Bio/LiveSeq/Mutation.pm

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