Bio/Map/Clone.pm

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