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1 # BioPerl module for Bio::Map::LinkageMap
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2 #
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3 # Cared for by Chad Matsalla <bioinformatics1@dieselwurks.com>
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4 #
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5 # Copyright Chad Matsalla
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6 #
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7 # You may distribute this module under the same terms as perl itself
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8
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9 # POD documentation - main docs before the code
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10
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11 =head1 NAME
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12
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13 Bio::Map::LinkageMap - A representation of a genetic linkage map.
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14
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15 =head1 SYNOPSIS
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16
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17 use Bio::Map::LinkageMap;
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18 # create a new map
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19 my $map = new Bio::Map::LinkageMap(-name => 'Chads Superterriffic Map',
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20 -type => 'Linkage',
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21 -units=> 'cM');
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22 # create the location of a marker for that map
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23 my $position = new Bio::Map::LinkagePosition( -positions => 1,
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24 -distance => "22.3");
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25 # create a marker and place it at that position
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26 my $marker = new Bio::Map::Marker::Microsatellite(
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27 -name => 'SuuuperMarker',
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28 -position => $position);
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29 # place that marker on that map
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30 $map->add_element($marker);
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31
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32 # done!
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33
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34 =head1 DESCRIPTION
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35
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36 This object describes the basic functionality of a genetic linkage map in
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37 Bioperl. Each 'position' can have one or more markers that map some number of
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38 units from the markers at the previous position.
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39
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40 =head1 FEEDBACK
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41
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42 =head2 Mailing Lists
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43
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44 User feedback is an integral part of the evolution of this and other
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45 Bioperl modules. Send your comments and suggestions preferably to
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46 the Bioperl mailing list. Your participation is much appreciated.
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47
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48 bioperl-l@bioperl.org - General discussion
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49 http://bioperl.org/MailList.shtml - About the mailing lists
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50
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51 =head2 Reporting Bugs
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52
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53 Report bugs to the Bioperl bug tracking system to help us keep track
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54 of the bugs and their resolution. Bug reports can be submitted via
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55 email or the web:
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56
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57 bioperl-bugs@bioperl.org
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58 http://bugzilla.bioperl.org/
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59
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60 =head1 AUTHOR - Chad Matsalla
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61
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62 Email bioinformatics1@dieselwurks.com
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63
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64 =head1 CONTRIBUTORS
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65
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66 Lincoln Stein lstein@cshl.org
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67 Heikki Lehvaslaiho heikki@ebi.ac.uk
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68 Jason Stajich jason@bioperl.org
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69
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70 =head1 APPENDIX
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71
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72 The rest of the documentation details each of the object methods.
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73 Internal methods are usually preceded with a _
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74
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75 =cut
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76
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77
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78 # Let the code begin...
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79
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80 package Bio::Map::LinkageMap;
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81 use vars qw(@ISA);
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82 use strict;
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83 use Bio::Map::SimpleMap;
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84
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85 @ISA = qw(Bio::Map::SimpleMap);
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86
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87 =head2 new
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88
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89 Title : new
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90 Usage : my $linkage_map = new Bio::Map::LinkageMap();
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91 Function: Builds a new Bio::Map::LinkageMap object
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92 Returns : Bio::Map::LinkageMap
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93 Args : -name => the name of the map (string) [optional]
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94 -type => the type of this map (string, defaults to Linkage) [optional]
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95 -species => species for this map (Bio::Species) [optional]
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96 -units => the map units (string, defaults to cM) [optional]
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97 -elements=> elements to initialize with
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98 (arrayref of Bio::Map::MappableI objects) [optional]
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99
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100 -uid => Unique ID of this map
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101 =cut
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102
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103 # new provided by SimpleMap
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104
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105
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106
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107 =head2 length()
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108
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109 Title : length()
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110 Usage : my $length = $map->length();
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111 Function: Retrieves the length of the map. In the case of a LinkageMap, the
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112 length is the sum of all marker distances.
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113 Returns : An integer representing the length of this LinkageMap. Will return
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114 undef if length is not calculateable
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115 Args : None.
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116
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117
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118 =cut
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119
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120 sub length {
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121 my ($self) = @_;
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122 my $total_distance;
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123 foreach (@{$self->{'_elements'}}) {
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124 if ($_) {
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125 $total_distance += ($_->position()->each_position_value($self))[0];
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126 }
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127 }
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128 return $total_distance;
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129 }
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130
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131 =head2 add_element($marker)
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132
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133 Title : add_element($marker)
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134 Usage : $map->add_element($marker)
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135 Function: Add a Bio::Map::MappableI object to the Map
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136 Returns : none
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137 Args : Bio::Map::MappableI object
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138 Notes : It is strongly recommended that you use a
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139 Bio::Map::LinkagePosition as the position in any
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140 Bio::Map::Mappable that you create to place on this
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141 map. Using some other Bio::Map::Position might work but might
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142 be unpredictable.
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143 N.B. I've added Bio::Map::OrderedPosition which should achieve
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144 similar things from LinkagePosition and will work for
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145 RH markers too.
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146 =cut
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147
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148 #'
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149 sub _add_element {
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150 my ($self,$marker) = @_;
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151
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152 my $o_position = $marker->position();
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153
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154 $self->debug( "marker position is ". $marker->position());
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155 # print("add_element: \$o_position is $o_position\n");
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156 # print("add_element: \$marker is $marker\n");
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157
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158 my $position;
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159 unless ( $o_position->isa('Bio::Map::LinkagePosition') ||
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160 $o_position->isa('Bio::Map::OrderedPosition')
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161 ) {
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162 $self->warn("You really should use a Linkage Position for this object. This insures that there is only one position. Trying anyway...");
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163 my @p = ( $o_position->each_position_value($self));
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164 $position = shift @p;
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165 if( ! defined $position ) {
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166 $self->throw("This marker ($marker) does not have a position in this map ($self)");
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167 }
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168 } else {
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169 $position = $o_position->order;
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170 }
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171
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172 if ($self->{'_elements'}[$position]) {
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173 $self->warn("Replacing the marker in position $position because in a linkage map the position is a key.");
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174 }
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175 $self->{'_elements'}[$position] = $marker;
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176 }
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177
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178 =head2 each_element
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179
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180 Title : each_element
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181 Usage : my @elements = $map->each_element;
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182 Function: Retrieves all the elements in a map
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183 _ordered_.
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184 Returns : An array containing MappableI objects.
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185 Args : None.
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186 Notes : This is a useless concept in the context of a linkage map but is
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187 included if you want a list of all of the marker names on the map.
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188
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189 =cut
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190
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191 sub each_element {
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192 my ($self) = @_;
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193 return @{$self->{'_elements'}};
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194 }
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195
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196 =head2 implemented by Bio::Map::SimpleMap
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197
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198 =cut
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199
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200 =head2 name($new_name)
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201
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202 Title : name($new_name)
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203 Usage : my $name = $map->name($new_name) _or_
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204 my $length = $map->name()
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205 Function: Get/set the name of the map.
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206 Returns : The current name of the map.
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207 Args : If provided, the name of the map is set to $new_name.
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208
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209 =head2 species
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210
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211 Title : species
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212 Usage : my $species = $map->species;
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213 Function: Get/Set Species for a map
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214 Returns : Bio::Species object
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215 Args : (optional) Bio::Species
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216
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217
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218 =head2 units
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219
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220 Title : units
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221 Usage : $map->units('cM');
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222 Function: Get/Set units for a map
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223 Returns : units for a map
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224 Args : units for a map (string)
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225
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226
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227 =head2 type
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228
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229 Title : type
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230 Usage : my $type = $map->type
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231 Function: Get/Set Map type
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232 Returns : String coding map type
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233 Args : (optional) string
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234
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235 =head2 unique_id
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236
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237 Title : unique_id
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238 Usage : my $id = $map->unique_id;
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239 Function: Get/Set the unique ID for this map
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240 Returns : a unique identifier
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241 Args : [optional] new identifier to set
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242
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243 =cut
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244
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245 1;
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