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1 # $Id: AAReverseMutate.pm,v 1.6 2002/10/22 07:38:49 lapp Exp $
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2 #
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3 # BioPerl module for Bio::Variation::AAReverseMutate
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4 #
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5 # Cared for by Heikki Lehvaslaiho <heikki@ebi.ac.uk>
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6 #
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7 # Copyright Heikki Lehvaslaiho
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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::Variation::AAReverseMutate - point mutation and codon
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16 information from single amino acid changes
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17
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18 =head1 SYNOPSIS
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19
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20 $aamut = new Bio::Variation::AAReverseMutate
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21 (-aa_ori => 'F',
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22 -aa_mut => 'S',
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23 -codon_ori => 'ttc', # optional
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24 -codon_table => '3' # defaults to 1
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25 );
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26
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27 @points = $aamut->each_Variant;
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28
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29 if (scalar @points > 0 ) {
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30 foreach $rnachange ( @points ) {
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31 # $rnachange is a Bio::Variation::RNAChange object
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32 print " ", $rnachange->allele_ori->seq, ">",
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33 $rnachange->allele_mut->seq, " in ",
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34 $rnachange->codon_ori, ">", $rnachange->codon_mut,
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35 " at position ", $rnachange->codon_pos, "\n";
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36 }
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37 } else {
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38 print "No point mutations possible\n",
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39 }
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40
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41 =head1 DESCRIPTION
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42
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43 Bio::Variation::AAReverseMutate objects take in reference and mutated
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44 amino acid information and deduces potential point mutations at RNA
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45 level leading to this change. The choice can be further limited by
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46 letting the object know what is the the codon in the reference
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47 sequence. The results are returned as L<Bio::Variation::RNAChange>
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48 objects.
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49
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50 =head1 FEEDBACK
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51
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52 =head2 Mailing Lists
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53
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54 User feedback is an integral part of the evolution of this and other
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55 Bioperl modules. Send your comments and suggestions preferably to the
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56 Bioperl mailing lists Your participation is much appreciated.
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57
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58 bioperl-l@bioperl.org - General discussion
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59 http://bio.perl.org/MailList.html - About the mailing lists
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60
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61 =head2 Reporting Bugs
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62
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63 report bugs to the Bioperl bug tracking system to help us keep track
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64 the bugs and their resolution. Bug reports can be submitted via
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65 email or the web:
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66
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67 bioperl-bugs@bio.perl.org
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68 http://bugzilla.bioperl.org/
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69
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70 =head1 AUTHOR - Heikki Lehvaslaiho
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71
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72 Email: heikki@ebi.ac.uk
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73 Address:
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74
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75 EMBL Outstation, European Bioinformatics Institute
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76 Wellcome Trust Genome Campus, Hinxton
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77 Cambs. CB10 1SD, United Kingdom
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78
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79
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80 =head1 APPENDIX
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81
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82 The rest of the documentation details each of the object
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83 methods. Internal methods are usually preceded with a _
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84
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85 =cut
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86
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87
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88 # Let the code begin...
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89
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90 package Bio::Variation::AAReverseMutate;
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91 my $VERSION=1.0;
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92 use vars qw(@ISA);
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93 use strict;
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94
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95 # Object preamble - inheritance
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96 use Bio::Tools::CodonTable;
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97 use Bio::Variation::RNAChange;
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98 use Bio::Variation::Allele;
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99
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100 @ISA = qw( Bio::Root::Root);
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101
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102 sub new {
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103 my($class,@args) = @_;
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104 my $self = $class->SUPER::new(@args);
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105
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106 my ($aa_ori, $aa_mut, $codon_ori, $codon_table) =
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107 $self->_rearrange([qw(AA_ORI
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108 AA_MUT
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109 CODON
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110 CODON_TABLE
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111 )],@args);
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112
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113 $aa_ori && $self->aa_ori($aa_ori);
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114 $aa_mut && $self->aa_mut($aa_mut);
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115 $codon_ori && $self->codon_ori($codon_ori);
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116 $codon_table && $self->codon_table($codon_table);
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117
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118 return $self; # success - we hope!
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119
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120 }
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121
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122
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123 =head2 aa_ori
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124
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125 Title : aa_ori
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126 Usage : $obj->aa_ori();
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127 Function:
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128
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129 Sets and returns original aa sequence. If value is not
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130 set, returns false.
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131
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132 Amino acid sequences are stored in upper case characters,
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133 others in lower case.
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134
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135 Example :
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136 Returns : string
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137 Args : single character amino acid code
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138
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139 =cut
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140
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141 sub aa_ori {
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142 my ($self,$value) = @_;
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143 if( defined $value) {
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144 if ( uc($value) !~ /^[ARNDCQEGHILKMFPSTWYVBZX*]$/ ) {
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145 $self->throw("'$value' is not a valid one letter amino acid symbol\n");
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146 } else {
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147 $self->{'aa_ori'} = uc $value;
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148 }
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149 }
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150 return $self->{'aa_ori'};
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151 }
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152
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153
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154 =head2 aa_mut
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155
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156 Title : aa_mut
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157 Usage : $obj->aa_mut();
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158 Function:
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159
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160 Sets and returns the mutated allele sequence. If value is not
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161 set, returns false.
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162
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163 Example :
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164 Returns : string
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165 Args : single character amino acid code
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166
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167 =cut
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168
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169
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170 sub aa_mut {
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171 my ($self,$value) = @_;
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172 if( defined $value) {
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173 if ( uc($value) !~ /^[ARNDCQEGHILKMFPSTWYVBZX*]$/ ) {
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174 $self->throw("'$value' is not a valid one letter amino acid symbol\n");
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175 } else {
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176 $self->{'aa_mut'} = uc $value;
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177 }
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178 }
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179 return $self->{'aa_mut'};
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180 }
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181
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182
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183 =head2 codon_ori
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184
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185 Title : codon_ori
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186 Usage : $obj->codon_ori();
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187 Function:
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188
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189 Sets and returns codon_ori triplet. If value is not set,
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190 returns false. The string has to be three characters
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191 long. The chracter content is not checked.
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192
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193 Example :
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194 Returns : string
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195 Args : string
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196
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197 =cut
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198
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199 sub codon_ori {
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200 my ($self,$value) = @_;
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201 if( defined $value) {
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202 if (length $value != 3 or lc $value =~ /[^atgc]/) {
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203 $self->warn("Codon string \"$value\" is not valid unique codon");
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204 }
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205 $self->{'codon_ori'} = lc $value;
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206 }
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207 return $self->{'codon_ori'};
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208 }
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209
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210 =head2 codon_table
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211
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212 Title : codon_table
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213 Usage : $obj->codon_table();
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214 Function:
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215
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216 Sets and returns the codon table id of the RNA
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217 If value is not set, returns 1, 'universal' code, as the default.
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218
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219 Example :
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220 Returns : integer
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221 Args : none if get, the new value if set
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222
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223 =cut
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224
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225
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226 sub codon_table {
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227 my ($self,$value) = @_;
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228 if( defined $value) {
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229 if ( not $value =~ /^\d+$/ ) {
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230 $self->throw("'$value' is not a valid codon table ID\n".
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231 "Has to be a positive integer. Defaulting to 1\n");
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232 } else {
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233 $self->{'codon_table'} = $value;
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234 }
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235 }
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236 if( ! exists $self->{'codon_table'} ) {
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237 return 1;
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238 } else {
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239 return $self->{'codon_table'};
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240 }
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241 }
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242
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243
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244 =head2 each_Variant
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245
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246 Title : each_Variant
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247 Usage : $obj->each_Variant();
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248 Function:
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249
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250 Returns a list of Variants.
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251
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252 Example :
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253 Returns : list of Variants
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254 Args : none
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255
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256 =cut
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257
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258 sub each_Variant{
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259 my ($self,@args) = @_;
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260
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261 $self->throw("aa_ori is not defined\n") if not defined $self->aa_ori;
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262 $self->throw("aa_mut is not defined\n") if not defined $self->aa_mut;
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263
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264 my (@points, $codon_pos, $allele_ori, $allele_mut);
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265 my $ct = Bio::Tools::CodonTable->new( '-id' => $self->codon_table );
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266 foreach my $codon_ori ($ct->revtranslate($self->aa_ori)) {
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267 next if $self->codon_ori and $self->codon_ori ne $codon_ori;
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268 foreach my $codon_mut ($ct->revtranslate($self->aa_mut)) {
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269 my $k = 0;
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270 my $length = 0;
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271 $codon_pos = $allele_ori = $allele_mut = undef;
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272 while ($k<3) {
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273 my $nt_ori = substr ($codon_ori, $k, 1);
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274 my $nt_mut = substr ($codon_mut, $k, 1);
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275 if ($nt_ori ne $nt_mut) {
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276 $length++;
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277 $codon_pos = $k+1;
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278 $allele_ori = $nt_ori;
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279 $allele_mut = $nt_mut;
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280 }
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281 $k++;
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282 }
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283 if ($length == 1) {
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284 my $rna = Bio::Variation::RNAChange->new
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285 ('-length' => '1',
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286 '-codon_ori' => $codon_ori,
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287 '-codon_mut' => $codon_mut,
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288 '-codon_pos' => $codon_pos,
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289 '-isMutation' => 1
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290 );
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291 my $all_ori = Bio::Variation::Allele->new('-seq'=>$allele_ori);
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292 $rna->allele_ori($all_ori);
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293 my $all_mut = Bio::Variation::Allele->new('-seq'=>$allele_mut);
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294 $rna->allele_mut($all_mut);
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295 push @points, $rna;
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296 }
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297 }
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298 }
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299 return @points;
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300 }
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301
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302 1;
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