->{'_dates'} = [];
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118 $self->{'_secondary_accession'} = [];
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119
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120 my ($dates, $xtra, $sv,
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121 $keywords, $pid, $mol,
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122 $division ) = $self->_rearrange([qw(DATES
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123 SECONDARY_ACCESSIONS
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124 SEQ_VERSION
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125 KEYWORDS
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126 PID
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127 MOLECULE
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128 DIVISION
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129 )],
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130 @args);
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131 defined $division && $self->division($division);
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132 defined $mol && $self->molecule($mol);
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133 defined $keywords && $self->keywords($keywords);
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134 defined $sv && $self->seq_version($sv);
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135 defined $pid && $self->pid($pid);
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136
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137 if( defined $dates ) {
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138 if( ref($dates) =~ /array/i ) {
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139 foreach ( @$dates) {
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140 $self->add_date($_);
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141 }
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142 } else {
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143 $self->add_date($dates);
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144 }
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145 }
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146
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147 if( defined $xtra ) {
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148 if( ref($xtra) =~ /array/i ) {
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149 foreach ( @$xtra) {
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150 $self->add_secondary_accession($_);
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151 }
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152 } else {
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153 $self->add_secondary_accession($xtra);
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154 }
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155 }
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156
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157 return $self;
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158 }
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159
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160
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161 =head2 division
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162
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163 Title : division
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164 Usage : $obj->division($newval)
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165 Function:
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166 Returns : value of division
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167 Args : newvalue (optional)
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168
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169
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170 =cut
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171
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172 sub division {
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173 my $obj = shift;
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174 if( @_ ) {
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175 my $value = shift;
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176 $obj->{'_division'} = $value;
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177 }
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178 return $obj->{'_division'};
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179
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180 }
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181
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182 =head2 molecule
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183
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184 Title : molecule
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185 Usage : $obj->molecule($newval)
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186 Function:
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187 Returns : type of molecule (DNA, mRNA)
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188 Args : newvalue (optional)
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189
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190
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191 =cut
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192
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193 sub molecule {
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194 my $obj = shift;
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195 if( @_ ) {
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196 my $value = shift;
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197 $obj->{'_molecule'} = $value;
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198 }
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199 return $obj->{'_molecule'};
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200
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201 }
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202
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203 =head2 add_date
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204
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205 Title : add_date
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206 Usage : $self->add_date($datestr)
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207 Function: adds a date
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208 Example :
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209 Returns : a date string or an array of such strings
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210 Args :
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211
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212
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213 =cut
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214
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215 sub add_date {
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216 my ($self,@dates) = @_;
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217 foreach my $dt ( @dates ) {
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218 push(@{$self->{'_dates'}},$dt);
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219 }
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220 }
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221
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222 =head2 get_dates
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223
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224 Title : get_dates
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225 Usage :
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226 Function:
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227 Example :
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228 Returns : an array of date strings
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229 Args :
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230
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231
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232 =cut
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233
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234 sub get_dates{
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235 my ($self) = @_;
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236 return @{$self->{'_dates'}};
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237 }
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238
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239
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240 =head2 pid
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241
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242 Title : pid
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243 Usage :
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244 Function: Get (and set, depending on the implementation) the PID property
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245 for the sequence.
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246 Example :
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247 Returns : a string
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248 Args :
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249
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250
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251 =cut
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252
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253 sub pid {
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254 my ($self,$pid) = @_;
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255
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256 if(defined($pid)) {
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257 $self->{'_pid'} = $pid;
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258 }
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259 return $self->{'_pid'};
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260 }
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261
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262
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263 =head2 accession
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264
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265 Title : accession
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266 Usage : $obj->accession($newval)
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267 Function: Whilst the underlying sequence object does not
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268 have an accession, so we need one here.
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269
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270 In this implementation this is merely a synonym for
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271 accession_number().
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272 Example :
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273 Returns : value of accession
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274 Args : newvalue (optional)
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275
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276
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277 =cut
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278
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279 sub accession {
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280 my ($obj,@args) = @_;
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281 return $obj->accession_number(@args);
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282 }
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283
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284 =head2 add_secondary_accession
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285
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286 Title : add_secondary_accession
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287 Usage : $self->add_domment($ref)
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288 Function: adds a secondary_accession
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289 Example :
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290 Returns :
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291 Args : a string or an array of strings
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292
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293
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294 =cut
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295
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296 sub add_secondary_accession {
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297 my ($self) = shift;
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298 foreach my $dt ( @_ ) {
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299 push(@{$self->{'_secondary_accession'}},$dt);
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300 }
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301 }
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302
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303 =head2 get_secondary_accessions
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304
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305 Title : get_secondary_accessions
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306 Usage :
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307 Function:
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308 Example :
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309 Returns : An array of strings
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310 Args :
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311
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312
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313 =cut
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314
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315 sub get_secondary_accessions{
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316 my ($self,@args) = @_;
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317 return @{$self->{'_secondary_accession'}};
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318 }
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319
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320 =head2 seq_version
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321
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322 Title : seq_version
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323 Usage : $obj->seq_version($newval)
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324 Function:
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325 Example :
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326 Returns : value of seq_version
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327 Args : newvalue (optional)
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328
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329
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330 =cut
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331
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332 sub seq_version{
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333 my ($obj,$value) = @_;
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334 if( defined $value) {
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335 $obj->{'_seq_version'} = $value;
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336 }
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337 return $obj->{'_seq_version'};
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338
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339 }
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340
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341
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342 =head2 keywords
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343
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344 Title : keywords
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345 Usage : $obj->keywords($newval)
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346 Function:
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347 Returns : value of keywords (a string)
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348 Args : newvalue (optional) (a string)
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349
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350
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351 =cut
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352
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353 sub keywords {
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354 my $obj = shift;
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355 if( @_ ) {
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356 my $value = shift;
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357 $obj->{'_keywords'} = $value;
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358 }
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359 return $obj->{'_keywords'};
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360
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361 }
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362
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363 #
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364 ##
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365 ### Deprecated methods kept for ease of transtion
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366 ##
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367 #
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368
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369 sub each_date {
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370 my ($self) = @_;
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371 $self->warn("Deprecated method... please use get_dates");
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372 return $self->get_dates;
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373 }
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374
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375
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376 sub each_secondary_accession {
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377 my ($self) = @_;
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378 $self->warn("each_secondary_accession - deprecated method. use get_secondary_accessions");
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379 return $self->get_secondary_accessions;
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380
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381 }
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382
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383 sub sv {
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384 my ($obj,$value) = @_;
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385 $obj->warn("sv - deprecated method. use seq_version");
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386 $obj->seq_version($value);
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387 }
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388
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389
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390 1;
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