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1 # $Id: SequenceFamily.pm,v 1.4 2002/12/01 00:34:58 jason Exp $
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2 #
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3 # BioPerl module for Bio::Cluster::SequenceFamily
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4 #
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5 # Cared for by Shawn Hoon <shawnh@fugu-sg.org>
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6 #
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7 # Copyright Shawn Hoon
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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::Cluster::SequenceFamily - Sequence Family object
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16
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17 =head1 SYNOPSIS
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18
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19 use Bio::Cluster::SequenceFamily
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20
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21 use Bio::SeqIO;
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22 use Bio::Cluster::SequenceFamily;
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23
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24 my $file = Bio::Root::IO->catfile('t','data','swiss.dat');
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25 my $seqio= new Bio::SeqIO('-format' => 'swiss',
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26 '-file' => $file);
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27 my @mem;
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28 while(my $seq = $seqio->next_seq){
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29 push @mem, $seq;
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30 }
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31
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32 #create the family
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33 my $family = Bio::Cluster::SequenceFamily->new(-family_id=>"Family_1",
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34 -description=>"Family Description Here",
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35 -annotation_score=>"100",
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36 -members=>\@mem);
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37
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38 #access the family
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39
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40 foreach my $mem ($family->get_members){
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41 print $mem->display_id."\t".$mem->desc."\n";
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42 }
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43
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44 #select members if members have a Bio::Species Object
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45
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46 my @mem = $family->get_members(-binomial=>"Homo sapiens");
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47 @mem = $family->get_members(-ncbi_taxid => 9606);
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48 @mem = $family->get_members(-common_name=>"Human");
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49 @mem = $family->get_members(-species=>"sapiens");
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50 @mem = $family->get_members(-genus=>"Homo");
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51
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52
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53
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54 =head1 DESCRIPTION
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55
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56 This is a simple Family object that may hold any group of object. For more
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57 specific families, one should derive from FamilyI.
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58
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59 =head1 FEEDBACK
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60
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61
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62 =head2 Mailing Lists
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63
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64 User feedback is an integral part of the evolution of this and other
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65 Bioperl modules. Send your comments and suggestions preferably to one
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66 of the Bioperl mailing lists. Your participation is much appreciated.
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67
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68 bioperl-l@bioperl.org - General discussion
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69 http://bio.perl.org/MailList.html - About the mailing lists
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70
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71 =head2 Reporting Bugs
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72
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73 Report bugs to the Bioperl bug tracking system to help us keep track
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74 the bugs and their resolution. Bug reports can be submitted via email
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75 or the web:
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76
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77 bioperl-bugs@bioperl.org
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78 http://bugzilla.bioperl.org/
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79
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80 =head1 AUTHOR - Shawn Hoon
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81
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82 Email shawnh@fugu-sg.org
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83
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84
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85 =head1 APPENDIX
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86
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87
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88 The rest of the documentation details each of the object
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89 methods. Internal methods are usually preceded with a "_".
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90
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91 =cut
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92
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93 # Let the code begin...
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94
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95
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96 package Bio::Cluster::SequenceFamily;
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97
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98 use strict;
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99 use vars qw(@ISA);
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100
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101
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102 use Bio::Root::Root;
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103 use Bio::Cluster::FamilyI;
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104
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105 @ISA = qw(Bio::Root::Root Bio::Cluster::FamilyI);
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106
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107
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108 =head2 new
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109
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110 Title : new
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111 Usage : my $family = Bio::Cluster::SequenceFamily->new(-family_id=>"Family_1",
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112 -description=>"Family Description Here",
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113 -annotation_score=>"100",
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114 -members=>\@mem);
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115 Function: Constructor for SequenceFamily object
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116 Returns : L<Bio::Cluster::SequenceFamily> object
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117
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118 =cut
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119
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120 sub new {
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121 my ($class,@args) = @_;
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122 my $self = $class->SUPER::new(@args);
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123 my ($id,$description,$version,$annot_score,
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124 $family_score,$members) = $self->_rearrange([qw(FAMILY_ID DESCRIPTION VERSION
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125 ANNOTATION_SCORE
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126 FAMILY_SCORE MEMBERS)],@args);
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127 $self->{'_members'} = [];
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128 $id && $self->family_id($id);
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129 $description && $self->description($description);
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130 $version && $self->version($version);
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131 $annot_score && $self->annotation_score($annot_score);
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132 $family_score && $self->family_score($family_score);
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133 $members && $self->add_members($members);
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134
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135 return $self;
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136
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137 }
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138
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139 =head2 version
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140
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141 Title : version
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142 Usage : $family->version("1.0");
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143 Function: get/set for version
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144 Returns : a string version of the family generated.
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145
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146 =cut
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147
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148 sub version{
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149 my ($self,$value) = @_;
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150 if($value){
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151 $self->{'_version'} =$value;
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152 }
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153 return $self->{'_version'};
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154 }
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155
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156 =head2 annotation_score
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157
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158 Title : annotation_score
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159 Usage : $family->annotation_score(100);
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160 Function: get/set for annotation_score which
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161 represent the confidence in which the
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162 consensus description has been assigned
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163 to the family.
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164 Returns : L<Bio::SimpleAlign>
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165
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166 =cut
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167
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168 sub annotation_score{
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169 my ($self,$score) = @_;
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170 if($score){
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171 $self->{'_annotation_score'} = $score;
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172 }
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173 return $self->{'_annotation_score'};
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174 }
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175
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176 =head2 alignment
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177
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178 Title : alignment
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179 Usage : $family->alignment($align);
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180 Function: get/set for an alignment object representing
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181 the multiple alignment of the members of the family.
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182 Returns : L<Bio::SimpleAlign>
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183
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184 =cut
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185
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186 sub alignment {
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187 my ($self,$align) = @_;
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188 if($align){
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189 $self->{'_alignment'} = $align;
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190 }
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191 return $self->{'_alignment'};
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192 }
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193
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194 =head2 tree
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195
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196 Title : tree
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197 Usage : $family->tree($tree);
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198 Function: get/set for an tree object representing
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199 the phylogenetic tree of the family.
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200 Returns : L<Bio::Tree>
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201
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202 =cut
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203
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204 sub tree {
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205 my ($self,$tree) = @_;
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206 if($tree) {
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207 $self->{'_tree'} = $tree;
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208 }
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209 return $self->{'_tree'};
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210 }
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211
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212 =head1 L<Bio::Cluster::FamilyI> methods
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213
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214 =cut
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215
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216 =head2 family_score
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217
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218 Title : family_score
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219 Usage : Bio::Cluster::FamilyI->family_score(95);
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220 Function: get/set for the score of algorithm used to generate
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221 the family if present
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222
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223 This is aliased to cluster_score().
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224
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225 Returns : the score
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226 Args : the score
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227
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228 =cut
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229
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230 sub family_score {
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231 return shift->cluster_score(@_);
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232 }
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233
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234
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235 =head2 family_id
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236
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237 Title : family_id
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238 Usage : $family->family_id("Family_1");
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239 Function: get/set for family id
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240
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241 This is aliased to display_id().
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242
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243 Returns : a string specifying identifier of the family
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244
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245 =cut
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246
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247 sub family_id{
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248 return shift->display_id(@_);
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249 }
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250
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251 =head1 L<Bio::ClusterI> methods
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252
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253 =cut
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254
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255 =head2 display_id
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256
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257 Title : display_id
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258 Usage :
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259 Function: Get/set the display name or identifier for the cluster
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260 Returns : a string
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261 Args : optional, on set the display ID ( a string)
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262
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263 =cut
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264
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265 sub display_id{
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266 my ($self,$id) = @_;
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267 if($id){
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268 $self->{'_cluster_id'} = $id;
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269 }
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270 return $self->{'_cluster_id'};
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271 }
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272
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273 =head2 description
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274
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275 Title : description
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276 Usage : $fam->description("POLYUBIQUITIN")
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277 Function: get/set for the consensus description of the cluster
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278 Returns : the description string
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279 Args : Optional the description string
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280
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281 =cut
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282
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283 sub description{
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284 my ($self,$desc) = @_;
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285 if($desc){
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286 $self->{'_description'} = $desc;
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287 }
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288 return $self->{'_description'};
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289 }
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290
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291 =head2 get_members
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292
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293 Title : get_members
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294 Usage : Valid criteria:
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295 -common_name
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296 -binomial
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297 -ncbi_taxid
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298 -organelle
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299 -genus
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300 $family->get_members(-common_name =>"human");
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301 $family->get_members(-species =>"homo sapiens");
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302 $family->get_members(-ncbi_taxid => 9606);
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303 For now, multiple critieria are ORed.
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304
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305 Will return all members if no criteria are provided.
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306
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307 Function: get members using methods from L<Bio::Species>
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308 the phylogenetic tree of the family.
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309 Returns : an array of objects that are member of this family.
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310
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311 =cut
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312
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313 sub get_members {
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314 my $self = shift;
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315 my @ret;
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316
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317 if(@_) {
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318 my %hash = @_;
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319 foreach my $mem ( @{$self->{'_members'}} ) {
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320 foreach my $key ( keys %hash){
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321 my $method = $key;
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322 $method=~s/-//g;
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323 if($mem->can('species')){
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324 my $species = $mem->species;
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325 $species->can($method) ||
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326 $self->throw("$method is an invalid criteria");
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327 if($species->$method() eq $hash{$key} ){
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328 push @ret, $mem;
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329 }
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330 }
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331 }
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332 }
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333 return @ret;
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334 }
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335 return @{$self->{'_members'}};
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336 }
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337
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338 =head2 size
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339
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340 Title : size
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341 Usage : $fam->size();
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342 Function: get/set for the size of the family,
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343 calculated from the number of members
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344 Returns : the size of the family
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345 Args :
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346
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347 =cut
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348
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349 sub size {
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350 my ($self) = @_;
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351
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352 return scalar(@{$self->{'_members'}});
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353
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354 }
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355
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356 =head2 cluster_score
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357
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358 Title : cluster_score
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359 Usage : $fam->cluster_score(100);
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360 Function: get/set for cluster_score which
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361 represent the score in which the clustering
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362 algorithm assigns to this cluster.
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363 Returns : a number
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364
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365 =cut
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366
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367 sub cluster_score{
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368 my ($self,$score) = @_;
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369 if($score){
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370 $self->{'_cluster_score'} = $score;
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371 }
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372 return $self->{'_cluster_score'};
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373 }
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374
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375
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376 =head1 Implementation specific methods
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377
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378 These are mostly for adding/removing/changing.
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379
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380 =cut
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381
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382 =head2 add_members
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383
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384 Title : add_members
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385 Usage : $fam->add_member([$seq1,$seq1]);
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386 Function: add members to a family
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387 Returns :
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388 Args : the member(s) to add, as an array or arrayref
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389
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390 =cut
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391
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392 sub add_members{
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393 my ($self,@mems) = @_;
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394
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395 my $mem = shift(@mems);
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396 if(ref($mem) eq "ARRAY"){
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397 push @{$self->{'_members'}},@{$mem};
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398 } else {
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399 push @{$self->{'_members'}},$mem;
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400 }
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401 push @{$self->{'_members'}}, @mems;
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402
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403 return 1;
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404 }
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405
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406 =head2 remove_members
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407
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408 Title : remove_members
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409 Usage : $fam->remove_members();
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410 Function: remove all members from a family
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411 Returns : the previous array of members
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412 Args : none
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413
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414 =cut
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415
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416 sub remove_members{
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417 my ($self) = @_;
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418 my $mems = $self->{'_members'};
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419 $self->{'_members'} = [];
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420 return @$mems;
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421 }
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422
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423 #####################################################################
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424 # aliases for naming consistency or other reasons #
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425 #####################################################################
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426
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427 *flush_members = \&remove_members;
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428 *add_member = \&add_members;
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429
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430 sub members{
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431 my $self = shift;
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432 if(@_) {
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433 # this is in set mode
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434 $self->warn("setting members() in ".ref($self)." is deprecated.\n".
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435 "Use add_members() instead.");
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436 return $self->add_members(@_);
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437 } else {
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438 # get mode
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439 $self->warn("members() in ".ref($self)." is deprecated.\n".
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440 "Use get_members() instead.");
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441 return $self->get_members();
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442 }
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443 }
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444
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445 1;
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