Bio/LiveSeq/Mutation.pm

   1 #
   2 # BioPerl module for Bio::LiveSeq::Mutation
   3 #
   4 # Please direct questions and support issues to <bioperl-l@bioperl.org>
   5 #
   6 # Cared for by Heikki Lehvaslaiho <heikki-at-bioperl-dot-org>
   7 #
   8 # Copyright Heikki Lehvaslaiho
   9 #
  10 # You may distribute this module under the same terms as perl itself
  11
  12 # POD documentation - main docs before the code
  13
  14 =head1 NAME
  15
  16 Bio::LiveSeq::Mutation - Mutation event descriptor class
  17
  18 =head1 SYNOPSIS
  19
  20   # full description of a point mutation
  21   $mutation1a = Bio::LiveSeq::Mutation->new ( -seq => 'A',
  22                                               -seqori => 'T',
  23                                               -pos  => 100,
  24                                               -len => 1 # optional, defaults to length(seq)
  25                                              );
  26
  27   # minimal information for a point mutation
  28   $mutation1b = Bio::LiveSeq::Mutation->new ( -seq => 'A',
  29                                               -pos  => 100
  30                                               );
  31   # insertion
  32   $mutation2 = Bio::LiveSeq::Mutation->new ( -seq => 'ATT',
  33                                              -pos  => 100,
  34                                              -len => 0
  35                                              );
  36   # deletion
  37   $mutation3 = Bio::LiveSeq::Mutation->new ( -seq => '',  # optional
  38                                              -seqori => 'TTG',  # optional
  39                                              -pos  => 100
  40                                              -len => 3
  41                                              );
  42   # complex
  43   $mutation4 = Bio::LiveSeq::Mutation->new ( -seq => 'CC',
  44                                              -seqori => 'TTG',  # optional
  45                                              -pos  => 100
  46                                              -len => 3
  47                                              );
  48
  49
  50 =head1 DESCRIPTION
  51
  52 This class describes a local mutation event using minimalistic
  53 description.  It is not necessary to know anything about the original
  54 sequence. You need to give the changed sequence, the position of the
  55 mutation in the (unidentified) reference sequence, and the length of
  56 the affected subsequence in the reference sequence. If the original
  57 allele sequence is given, the objects applying the mutation into the
  58 reference sequence (e.g. L<Bio::LiveSeq::Mutator>) might check for its
  59 validity.
  60
  61 =head1 FEEDBACK
  62
  63 =head2 Mailing Lists
  64
  65 User feedback is an integral part of the evolution of this and other
  66 Bioperl modules. Send your comments and suggestions preferably to the
  67 Bioperl mailing lists  Your participation is much appreciated.
  68
  69   bioperl-l@bioperl.org                  - General discussion
  70   http://bioperl.org/wiki/Mailing_lists  - About the mailing lists
  71
  72 =head2 Support
  73
  74 Please direct usage questions or support issues to the mailing list:
  75
  76 I<bioperl-l@bioperl.org>
  77
  78 rather than to the module maintainer directly. Many experienced and
  79 reponsive experts will be able look at the problem and quickly
  80 address it. Please include a thorough description of the problem
  81 with code and data examples if at all possible.
  82
  83 =head2 Reporting Bugs
  84
  85 report bugs to the Bioperl bug tracking system to help us keep track
  86 the bugs and their resolution.  Bug reports can be submitted via the
  87 web:
  88
  89   https://github.com/bioperl/bioperl-live/issues
  90
  91 =head1 AUTHOR - Heikki Lehvaslaiho
  92
  93 Email:  heikki-at-bioperl-dot-org
  94
  95 =head1 APPENDIX
  96
  97 The rest of the documentation details each of the object
  98 methods. Internal methods are usually preceded with a _
  99
 100 =cut
 101
 102
 103 # Let the code begin...
 104
 105 package Bio::LiveSeq::Mutation;
 106 use strict;
 107
 108 # Object preamble - inheritance
 109
 110
 111 use base qw(Bio::Root::Root);
 112
 113 sub new {
 114     my($class,@args) = @_;
 115     my $self;
 116     $self = {};
 117     bless $self, $class;
 118
 119     my ($seq, $seqori, $pos, $len, $label) =
 120             $self->_rearrange([qw(SEQ
 121                                   SEQORI
 122                                   POS
 123                                   LEN
 124                                   )],
 125                               @args);
 126
 127     $seq && $self->seq($seq);
 128     $seqori && $self->seqori($seqori);
 129     $pos && $self->pos($pos);
 130     defined($len) && $self->len($len); # defined() added otherwise won't work for len==0
 131
 132     return $self; # success - we hope!
 133 }
 134
 135
 136 =head2 seq
 137
 138  Title   : seq
 139  Usage   : $obj->seq();
 140  Function:
 141
 142             Sets and returns the mutated sequence. No checking is done
 143             to validate the symbols.
 144
 145  Example :
 146  Returns : string
 147  Args    : integer
 148
 149 =cut
 150
 151
 152 sub seq {
 153     my ($self,$value) = @_;
 154     if( defined $value) {
 155         $self->{'seq'} = $value;
 156     }
 157     return $self->{'seq'} || '';
 158 }
 159
 160
 161 =head2 seqori
 162
 163  Title   : seqori
 164  Usage   : $obj->seqori();
 165  Function:
 166
 167             Sets and returns the original subsequence in the reference
 168             sequence. No checking is done to validate the symbols.
 169             Optional value.
 170
 171  Example :
 172  Returns : string
 173  Args    : string
 174
 175 =cut
 176
 177
 178 sub seqori {
 179     my ($self,$value) = @_;
 180     if( defined $value) {
 181         $self->{'seqori'} = $value;
 182     }
 183     return $self->{'seqori'} || '';
 184 }
 185
 186
 187 =head2 pos
 188
 189  Title   : pos
 190  Usage   : $obj->pos();
 191  Function:
 192
 193             Sets and returns the position of the first element in the
 194             sequence.
 195
 196  Example :
 197  Returns : string
 198  Args    : integer
 199
 200 =cut
 201
 202
 203 sub pos {
 204     my ($self,$value) = @_;
 205     if( defined $value) {
 206         if ( $value !~ /^([+-])?\d+$/ ) {
 207             $self->throw("[$value] for pos has to be an integer\n");
 208         } else {
 209             $self->{'pos'} = $value;
 210         }
 211     }
 212     return $self->{'pos'};
 213 }
 214
 215 =head2 len
 216
 217  Title   : len
 218  Usage   : $obj->len();
 219  Function:
 220
 221             Sets and returns the len of the affected original allele
 222             sequence.  If value is not set, defaults to the length of
 223             the mutated sequence (seq).
 224
 225  Example :
 226  Returns : string
 227  Args    : string
 228
 229 =cut
 230
 231 sub len {
 232    my ($self,$value) = @_;
 233    if ( defined $value) {
 234        $self->{'len'} = $value;
 235   }
 236    if ( ! exists $self->{'len'} ) {
 237        return length $self->{'seq'};
 238    }
 239    return $self->{'len'};
 240 }
 241
 242 =head2 label
 243
 244  Title   : label
 245  Usage   : $obj->label();
 246  Function:
 247
 248             Sets and returns the label of the affected original allele
 249             location. Label is a stable identifier whereas location
 250             can be changed by mutations. Label comes from
 251             l<Bio::LiveSeq::Gene>.
 252
 253  Example :
 254  Returns : string
 255  Args    : string
 256
 257 =cut
 258
 259 sub label {
 260    my ($self,$value) = @_;
 261    if ( defined $value) {
 262        $self->{'label'} = $value;
 263    }
 264    if ( ! exists $self->{'label'} ) {
 265        return;
 266    }
 267    return $self->{'label'};
 268 }
 269
 270
 271 =head2 transpos
 272
 273  Title   : transpos
 274  Usage   : $obj->transpos();
 275  Function:
 276
 277             Sets and returns the transcript position of the mutation.
 278             Set when associated with a reference sequence. Value
 279             depends on reference molecule and the co-ordinate system
 280             used.
 281
 282  Example :
 283  Returns : string
 284  Args    : integer
 285
 286 =cut
 287
 288
 289 sub transpos {
 290     my ($self,$value) = @_;
 291     if( defined $value) {
 292         if ( $value !~ /^([+-])?\d+$/ ) {
 293             $self->throw("[$value] for transpos has to be an integer\n");
 294         } else {
 295             $self->{'transpos'} = $value;
 296         }
 297     }
 298     return $self->{'transpos'};
 299 }
 300
 301
 302 =head2 issue
 303
 304  Title   : issue
 305  Usage   : $obj->issue();
 306  Function:
 307
 308             Sets and returns the position of the mutation in an array
 309             of mutations to be issued. Set after the validity of the
 310             mutation has been confirmed.
 311
 312  Example :
 313  Returns : string
 314  Args    : integer
 315
 316 =cut
 317
 318
 319 sub issue {
 320     my ($self,$value) = @_;
 321     if( defined $value) {
 322         if ( $value !~ /^([+-])?\d+$/ ) {
 323             $self->throw("[$value] for issue has to be an integer\n");
 324         } else {
 325             $self->{'issue'} = $value;
 326         }
 327     }
 328     return $self->{'issue'};
 329 }
 330
 331
 332 =head2 prelabel
 333
 334  Title   : prelabel
 335  Usage   : $obj->prelabel();
 336  Function:
 337
 338             Sets and returns the prelabel of the affected original allele
 339             location. Prelabel is a stable identifier whereas location
 340             can be changed by mutations. Prelabel comes from
 341             l<Bio::LiveSeq::Gene>.
 342
 343  Example :
 344  Returns : string
 345  Args    : string
 346
 347 =cut
 348
 349 sub prelabel {
 350    my ($self,$value) = @_;
 351    if ( defined $value) {
 352        $self->{'prelabel'} = $value;
 353    }
 354    if ( ! exists $self->{'prelabel'} ) {
 355        return;
 356    }
 357    return $self->{'prelabel'};
 358 }
 359
 360
 361 =head2 postlabel
 362
 363  Title   : postlabel
 364  Usage   : $obj->postlabel();
 365  Function:
 366
 367             Sets and returns the postlabel of the affected original allele
 368             location. Postlabel is a stable identifier whereas location
 369             can be changed by mutations. Postlabel comes from
 370             l<Bio::LiveSeq::Gene>.
 371
 372  Example :
 373  Returns : string
 374  Args    : string
 375
 376 =cut
 377
 378 sub postlabel {
 379    my ($self,$value) = @_;
 380    if ( defined $value) {
 381        $self->{'postlabel'} = $value;
 382    }
 383    if ( ! exists $self->{'postlabel'} ) {
 384        return;
 385    }
 386    return $self->{'postlabel'};
 387 }
 388
 389
 390 =head2 lastlabel
 391
 392  Title   : lastlabel
 393  Usage   : $obj->lastlabel();
 394  Function:
 395
 396             Sets and returns the lastlabel of the affected original allele
 397             location. Lastlabel is a stable identifier whereas location
 398             can be changed by mutations. Lastlabel comes from
 399             l<Bio::LiveSeq::Gene>.
 400
 401  Example :
 402  Returns : string
 403  Args    : string
 404
 405 =cut
 406
 407 sub lastlabel {
 408    my ($self,$value) = @_;
 409    if ( defined $value) {
 410        $self->{'lastlabel'} = $value;
 411    }
 412    if ( ! exists $self->{'lastlabel'} ) {
 413        return;
 414    }
 415    return $self->{'lastlabel'};
 416 }
 417
 418 1;