Bio/Map/Clone.pm

   1 # $Id$
   2 #
   3 # BioPerl module for Bio::Map::clone
   4 #
   5 # Please direct questions and support issues to <bioperl-l@bioperl.org>
   6 #
   7 # Cared for by Sendu Bala <bix@sendu.me.uk>
   8 #
   9 # Copyright Gaurav Gupta
  10 #
  11 # You may distribute this module under the same terms as perl itself
  12
  13 # POD documentation - main docs before the code
  14
  15 =head1 NAME
  16
  17 Bio::Map::Clone - An central map object representing a clone
  18
  19 =head1 SYNOPSIS
  20
  21    # get the clone object of $clone from the Bio::Map::Clone
  22    my $cloneobj = $physical->get_cloneobj($clone);
  23
  24    # acquire all the markers that hit this clone
  25    foreach my $marker ($cloneobj->each_markerid()) {
  26        print "   +++$marker\n";
  27    }
  28
  29 See L<Bio::Map::Position> and L<Bio::Map::PositionI> for more information.
  30
  31 =head1 DESCRIPTION
  32
  33 This object handles the notion of a clone. This clone will
  34 have a name and a position in a map.
  35
  36 This object is intended to be used by a map parser like fpc.pm.
  37
  38 =head1 FEEDBACK
  39
  40 =head2 Mailing Lists
  41
  42 User feedback is an integral part of the evolution of this and other
  43 Bioperl modules. Send your comments and suggestions preferably to
  44 the Bioperl mailing list.  Your participation is much appreciated.
  45
  46   bioperl-l@bioperl.org                  - General discussion
  47   http://bioperl.org/wiki/Mailing_lists  - About the mailing lists
  48
  49 =head2 Support
  50
  51 Please direct usage questions or support issues to the mailing list:
  52
  53 L<bioperl-l@bioperl.org>
  54
  55 rather than to the module maintainer directly. Many experienced and
  56 reponsive experts will be able look at the problem and quickly
  57 address it. Please include a thorough description of the problem
  58 with code and data examples if at all possible.
  59
  60 =head2 Reporting Bugs
  61
  62 Report bugs to the Bioperl bug tracking system to help us keep track
  63 of the bugs and their resolution. Bug reports can be submitted via the
  64 web:
  65
  66   http://bugzilla.open-bio.org/
  67
  68 =head1 AUTHOR - Gaurav Gupta
  69
  70 Email gaurav@genome.arizona.edu
  71
  72 =head1 CONTRIBUTORS
  73
  74 Sendu Bala  bix@sendu.me.uk
  75
  76 =head1 PROJECT LEADERS
  77
  78 Jamie Hatfield      jamie@genome.arizona.edu
  79 Dr. Cari Soderlund  cari@genome.arizona.edu
  80
  81 =head1 PROJECT DESCRIPTION
  82
  83 The project was done in Arizona Genomics Computational Laboratory (AGCoL)
  84 at University of Arizona.
  85
  86 This work was funded by USDA-IFAFS grant #11180 titled "Web Resources for
  87 the Computation and Display of Physical Mapping Data".
  88
  89 For more information on this project, please refer:
  90   http://www.genome.arizona.edu
  91
  92 =head1 APPENDIX
  93
  94 The rest of the documentation details each of the object methods.
  95 Internal methods are usually preceded with a _
  96
  97 =cut
  98
  99 # Let the code begin...
 100
 101 package Bio::Map::Clone;
 102 use strict;
 103 use Bio::Map::Position;
 104
 105 use base qw(Bio::Root::Root Bio::Map::MappableI);
 106
 107 =head2 new
 108
 109  Title   : new
 110  Usage   : my $clone = Bio::Map::Clone->new
 111                       (
 112                        -name    => $clone,
 113                        -markers => \@markers,
 114                        -contig  => $contig,
 115                        -type    => $type,
 116                        -bands   => $bands,
 117                        -gel     => $gel,
 118                        -group   => $group,
 119                        -remark  => $remark,
 120                        -fpnumber=> $fp_number,
 121                        -sequencetype  => $seq_type,
 122                        -sequencestatus=> $seq_status,
 123                        -fpcremark => $fpc_remark,
 124                        -matche    => \@ematch,
 125                        -matcha    => \@amatch,
 126                        -matchp    => \@pmatch,
 127                        -range     => Bio::Range->new(-start => $startrange,
 128                                                      -end   => $endrange)
 129                        );
 130  Function: Initialize a new Bio::Map::Clone object
 131            Most people will not use this directly but get Clones
 132            through L<Bio::MapIO::fpc>
 133  Returns : L<Bio::Map::Clone> object
 134  Args    :   -name => marker name string,
 135              -markers => array ref of markers,
 136              -contig  => contig name string,
 137              -type    => type string,
 138              -bands   => band string,
 139              -gel     => gel string,
 140              -group   => group name string,
 141              -remark  => remark string,
 142              -fpnumber=> FP number string,
 143              -sequencetype  => seq type string,
 144              -sequencestatus=> seq status string,
 145              -fpcremark => FPC remark,
 146              -matche    => array ref,
 147              -matcha    => array ref,
 148              -matchp    => array ref,
 149              -range     => L<Bio::Range> object,
 150
 151 =cut
 152
 153 sub new {
 154    my ($class,@args) = @_;
 155    my $self= $class->SUPER::new(@args);
 156
 157    my ($name,$markers,$contig,$type,$bands,$gel,$group,
 158        $remark,$fpnumber,$seqtype,$seqstatus,$fpcremark,
 159        $matche,$matcha,$matchp,
 160        $range) = $self->_rearrange([qw(NAME  MARKERS CONTIG TYPE
 161                                        BANDS GEL GROUP REMARK FPNUMBER
 162                                        SEQUENCETYPE SEQUENCESTATUS
 163                                        FPCREMARK MATCHE MATCHA MATCHP
 164                                        RANGE)],@args);
 165
 166    $self->name($name)                  if defined $name;
 167    $self->markers($markers)            if defined $markers;
 168    $self->contigid($contig)            if defined $contig;
 169    $self->type($type)                  if defined $type;
 170    $self->bands($bands)                if defined $bands;
 171    $self->gel($gel)                    if defined $gel;
 172    $self->group($group)                if defined $group;
 173    $self->remark($remark)              if defined $remark;
 174    $self->fp_number($fpnumber)         if defined $fpnumber;
 175    $self->sequence_type($seqtype)     if defined $seqtype;
 176    $self->sequence_status($seqstatus) if defined $seqstatus;
 177    $self->fpc_remark($fpcremark)       if defined $fpcremark;
 178    $self->range($range)                if defined $range;
 179
 180    $self->set_match('approx', $matcha) if defined $matcha;
 181    $self->set_match('pseudo', $matchp) if defined $matchp;
 182    $self->set_match('exact',  $matche) if defined $matche;
 183
 184    return $self;
 185 }
 186
 187 =head1 Access Methods
 188
 189 These methods let you get and set the member variables
 190
 191 =head2 name
 192
 193  Title   : name
 194  Usage   : my $name = $cloneobj->name();
 195  Function: Get/set the name for this Clone
 196  Returns : scalar representing the current name of this clone
 197  Args    : none to get, OR string to set
 198
 199 =cut
 200
 201 sub name {
 202     my ($self) = shift;
 203     return $self->{'_name'} = shift if @_;
 204     return $self->{'_name'};
 205 }
 206
 207 =head2 type
 208
 209  Title   : type
 210  Usage   : my $type = $cloneobj->type();
 211  Function: Get/set the type for this clone
 212  Returns : scalar representing the current type of this clone
 213  Args    : none to get, OR string to set
 214
 215 =cut
 216
 217 sub type {
 218     my ($self) = shift;
 219     return $self->{'_type'} = shift if @_;
 220     return $self->{'_type'};
 221 }
 222
 223 =head2 range
 224
 225  Title   : range
 226  Usage   : my $range = $cloneobj->range();
 227  Function: Get/set the range of the contig that this clone covers
 228  Returns : Bio::Range representing the current range of this contig,
 229            start and end of the contig can be thus found using:
 230            my $start = $contigobj->range()->start();
 231            my $end   = $contigobj->range()->end();
 232  Args    : none to get, OR Bio::Range to set
 233
 234 =cut
 235
 236 sub range {
 237     my ($self) = shift;
 238     return $self->{'_range'} = shift if @_;
 239     return $self->{'_range'};
 240 }
 241
 242 =head2 match
 243
 244  Title   : match
 245  Usage   : @eclone = $cloneobj->match('exact');
 246            @aclone = $cloneobj->match('approximate');
 247            @pclone = $cloneobj->match('pseudo');
 248  Function: get all matching clones
 249  Returns : list
 250  Args    : scalar representing the type of clone to be
 251            queried.
 252
 253 =cut
 254
 255 sub match {
 256   my ($self,$type) = @_;
 257
 258   $type = "_match" . lc(substr($type, 0, 1));
 259   return @{$self->{$type} || []};
 260 }
 261
 262 =head2 each_match
 263
 264  Title   : each_match
 265  Function: Synonym of the match() method.
 266
 267 =cut
 268
 269 *each_match = \&match;
 270
 271 =head2 set_match
 272
 273  Title   : set_match
 274  Usage   : $clone->set_match($type,$values);
 275  Function: Set the Matches per type
 276  Returns : None
 277  Args    : type (one of 'exact' 'approx' 'pseudo')
 278            array ref of match values
 279
 280 =cut
 281
 282 sub set_match{
 283    my ($self,$type,$val) = @_;
 284    $type = "_match" . lc(substr($type, 0, 1));
 285    $self->{$type} = $val;
 286 }
 287
 288 =head2 gel
 289
 290  Title   : gel
 291  Usage   : $clonegel = $cloneobj->gel();
 292  Function: Get/set the gel number for this clone
 293  Returns : scalar representing the gel number of this clone
 294  Args    : none to get, OR string to set
 295
 296 =cut
 297
 298 sub gel {
 299     my ($self) = shift;
 300     return $self->{'_gel'} = shift if @_;
 301     return $self->{'_gel'};
 302 }
 303
 304 =head2 remark
 305
 306  Title   : remark
 307  Usage   : $cloneremark = $cloneobj->remark();
 308  Function: Get/set the remark for this clone
 309  Returns : scalar representing the current remark of this clone
 310  Args    : none to get, OR string to set
 311
 312 =cut
 313
 314 sub remark {
 315     my ($self) = shift;
 316     return $self->{'_remark'} = shift if @_;
 317     return $self->{'_remark'};
 318 }
 319
 320 =head2 fp_number
 321
 322  Title   : fp_number
 323  Usage   : $clonefpnumber = $cloneobj->fp_number();
 324  Function: Get/set the fp number for this clone
 325  Returns : scalar representing the fp number of this clone
 326  Args    : none to get, OR string to set
 327
 328 =cut
 329
 330 sub fp_number {
 331     my ($self) = shift;
 332     return $self->{'_fpnumber'} = shift if @_;
 333     return $self->{'_fpnumber'};
 334 }
 335
 336 =head2 sequence_type
 337
 338  Title   : sequence_type
 339  Usage   : $cloneseqtype = $cloneobj->sequence_type();
 340  Function: Get/set the sequence type for this clone
 341  Returns : scalar representing the sequence type of this clone
 342  Args    : none to get, OR string to set
 343
 344 =cut
 345
 346 sub sequence_type {
 347     my ($self) = shift;
 348     return $self->{'_sequencetype'} = shift if @_;
 349     return $self->{'_sequencetype'};
 350 }
 351
 352 =head2 sequence_status
 353
 354  Title   : sequence_status
 355  Usage   : $cloneseqstatus = $cloneobj->sequence_status();
 356  Function: Get/set the sequence status for this clone
 357  Returns : scalar representing the sequence status of this clone
 358  Args    : none to get, OR string to set
 359
 360 =cut
 361
 362 sub sequence_status {
 363     my ($self) = shift;
 364     return $self->{'_sequencestatus'} = shift if @_;
 365     return $self->{'_sequencestatus'};
 366 }
 367
 368 =head2 fpc_remark
 369
 370  Title   : fpc_remark
 371  Usage   : $clonefpcremark = $cloneobj->fpc_remark();
 372  Function: Get/set the fpc remark for this clone
 373  Returns : scalar representing the fpc remark of this clone
 374  Args    : none to get, OR string to set
 375
 376 =cut
 377
 378 sub fpc_remark {
 379     my ($self) = shift;
 380     return $self->{'_fpcremark'} = shift if @_;
 381     return $self->{'_fpcremark'};
 382 }
 383
 384 =head2 bands
 385
 386  Title   : bands
 387  Usage   : @clonebands = $cloneobj->bands();
 388  Function: Get/set the bands for this clone
 389  Returns : liat representing the band of this clone, if
 390            readcor = 1 while creating the MapIO object and the
 391            .cor exists
 392  Args    : none to get, OR string to set
 393
 394 =cut
 395
 396 sub bands {
 397     my ($self) = shift;
 398     return $self->{'_bands'} = shift if @_;
 399     return $self->{'_bands'};
 400 }
 401
 402 =head2 group
 403
 404  Title   : group
 405  Usage   : $cloneobj->group($chrno);
 406  Function: Get/set the group number for this clone.
 407            This is a generic term, used for Linkage-Groups as well as for
 408            Chromosomes.
 409  Returns : scalar representing the group number of this clone
 410  Args    : none to get, OR string to set
 411
 412 =cut
 413
 414 sub group {
 415     my ($self) = shift;
 416     return $self->{'_group'} = shift if @_;
 417     return $self->{'_group'};
 418 }
 419
 420 =head2 contigid
 421
 422  Title   : contigid
 423  Usage   : my $ctg = $cloneobj->contigid();
 424  Function: Get/set the contig this clone belongs to
 425  Returns : scalar representing the contig
 426  Args    : none to get, OR string to set
 427
 428 =cut
 429
 430 sub contigid {
 431     my ($self) = shift;
 432     $self->{'_contig'} = shift if @_;
 433     return $self->{'_contig'} || 0;
 434 }
 435
 436 =head2 each_markerid
 437
 438  Title   : each_markerid
 439  Usage   : @markers = $cloneobj->each_markerid();
 440  Function: retrieves all the elements in a map unordered
 441  Returns : list of strings (ids)
 442  Args    : none
 443
 444  *** This only supplies the ids set with the set_markers method ***
 445  *** It has nothing to do with actual Bio::Map::MarkerI objects ***
 446
 447 =cut
 448
 449 sub each_markerid {
 450   my ($self,$value) = @_;
 451   return @{$self->{"_markers"}};
 452 }
 453
 454 =head2 set_markers
 455
 456  Title   : markers
 457  Usage   : $obj->set_markers($newval)
 458  Function: Set list of Marker ids (arrayref)
 459  Returns : None
 460  Args    : arrayref of strings (ids)
 461
 462  *** This only sets a list of ids ***
 463  *** It has nothing to do with actual Bio::Map::MarkerI objects ***
 464
 465 =cut
 466
 467 sub set_markers {
 468     my ($self,$markers) = @_;
 469     if( defined $markers && ref($markers) =~ /ARRAY/ ) {
 470         $self->{'_markers'} = $markers;
 471     }
 472 }
 473
 474 1;