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1 # BioPerl module for Bio::Map::Microsatellite
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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::Microsatellite - An object representing a Microsatellite marker.
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14
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15 =head1 SYNOPSIS
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16
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17 $o_usat = new Bio::Map::Microsatellite
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18 (-name=>'Chad Super Marker 2',
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19 -sequence => 'gctgactgatcatatatatatatatatatatatatatatatcgcgatcgtga',
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20 -motif => 'at',
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21 -repeats => 15,
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22 -repeat_start_position => 11
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23 );
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24
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25 $sequence_before_usat = $o_usat->get_leading_flank();
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26 $sequence_after_usat = $o_usat->get_trailing_flank();
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27
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28
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29 =head1 DESCRIPTION
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30
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31 This object handles the notion of an Microsatellite. This microsatellite can
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32 be placed on a (linear) Map or used on its own. If this Microsatellites
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33 will be used in a mapping context (it doesn't have to, you know) it can have
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34 multiple positions in a map. For information about a Microsatellite's position
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35 in a map one must query the associate PositionI object which is accessible
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36 through the position() method.
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37
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38 =head1 FEEDBACK
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39
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40 =head2 Mailing Lists
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41
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42 User feedback is an integral part of the evolution of this and other
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43 Bioperl modules. Send your comments and suggestions preferably to
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44 the Bioperl mailing list. Your participation is much appreciated.
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45
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46 bioperl-l@bioperl.org - General discussion
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47 http://bioperl.org/MailList.shtml - About the mailing lists
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48
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49 =head2 Reporting Bugs
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50
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51 Report bugs to the Bioperl bug tracking system to help us keep track
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52 of the bugs and their resolution. Bug reports can be submitted via
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53 email or the web:
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54
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55 bioperl-bugs@bioperl.org
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56 http://bugzilla.bioperl.org/
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57
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58 =head1 AUTHOR - Chad Matsalla
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59
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60 Email bioinformatics1@dieselwurks.com
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61
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62 =head1 CONTRIBUTORS
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63
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64 Heikki Lehvaslaiho heikki@ebi.ac.uk
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65 Lincoln Stein lstein@cshl.org
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66 Jason Stajich jason@bioperl.org
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67
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68 =head1 APPENDIX
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69
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70 The rest of the documentation details each of the object methods.
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71 Internal methods are usually preceded with a _
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72
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73 =cut
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74
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75 # Let the code begin...
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76
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77 package Bio::Map::Microsatellite;
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78 use vars qw(@ISA);
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79 use strict;
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80 use Bio::Root::Root;
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81 use Bio::Map::Marker;
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82
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83 @ISA = qw(Bio::Map::Marker);
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84
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85 =head2 new
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86
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87 Title : new
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88 Usage : $o_usat =
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89 Function: Builds a new Bio::Map::Microsatellite object
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90 Returns : Bio::Map::Microsatellite
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91 Args :
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92 -name => name of this microsatellite (optional, string,
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93 default 'Unknown microsatellite')
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94 -positions => position(s) for this marker in maps[optional],
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95 An array reference of tuples (array refs themselves)
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96 Each tuple conatins a Bio::Map::MapI-inherited object and a
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97 Bio::Map::PositionI-inherited obj, no default)
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98 -sequence => the sequence of this microsatellite (optional,
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99 scalar, no default)
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100 -motif => the repeat motif of this microsatellite (optional,
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101 scalar, no default)
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102 -repeats => the number of motif repeats for this microsatellite
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103 (optional, scalar, no default)
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104 -repeat_start_position => the starting position of the
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105 microsatellite in this sequence. The first base of the
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106 sequence is position "1". (optional, scalar, no default)
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107
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108 Note : Creating a Bio::Map::Microsatellite object with no position
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109 might be useful for microsatellite people wanting to embrace
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110 and extend this module. <raising hand> Me! Me! Me!
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111 - using repeat_start_position will trigger a mechinism to
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112 calculate a value for repeat_end_position.
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113
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114
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115 =cut
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116
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117 sub new {
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118 my ($class,@args) = @_;
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119 my $self = $class->SUPER::new(@args);
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120 my ($map, $position, $sequence, $motif, $repeats, $start) =
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121 $self->_rearrange([qw(MAP
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122 POSITION
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123 SEQUENCE
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124 MOTIF
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125 REPEATS
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126 REPEAT_START_POSITION
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127 )], @args);
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128 if( ! $self->name ) {
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129 $self->name('Unnamed microsatellite');
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130 }
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131 $map && $self->map($map);
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132 $position && $self->position($position);
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133 $sequence && $self->sequence($sequence);
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134 $self->motif(defined $motif ? $motif : 'Unknown motif');
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135 $repeats && $self->repeats($repeats);
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136 $start && $self->repeat_start_position($start);
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137 return $self;
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138 }
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139
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140 =head2 Bio::Map::Marker methods
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141
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142 =cut
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143
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144 =head2 position
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145
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146 Title : position
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147 Usage : my $position = $mappable->position($map); OR
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148 $mappable->position($map,$position); OR
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149 Function: Get/Set the Bio::Map::PositionI for a mappable element
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150 in a specific Map
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151 Returns : Bio::Map::PositionI
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152 Args : $map =Bio::Map::MapI # Map we are talking about
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153 $position = Bio::Map::PositionI # Position we want to set
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154
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155
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156 =head2 name($new_name)
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157
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158 Title : name($new_name)
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159 Usage : $o_usat->name($new_name) _or_
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160 my $name = $o_usat->name()
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161 Function: Get/Set the name for this Microsatellite
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162 Returns : A scalar representing the current name of this Microsatellite
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163 Args : If provided, the current name of this Microsatellite
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164 will be set to $new_name.
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165
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166 =head2 motif($new_motif)
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167
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168 Title : motif($new_motif)
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169 Usage : my $motif = $o_usat->motif($new_motif) _or_
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170 my $motif = $o_usat->motif()
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171 Function: Get/Set the repeat motif for this Microsatellite
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172 Returns : A scalar representing the current repeat motif of this
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173 Microsatellite.
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174 Args : If provided, the current repeat motif of this Microsatellite
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175 will be set to $new_motif.
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176
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177 =cut
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178
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179 sub motif {
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180 my ($self,$motif) = @_;
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181 if ($motif) {
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182 $self->{'_motif'} = $motif;
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183 }
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184 return $self->{'_motif'};
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185 }
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186
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187 =head2 sequence($new_sequence)
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188
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189 Title : sequence($new_sequence)
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190 Usage : my $sequence = $o_usat->sequence($new_sequence) _or_
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191 my $sequence = $o_usat->sequence()
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192 Function: Get/Set the sequence for this Microsatellite
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193 Returns : A scalar representing the current sequence of this
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194 Microsatellite.
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195 Args : If provided, the current sequence of this Microsatellite
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196 will be set to $new_sequence.
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197
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198 =cut
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199
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200 sub sequence {
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201 my ($self,$sequence) = @_;
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202 if ($sequence) {
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203 $self->{'_sequence'} = $sequence;
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204 }
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205 return $self->{'_sequence'};
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206 }
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207
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208 =head2 repeats($new_repeats)
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209
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210 Title : repeats($new_repeats)
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211 Usage : my $repeats = $o_usat->repeats($new_repeats) _or_
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212 my $repeats = $o_usat->repeats()
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213 Function: Get/Set the repeat repeats for this Microsatellite
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214 Returns : A scalar representing the current number of repeats of this
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215 Microsatellite.
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216 Args : If provided, the current number of repeats of this
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217 Microsatellite will be set to $new_repeats.
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218
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219 =cut
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220
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221 sub repeats {
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222 my ($self,$repeats) = @_;
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223 if ($repeats) {
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224 $self->{'_repeats'} = $repeats;
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225 }
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226 return $self->{'_repeats'};
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227 }
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228
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229 =head2 repeat_start_position($new_repeat_start_position)
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230
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231 Title : repeat_start_position($new_repeat_start_position)
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232 Usage : my $repeat_start_position =
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233 $o_usat->repeat_start_position($new_repeat_start_position) _or_
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234 my $repeat_start_position = $o_usat->repeat_start_position()
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235 Function: Get/Set the repeat repeat_start_position for this
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236 Microsatellite
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237 Returns : A scalar representing the repeat start position for this
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238 Microsatellite.
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239 Args : If provided, the current repeat start position of this
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240 Microsatellite will be set to $new_repeat_start_position.
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241 This method will also try to set the repeat end position. This
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242 depends on having information for the motif and the number of
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243 repeats. If you want to use methods like get_trailing_flank or
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244 get_leading flank, be careful to include the right information.
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245
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246 =cut
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247
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248 sub repeat_start_position {
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249 my ($self,$repeat_start_position) = @_;
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250 if ($repeat_start_position) {
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251 $self->{'_repeat_start_position'} = $repeat_start_position;
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252 $self->repeat_end_position("set");
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253 }
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254 return $self->{'_repeat_start_position'};
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255 }
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256
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257 =head2 repeat_end_position($value)
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258
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259 Title : repeat_end_position($set)
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260 Usage : $new_repeat_end_position =
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261 $o_usat->repeat_end_position("set"); _or_
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262 $new_repeat_end_position =
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263 $o_usat->repeat_end_position($value); _or_
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264 $current_repeat_end_position = $o_usat->repeat_end_position();
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265 Function: get/set the end position of the repeat in this sequence
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266 Returns : A scalar representing the base index of the end of the
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267 repeat in this Microsatellite. The first base in the sequence
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268 is base 1.
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269 Args : A scalar representing a value, the string "set", or no
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270 argument (see Notes).
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271 Notes : If you do not provide an argument to this method, the current
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272 end position of the repeat in this Microsatellite will be
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273 returned (a scalar).
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274 If you provide the string "set" to this method it will set the
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275 end position based on the start position, the length of the
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276 motif, and the nuimber of repeats.
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277 If you specify a value the current end position of the repeat
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278 will be set to that value. This is a really bad idea. Don't do
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279 it.
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280
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281 =cut
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282
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283 #'
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284 sub repeat_end_position {
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285 my ($self,$caller) = @_;
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286 if( defined $caller ) {
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287 if ($caller eq "set") {
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288 $self->{'_repeat_end_position'} =
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289 $self->{'_repeat_start_position'} +
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290 (length($self->motif()) * $self->repeats());
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291 }
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292 elsif ($caller) {
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293 $self->{'_repeat_end_position'} = $caller;
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294 }
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295 }
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296 return $self->{'_repeat_end_position'};
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297 }
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298
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299 =head2 equals
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300
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301 Title : equals
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302 Usage : if( $mappable->equals($mapable2)) ...
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303 Function: Test if a position is equal to another position
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304 Returns : boolean
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305 Args : Bio::Map::MappableI
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306
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307 =cut
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308
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309 sub equals {
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310 my ($self,@args) = @_;
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311 $self->warn("equals is not yet implemented in ".
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312 ref($self)." yet. Check back real soon!");
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313 }
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314
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315 =head2 less_than
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316
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317 Title : less_than
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318 Usage : if( $mappable->less_than($m2) ) ...
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319 Function: Tests if a position is less than another position
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320 Returns : boolean
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321 Args : Bio::Map::MappableI
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322
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323 =cut
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324
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325 sub less_than {
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326 my ($self,@args) = @_;
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327 $self->warn("less_then is not yet implemented in ".
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328 ref($self)." yet. Check back real soon!");
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329 }
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330
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331 =head2 greater_than
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332
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333 Title : greater_than
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334 Usage : if( $mappable->greater_than($m2) ) ...
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335 Function: Tests if position is greater than another position
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336 Returns : boolean
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337 Args : Bio::Map::MappableI
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338
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339 =cut
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340
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341 sub greater_than {
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342 my ($self,@args) = @_;
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343 $self->warn("greater_then is not yet implemented in ".
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344 ref($self)." yet. Check back real soon!");
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345 }
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346
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347 =head2 get_leading_flank()
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348
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349 Title : get_leading_flank()
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350 Usage : $leading_sequence = $o_usat->get_leading_flank();
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351 Returns : A scalar representing the sequence before the repeats in this
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352 Microsatellite.
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353 Args : None.
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354
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355 =cut
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356
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357 sub get_leading_flank {
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358 my $self = shift;
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359 return substr $self->sequence(),0,$self->repeat_start_position-1;
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360
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361 }
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362
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363 =head2 get_trailing_flank()
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364
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365 Title : get_trailing_flank()
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366 Usage : $trailing_flank = $o_usat->get_trailing_flank();
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367 Returns : A scalar representing the sequence after the repeats in this
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368 Microsatellite.
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369 Args : None.
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370
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371 =cut
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372
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373 sub get_trailing_flank {
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374 my $self = shift;
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375 return substr $self->sequence(),$self->repeat_end_position()-1;
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376 }
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377
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378
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379 1;
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380
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381
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