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1 # $Id: AAChange.pm,v 1.13 2002/10/22 07:38:49 lapp Exp $
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2 #
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3 # BioPerl module for Bio::Variation::AAChange
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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::AAChange - Sequence change class for polypeptides
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16
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17 =head1 SYNOPSIS
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18
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19 $aamut = Bio::Variation::AAChange->new
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20 ('-start' => $start,
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21 '-end' => $end,
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22 '-length' => $len,
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23 '-proof' => $proof,
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24 '-isMutation' => 1,
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25 '-mut_number' => $mut_number
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26 );
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27
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28 my $a1 = Bio::Variation::Allele->new;
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29 $a1->seq($ori) if $ori;
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30 $aamut->allele_ori($a1);
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31 my $a2 = Bio::Variation::Allele->new;
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32 $a2->seq($mut) if $mut;
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33 $aachange->add_Allele($a2);
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34 $aachange->allele_mut($a2);
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35
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36 print "\n";
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37
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38 # add it to a SeqDiff container object
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39 $seqdiff->add_Variant($rnachange);
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40
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41 # and create links to and from RNA level variant objects
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42 $aamut->RNAChange($rnachange);
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43 $rnachange->AAChange($rnachange);
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44
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45 =head1 DESCRIPTION
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46
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47 The instantiable class Bio::Variation::RNAChange describes basic
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48 sequence changes at polypeptide level. It uses methods defined in
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49 superclass Bio::Variation::VariantI, see L<Bio::Variation::VariantI>
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50 for details.
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51
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52 If the variation described by a AAChange object has a known
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53 Bio::Variation::RNAAChange object, create the link with method
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54 AAChange(). See L<Bio::Variation::AAChange> for more information.
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55
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56 =head1 FEEDBACK
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57
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58 =head2 Mailing Lists
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59
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60 User feedback is an integral part of the evolution of this and other
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61 Bioperl modules. Send your comments and suggestions preferably to the
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62 Bioperl mailing lists Your participation is much appreciated.
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63
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64 bioperl-l@bioperl.org - General discussion
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65 http://bio.perl.org/MailList.html - About the mailing lists
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66
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67 =head2 Reporting Bugs
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68
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69 report bugs to the Bioperl bug tracking system to help us keep track
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70 the bugs and their resolution. Bug reports can be submitted via
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71 email or the web:
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72
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73 bioperl-bugs@bio.perl.org
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74 http://bugzilla.bioperl.org/
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75
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76 =head1 AUTHOR - Heikki Lehvaslaiho
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77
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78 Email: heikki@ebi.ac.uk
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79
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80 Address:
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81
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82 EMBL Outstation, European Bioinformatics Institute
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83 Wellcome Trust Genome Campus, Hinxton
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84 Cambs. CB10 1SD, United Kingdom
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85
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86 =head1 APPENDIX
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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
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94 # Let the code begin...
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95
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96
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97 package Bio::Variation::AAChange;
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98 my $VERSION=1.0;
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99 use vars qw(@ISA $MATRIX);
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100 use strict;
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101
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102 # Object preamble - inheritance
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103 use Bio::Variation::VariantI;
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104
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105 @ISA = qw( Bio::Variation::VariantI );
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106
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107 BEGIN {
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108
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109 my $matrix = << "__MATRIX__";
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110 # Matrix made by matblas from blosum62.iij
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111 # * column uses minimum score
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112 # BLOSUM Clustered Scoring Matrix in 1/2 Bit Units
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113 # Blocks Database = /data/blocks_5.0/blocks.dat
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114 # Cluster Percentage: >= 62
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115 # Entropy = 0.6979, Expected = -0.5209
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116 A R N D C Q E G H I L K M F P S T W Y V B Z X *
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117 A 4 -1 -2 -2 0 -1 -1 0 -2 -1 -1 -1 -1 -2 -1 1 0 -3 -2 0 -2 -1 0 -4
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118 R -1 5 0 -2 -3 1 0 -2 0 -3 -2 2 -1 -3 -2 -1 -1 -3 -2 -3 -1 0 -1 -4
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119 N -2 0 6 1 -3 0 0 0 1 -3 -3 0 -2 -3 -2 1 0 -4 -2 -3 3 0 -1 -4
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120 D -2 -2 1 6 -3 0 2 -1 -1 -3 -4 -1 -3 -3 -1 0 -1 -4 -3 -3 4 1 -1 -4
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121 C 0 -3 -3 -3 9 -3 -4 -3 -3 -1 -1 -3 -1 -2 -3 -1 -1 -2 -2 -1 -3 -3 -2 -4
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122 Q -1 1 0 0 -3 5 2 -2 0 -3 -2 1 0 -3 -1 0 -1 -2 -1 -2 0 3 -1 -4
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123 E -1 0 0 2 -4 2 5 -2 0 -3 -3 1 -2 -3 -1 0 -1 -3 -2 -2 1 4 -1 -4
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124 G 0 -2 0 -1 -3 -2 -2 6 -2 -4 -4 -2 -3 -3 -2 0 -2 -2 -3 -3 -1 -2 -1 -4
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125 H -2 0 1 -1 -3 0 0 -2 8 -3 -3 -1 -2 -1 -2 -1 -2 -2 2 -3 0 0 -1 -4
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126 I -1 -3 -3 -3 -1 -3 -3 -4 -3 4 2 -3 1 0 -3 -2 -1 -3 -1 3 -3 -3 -1 -4
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127 L -1 -2 -3 -4 -1 -2 -3 -4 -3 2 4 -2 2 0 -3 -2 -1 -2 -1 1 -4 -3 -1 -4
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128 K -1 2 0 -1 -3 1 1 -2 -1 -3 -2 5 -1 -3 -1 0 -1 -3 -2 -2 0 1 -1 -4
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129 M -1 -1 -2 -3 -1 0 -2 -3 -2 1 2 -1 5 0 -2 -1 -1 -1 -1 1 -3 -1 -1 -4
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130 F -2 -3 -3 -3 -2 -3 -3 -3 -1 0 0 -3 0 6 -4 -2 -2 1 3 -1 -3 -3 -1 -4
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131 P -1 -2 -2 -1 -3 -1 -1 -2 -2 -3 -3 -1 -2 -4 7 -1 -1 -4 -3 -2 -2 -1 -2 -4
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132 S 1 -1 1 0 -1 0 0 0 -1 -2 -2 0 -1 -2 -1 4 1 -3 -2 -2 0 0 0 -4
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133 T 0 -1 0 -1 -1 -1 -1 -2 -2 -1 -1 -1 -1 -2 -1 1 5 -2 -2 0 -1 -1 0 -4
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134 W -3 -3 -4 -4 -2 -2 -3 -2 -2 -3 -2 -3 -1 1 -4 -3 -2 11 2 -3 -4 -3 -2 -4
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135 Y -2 -2 -2 -3 -2 -1 -2 -3 2 -1 -1 -2 -1 3 -3 -2 -2 2 7 -1 -3 -2 -1 -4
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136 V 0 -3 -3 -3 -1 -2 -2 -3 -3 3 1 -2 1 -1 -2 -2 0 -3 -1 4 -3 -2 -1 -4
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137 B -2 -1 3 4 -3 0 1 -1 0 -3 -4 0 -3 -3 -2 0 -1 -4 -3 -3 4 1 -1 -4
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138 Z -1 0 0 1 -3 3 4 -2 0 -3 -3 1 -1 -3 -1 0 -1 -3 -2 -2 1 4 -1 -4
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139 X 0 -1 -1 -1 -2 -1 -1 -1 -1 -1 -1 -1 -1 -1 -2 0 0 -2 -1 -1 -1 -1 -1 -4
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140 * -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 1
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141 __MATRIX__
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142
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143 my %blosum = ();
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144 $matrix =~ /^ +(.+)$/m;
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145 my @aas = split / +/, $1;
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146 foreach my $aa (@aas) {
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147 my $tmp = $aa;
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148 $tmp = "\\$aa" if $aa eq '*';
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149 $matrix =~ /^($tmp) +([-+]?\d.*)$/m;
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150 my @scores = split / +/, $2 if defined $2;
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151 my $count = 0;
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152 foreach my $ak (@aas) {
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153 $blosum{$aa}->{$aas[$count]} = $scores[$count];
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154 $count++;
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155 }
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156 }
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157 sub _matrix;
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158 $MATRIX = \%blosum;
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159 }
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160
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161 sub new {
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162 my($class,@args) = @_;
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163 my $self = $class->SUPER::new(@args);
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164
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165 my ($start, $end, $length, $strand, $primary, $source,
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166 $frame, $score, $gff_string,
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167 $allele_ori, $allele_mut, $upstreamseq, $dnstreamseq,
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168 $label, $status, $proof, $re_changes, $region, $region_value,
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169 $region_dist,
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170 $numbering, $mut_number, $ismutation) =
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171 $self->_rearrange([qw(START
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172 END
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173 LENGTH
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174 STRAND
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175 PRIMARY
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176 SOURCE
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177 FRAME
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178 SCORE
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179 GFF_STRING
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180 ALLELE_ORI
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181 ALLELE_MUT
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182 UPSTREAMSEQ
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183 DNSTREAMSEQ
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184 LABEL
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185 STATUS
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186 PROOF
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187 RE_CHANGES
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188 REGION
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189 REGION_VALUE
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190 REGION_DIST
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191 NUMBERING
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192 MUT_NUMBER
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193 ISMUTATION
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194 )],@args);
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195
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196 $self->primary_tag("Variation");
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197
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198 $self->{ 'alleles' } = [];
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199
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200 $start && $self->start($start);
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201 $end && $self->end($end);
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202 $length && $self->length($length);
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203 $strand && $self->strand($strand);
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204 $primary && $self->primary_tag($primary);
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205 $source && $self->source_tag($source);
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206 $frame && $self->frame($frame);
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207 $score && $self->score($score);
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208 $gff_string && $self->_from_gff_string($gff_string);
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209
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210 $allele_ori && $self->allele_ori($allele_ori);
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211 $allele_mut && $self->allele_mut($allele_mut);
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212 $upstreamseq && $self->upstreamseq($upstreamseq);
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213 $dnstreamseq && $self->dnstreamseq($dnstreamseq);
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214
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215 $label && $self->label($label);
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216 $status && $self->status($status);
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217 $proof && $self->proof($proof);
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218 $region && $self->region($region);
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219 $region_value && $self->region_value($region_value);
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220 $region_dist && $self->region_dist($region_dist);
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221 $numbering && $self->numbering($numbering);
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222 $mut_number && $self->mut_number($mut_number);
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223 $ismutation && $self->isMutation($ismutation);
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224
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225 return $self; # success - we hope!
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226 }
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227
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228 =head2 RNAChange
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229
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230 Title : RNAChange
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231 Usage : $mutobj = $self->RNAChange;
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232 : $mutobj = $self->RNAChange($objref);
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233 Function: Returns or sets the link-reference to a mutation/change object.
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234 If there is no link, it will return undef
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235 Returns : an obj_ref or undef
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236
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237 =cut
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238
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239 sub RNAChange {
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240 my ($self,$value) = @_;
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241 if (defined $value) {
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242 if( ! $value->isa('Bio::Variation::RNAChange') ) {
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243 $self->throw("Is not a Bio::Variation::RNAChange object but a [$self]");
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244 return (undef);
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245 }
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246 else {
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247 $self->{'RNAChange'} = $value;
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248 }
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249 }
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250 unless (exists $self->{'RNAChange'}) {
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251 return (undef);
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252 } else {
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253 return $self->{'RNAChange'};
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254 }
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255 }
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256
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257
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258
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259 =head2 label
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260
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261 Title : label
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262 Usage : $obj->label();
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263 Function:
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264
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265 Sets and returns mutation event label(s). If value is not
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266 set, or no argument is given returns false. Each
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267 instantiable subclass of L<Bio::Variation::VariantI> needs
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268 to implement this method. Valid values are listed in
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269 'Mutation event controlled vocabulary' in
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270 http://www.ebi.ac.uk/mutations/recommendations/mutevent.html.
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271
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272 Example :
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273 Returns : string
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274 Args : string
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275
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276 =cut
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277
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278
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279 sub label {
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280 my ($self) = @_;
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281 my ($o, $m, $type);
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282 $o = $self->allele_ori->seq if $self->allele_ori and $self->allele_ori->seq;
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283 $m = $self->allele_mut->seq if $self->allele_mut and $self->allele_mut->seq;
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284
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285 if ($self->start == 1 ) {
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286 if ($o and substr($o, 0, 1) ne substr($m, 0, 1)) {
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287 $type = 'no translation';
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288 }
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289 elsif ($o and $m and $o eq $m ) {
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290 $type = 'silent';
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291 }
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292 # more ...
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293 }
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294 elsif ($o and substr($o, 0, 1) eq '*' ) {
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295 if ($m and substr($o, 0, 1) ne substr($m, 0, 1)) {
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296 $type = 'post-elongation';
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297 }
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298 elsif ($m and $o eq $m ) {
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299 $type = 'silent, conservative';
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300 }
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301 }
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302 elsif ($o and $m and $o eq $m) {
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303 $type = 'silent, conservative';
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304 }
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305 elsif ($m and $m eq '*') {
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306 $type = 'truncation';
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307 }
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308 elsif ($o and $m and $o eq $m) {
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309 $type = 'silent, conservative';
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310 }
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311 elsif (not $m or
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312 ($o and $m and length($o) > length($m) and
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313 substr($m, -1, 1) ne '*')) {
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314 $type = 'deletion';
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315 if ($o and $m and $o !~ $m and $o !~ $m) {
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316 $type .= ', complex';
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317 }
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318 }
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319 elsif (not $o or
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320 ($o and $m and length($o) < length($m) and
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321 substr($m, -1, 1) ne '*' ) ) {
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322 $type = 'insertion';
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323 if ($o and $m and $o !~ $m and $o !~ $m) {
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324 $type .= ', complex';
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325 }
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326 }
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327 elsif ($o and $m and $o ne $m and
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328 length $o == 1 and length $m == 1 ) {
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329 $type = 'substitution';
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330 my $value = $self->similarity_score;
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331 if (defined $value) {
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332 my $cons = ($value < 0) ? 'nonconservative' : 'conservative';
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333 $type .= ", ". $cons;
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334 }
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335 } else {
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336 $type = 'out-of-frame translation, truncation';
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337 }
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338 $self->{'label'} = $type;
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339 return $self->{'label'};
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340 }
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341
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342
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343 =head2 similarity_score
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344
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345 Title : similarity_score
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346 Usage : $self->similarity_score
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347 Function: Measure for evolutionary conservativeness
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348 of single amino substitutions. Uses BLOSUM62.
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349 Negative numbers are noncoservative changes.
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350 Returns : integer, undef if not single amino acid change
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351
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352 =cut
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353
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354 sub similarity_score {
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355 my ($self) = @_;
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356 my ($o, $m, $type);
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357 $o = $self->allele_ori->seq if $self->allele_ori and $self->allele_ori->seq;
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358 $m = $self->allele_mut->seq if $self->allele_mut and $self->allele_mut->seq;
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359 return undef unless $o and $m and length $o == 1 and length $m == 1;
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360 return undef unless $o =~ /[ARNDCQEGHILKMFPSTWYVBZX*]/i and
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361 $m =~ /[ARNDCQEGHILKMFPSTWYVBZX*]/i;
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362 return $MATRIX->{"\U$o"}->{"\U$m"};
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363 }
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364
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365 =head2 trivname
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366
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367 Title : trivname
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368 Usage : $self->trivname
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369 Function:
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370
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371 Given a Bio::Variation::AAChange object with linked
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372 Bio::Variation::RNAChange and Bio::Variation::DNAMutation
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373 objects, this subroutine creates a string corresponding to
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374 the 'trivial name' of the mutation. Trivial name is
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375 specified in Antonorakis & MDI Nomenclature Working Group:
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376 Human Mutation 11:1-3, 1998.
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377 http://www.interscience.wiley.com/jpages/1059-7794/nomenclature.html
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378
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379 Returns : string
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380
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381 =cut
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382
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383
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384 sub trivname {
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385 my ($self,$value) = @_;
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386 if( defined $value) {
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387 $self->{'trivname'} = $value;
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388 } else {
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389 my ( $aaori, $aamut,$aamutsymbol, $aatermnumber, $aamutterm) =
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390 ('', '', '', '', '');
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391 my $o = $self->allele_ori->seq if $self->allele_ori and $self->allele_ori->seq;
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392 #my $m = $self->allele_mut->seq if $self->allele_mut and $self->allele_mut->seq;
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393
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394 $aaori = substr ($o, 0, 1) if $o;
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395 $aaori =~ tr/\*/X/;
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396
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397 my $sep;
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398 if ($self->isMutation) {
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399 $sep = '>';
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400 } else {
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401 $sep = '|';
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402 }
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403 my $trivname = $aaori. $self->start;
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404 $trivname .= $sep if $sep eq '|';
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405
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406 my @alleles = $self->each_Allele;
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407 foreach my $allele (@alleles) {
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408 my $m = $allele->seq if $allele->seq;
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409
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410 $self->allele_mut($allele);
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411 #$trivname .= $sep. uc $m if $m;
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412
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413 $aamutterm = substr ($m, -1, 1) if $m;
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414 if ($self->RNAChange->label =~ /initiation codon/ and
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415 ( $o and $m and $o ne $m)) {
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416 $aamut = 'X';
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417 }
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418 elsif (CORE::length($o) == 1 and CORE::length($m) == 1 ) {
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419 $aamutsymbol = '';
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420 $aamut = $aamutterm;
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421 }
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422 elsif ($self->RNAChange->label =~ /deletion/) {
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423 $aamutsymbol = 'del';
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424 if ($aamutterm eq '*') {
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425 $aatermnumber = $self->start + length($m) -1;
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426 $aamut = 'X'. $aatermnumber;
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427 }
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428 if ($self->RNAChange && $self->RNAChange->label =~ /inframe/){
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429 $aamut = '-'. length($self->RNAChange->allele_ori->seq)/3 ;
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430 }
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431 }
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432 elsif ($self->RNAChange->label =~ /insertion/) {
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433 $aamutsymbol = 'ins';
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434 if (($aamutterm eq '*') && (length($m)-1 != 0)) {
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435 $aatermnumber = $self->start + length($m)-1;
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436 $aamut = $aatermnumber. 'X';
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437 }
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438 if ($self->RNAChange->label =~ /inframe/){
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439 $aamut = '+'. int length($self->RNAChange->allele_mut->seq)/3 ;
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440 }
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441 }
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442 elsif ($self->RNAChange->label =~ /complex/ ) {
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443 my $diff = length($m) - length($o);
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444 if ($diff >= 0 ) {
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445 $aamutsymbol = 'ins';
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446 } else {
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447 $aamutsymbol = 'del' ;
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448 }
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449 if (($aamutterm eq '*') && (length($m)-1 != 0)) {
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450 $aatermnumber = $self->start + length($m)-1;
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451 $aamut = $aatermnumber. 'X';
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452 }
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453 if ($self->RNAChange->label =~ /inframe/){
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454
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455 if ($diff >= 0 ) {
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456 $aamut = '+'. $diff ;
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457 } else {
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458 $aamut = $diff ;
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459 }
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460 }
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461 }
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462 elsif ($self->label =~ /truncation/) {
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463 $aamut = $m;
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464 } else {
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465 $aamutsymbol = '';
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466 $aamut = $aamutterm;
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467 }
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468 $aamut =~ tr/\*/X/;
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469 $trivname .= $aamutsymbol. $aamut. $sep;
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470 }
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471 chop $trivname;
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472 $self->{'trivname'} = $trivname;
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473 }
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474 return $self->{'trivname'};
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475 }
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476
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477 1;
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