Bio/Map/FPCMarker.pm

   1 #
   2 # BioPerl module for Bio::Map::fpcmarker
   3 #
   4 # Please direct questions and support issues to <bioperl-l@bioperl.org>
   5 #
   6 # Cared for by Gaurav Gupta <gaurav@genome.arizona.edu>
   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::FPCMarker - An central map object representing a marker
  17
  18 =head1 SYNOPSIS
  19
  20    # get the marker object of $marker from the Bio::Map::FPCMarker
  21    my $markerobj = $physical->get_markerobj($marker);
  22
  23    # acquire all the clones that hit this marker
  24    foreach my $clone ($markerobj->each_cloneid()) {
  25        print "   +++$clone\n";
  26    }
  27
  28    # find the position of this marker in $contig
  29    print "Position in contig $contig"," = ",$markerobj->position($contig),
  30          "\n";
  31
  32    # find the group of the marker
  33    print "Group : ",$markerobj->group();
  34
  35
  36 See L<Bio::Map::Position> and L<Bio::Map::PositionI> for more information.
  37
  38 =head1 DESCRIPTION
  39
  40 This object handles the notion of a marker.
  41 This object is intended to be used by a map parser like fpc.pm.
  42
  43 =head1 FEEDBACK
  44
  45 =head2 Mailing Lists
  46
  47 User feedback is an integral part of the evolution of this and other
  48 Bioperl modules. Send your comments and suggestions preferably to
  49 the Bioperl mailing list.  Your participation is much appreciated.
  50
  51   bioperl-l@bioperl.org                  - General discussion
  52   http://bioperl.org/wiki/Mailing_lists  - About the mailing lists
  53
  54 =head2 Support
  55
  56 Please direct usage questions or support issues to the mailing list:
  57
  58 I<bioperl-l@bioperl.org>
  59
  60 rather than to the module maintainer directly. Many experienced and
  61 reponsive experts will be able look at the problem and quickly
  62 address it. Please include a thorough description of the problem
  63 with code and data examples if at all possible.
  64
  65 =head2 Reporting Bugs
  66
  67 Report bugs to the Bioperl bug tracking system to help us keep track
  68 of the bugs and their resolution. Bug reports can be submitted via the
  69 web:
  70
  71   https://github.com/bioperl/bioperl-live/issues
  72
  73 =head1 AUTHOR - Gaurav Gupta
  74
  75 Email gaurav@genome.arizona.edu
  76
  77 =head1 CONTRIBUTORS
  78
  79 Sendu Bala  bix@sendu.me.uk
  80
  81 =head1 PROJECT LEADERS
  82
  83 Jamie Hatfield      jamie@genome.arizona.edu
  84 Dr. Cari Soderlund  cari@genome.arizona.edu
  85
  86 =head1 PROJECT DESCRIPTION
  87
  88 The project was done in Arizona Genomics Computational Laboratory (AGCoL)
  89 at University of Arizona.
  90
  91 This work was funded by USDA-IFAFS grant #11180 titled "Web Resources for
  92 the Computation and Display of Physical Mapping Data".
  93
  94 For more information on this project, please refer:
  95   http://www.genome.arizona.edu
  96
  97 =head1 APPENDIX
  98
  99 The rest of the documentation details each of the object methods.
 100 Internal methods are usually preceded with a _
 101
 102 =cut
 103
 104 # Let the code begin...
 105
 106 package Bio::Map::FPCMarker;
 107 use strict;
 108 use Bio::Map::Position;
 109 use Time::Local;
 110
 111 use base qw(Bio::Root::Root Bio::Map::MappableI);
 112
 113 =head2 new
 114
 115  Title   : new
 116  Usage   : my $clone = Bio::Map::FPCMarker->new
 117                       (
 118                        -name    => $marker,
 119                        -type    => $type,
 120                        -global  => $global,
 121                        -frame   => $frame,
 122                        -group   => $group,
 123                        -subgroup=> $subgroup,
 124                        -anchor  => $anchor,
 125                        -clones  => \%clones,
 126                        -contigs => \%contigs,
 127                        -position => \%markerpos,
 128                -remark => $remark
 129                        );
 130
 131  Function: Initialize a new Bio::Map::FPCMarker object
 132            Most people will not use this directly but get Markers
 133            through L<Bio::MapIO::fpc>
 134  Returns : L<Bio::Map::FPCMarker> object
 135  Args    : -name     => marker name string,
 136                -type     => type string,
 137                -global   => global position for marker,
 138                -frame    => boolean if marker is framework or placement,
 139                -group    => group number for marker,
 140                -subgroup => subgroup number of marker,
 141                -anchor   => boolean if marker is anchored,
 142                -clones   => all the clone elements in map (hashref),
 143                -contigs  => all the contig elements (hasref),
 144                -position => mapping of marker names to map position (hasref),
 145            -remark   => remarks, separated by newlines
 146
 147 =cut
 148
 149 sub new {
 150    my ($class,@args) = @_;
 151    my $self= $class->SUPER::new(@args);
 152
 153    my ($name,$type,$global,$frame,$group,
 154        $subgroup, $anchor, $clones,$contigs,
 155        $positions, $remark) = $self->_rearrange([qw(NAME TYPE GLOBAL FRAME
 156                                            GROUP SUBGROUP ANCHOR
 157                                            CLONES CONTIGS POSITIONS REMARK)],@args);
 158
 159    $self->name($name)                  if defined $name;
 160    $self->type($type)                  if defined $type;
 161    $self->global($global)              if defined $global;
 162    $self->group($group)                if defined $group;
 163    $self->subgroup($group)             if defined $subgroup;
 164    $self->anchor($anchor)              if defined $anchor;
 165    $self->remark($remark)              if defined $remark;
 166
 167    $self->set_clones($clones)          if defined $clones;
 168    $self->set_contigs($contigs)        if defined $contigs;
 169    $self->set_positions($positions)    if defined $positions;
 170
 171    return $self;
 172 }
 173
 174 =head1 Access Methods
 175
 176 These methods let you get and set the member variables
 177
 178 =head2 name
 179
 180  Title   : name
 181  Usage   : my $name = $markerobj->name();
 182  Function: Get/set the name for this marker
 183  Returns : scalar representing the current name of this marker
 184  Args    : none to get, OR string to set
 185
 186 =cut
 187
 188 sub name {
 189     my ($self) = shift;
 190     return $self->{'_name'} = shift if @_;
 191     return $self->{'_name'};
 192 }
 193
 194 =head2 type
 195
 196  Title   : type
 197  Usage   : my $type = $markerobj->type();
 198  Function: Get/set the type for this marker
 199  Returns : scalar representing the current type of this marker
 200  Args    : none to get, OR string to set
 201
 202 =cut
 203
 204 sub type {
 205     my ($self) = shift;
 206     return $self->{'_type'} = shift if @_;
 207     return $self->{'_type'};
 208 }
 209
 210 =head2 global
 211
 212  Title   : global
 213  Usage   : my $type = $markerobj->global();
 214  Function: Get/set the global position for this marker
 215  Returns : scalar representing the current global position of this marker
 216  Args    : none to get, OR string to set
 217
 218 =cut
 219
 220 sub global {
 221     my ($self) = shift;
 222     return $self->{'_global'} = shift if @_;
 223     return $self->{'_global'};
 224 }
 225
 226 =head2 anchor
 227
 228  Title   : anchor
 229  Usage   : my $anchor = $markerobj->anchor();
 230  Function: indicate if the Marker is anchored or not (True | False)
 231  Returns : scalar representing the anchor (1 | 0) for this marker
 232  Args    : none to get, OR 1|0 to set
 233
 234 =cut
 235
 236 sub anchor {
 237     my ($self) = shift;
 238     return $self->{'_anchor'} = shift if @_;
 239     return $self->{'_anchor'};
 240 }
 241
 242 =head2 framework
 243
 244  Title   : framework
 245  Usage   : $frame = $markerobj->framework();
 246  Function: indicate if the Marker is framework or placement (1 | 0)
 247  Returns : scalar representing if the marker is framework
 248            (1 if framework, 0 if placement)
 249  Args    : none to get, OR 1|0 to set
 250
 251 =cut
 252
 253 sub framework {
 254     my ($self) = shift;
 255     return $self->{'_frame'} = shift if @_;
 256     return $self->{'_frame'};
 257 }
 258
 259 =head2 group
 260
 261  Title   : group
 262  Usage   : $grpno = $markerobj->group();
 263  Function: Get/set the group number for this marker. This is a generic term,
 264            used for Linkage-Groups as well as for Chromosomes.
 265  Returns : scalar representing the group number of this marker
 266  Args    : none to get, OR string to set
 267
 268 =cut
 269
 270 sub group {
 271     my ($self) = shift;
 272     $self->{'_group'} = shift if @_;
 273     return $self->{'_group'} || 0;
 274 }
 275
 276 =head2 subgroup
 277
 278  Title   : subgroup
 279  Usage   : $subgroup = $marker->subgroup();
 280  Function: Get/set the subgroup for this marker. This is a generic term:
 281            subgroup here could represent subgroup of a Chromosome or of a
 282            Linkage Group. The user must take care of which subgroup he/she is
 283            querying for.
 284  Returns : scalar representing the subgroup of this marker
 285  Args    : none to get, OR string to set
 286
 287 =cut
 288
 289 sub subgroup {
 290     my ($self) = shift;
 291     $self->{'_subgroup'} = shift if @_;
 292     return $self->{'_subgroup'} || 0;
 293 }
 294
 295 =head2 position
 296
 297  Title   : position
 298  Usage   : $markerpos = $markerobj->position($ctg);
 299  Function: get the position of the marker in the contig
 300  Returns : scalar representing the position of the markernumber of
 301            the contig
 302  Args    : $ctg is necessary to look for the position of the marker
 303            in that contig.
 304
 305  *** This has nothing to do with an actual Bio::Map::PositionI object ***
 306
 307 =cut
 308
 309 sub position {
 310     my ($self,$ctg) = @_;
 311     return 0 unless defined $ctg;
 312
 313     return 0 unless( defined $self->{'_position'} &&
 314                      defined $self->{'_position'}{$ctg});
 315     return $self->{'_position'}{$ctg};
 316 }
 317
 318 =head2 remark
 319
 320  Title   : remark
 321  Usage   : $markerremark = $markerobj->remark();
 322  Function: get the remarks for this marker
 323  Returns : scalar of newline-separated markers
 324  Args    : none
 325
 326 =cut
 327
 328 sub remark {
 329     my ($self) = shift;
 330     return $self->{'_remark'} = shift if @_;
 331     return $self->{'_remark'};
 332 }
 333
 334 =head2 each_cloneid
 335
 336  Title   : each_cloneid
 337  Usage   : my @clones  = $map->each_cloneid();
 338  Function: retrieves all the clone ids in a map unordered
 339  Returns : list of strings (ids)
 340  Args    : none
 341
 342  *** This only supplies the ids set with the set_clones method ***
 343  *** It has nothing to do with actual Bio::Map::MappableI objects ***
 344
 345 =cut
 346
 347 sub each_cloneid {
 348     my ($self) = @_;
 349     return $self->_each_element('clones');
 350 }
 351
 352 =head2 each_contigid
 353
 354  Title   : each_contigid
 355  Usage   : my @contigs = $map->each_contigid();
 356  Function: retrieves all the contig ids in a map unordered
 357  Returns : list of strings (ids)
 358  Args    : none
 359
 360  *** This only supplies the ids set with the set_contigs method ***
 361  *** It has nothing to do with actual Bio::Map::MapI objects ***
 362
 363 =cut
 364
 365 sub each_contigid {
 366     my ($self) = @_;
 367     return $self->_each_element('contigs');
 368 }
 369
 370 sub _each_element{
 371     my ($self, $type) = @_;
 372
 373     $type = 'clones' unless defined $type;
 374     $type = lc("_$type");
 375
 376     return keys %{$self->{$type} || {}};
 377 }
 378
 379 =head2 set_clones
 380
 381  Title   : set_clones
 382  Usage   : $marker->set_clones(\%clones)
 383  Function: Set the clone ids hashref
 384  Returns : None
 385  Args    : Hashref of clone ids
 386
 387  *** This only sets a hash of ids ***
 388  *** It has nothing to do with actual Bio::Map::MappableI objects ***
 389
 390 =cut
 391
 392 sub set_clones{
 393    my ($self,$clones) = @_;
 394    if( defined $clones && ref($clones) =~ /HASH/ ) {
 395        $self->{'_clones'} = $clones;
 396    }
 397 }
 398
 399 =head2 set_contigs
 400
 401  Title   : set_contigs
 402  Usage   : $marker->set_contigs(\%contigs)
 403  Function: Set the contig ids hashref
 404  Returns : None
 405  Args    : Hashref of contig ids
 406
 407  *** This only sets a hash of ids ***
 408  *** It has nothing to do with actual Bio::Map::MapI objects ***
 409
 410 =cut
 411
 412 sub set_contigs{
 413    my ($self,$contigs) = @_;
 414    if( defined $contigs && ref($contigs) =~ /HASH/ ) {
 415        $self->{'_contigs'} = $contigs;
 416    }
 417 }
 418
 419 =head2 set_positions
 420
 421  Title   : set_positions
 422  Usage   : $marker->set_positions(\%markerpos)
 423  Function: Set the positions hashref
 424  Returns : None
 425  Args    : Hashref of marker positions
 426
 427  *** This only sets a hash of numbers ***
 428  *** It has nothing to do with actual Bio::Map::PositionI objects ***
 429
 430 =cut
 431
 432 sub set_positions{
 433    my ($self,$pos) = @_;
 434    if( defined $pos && ref($pos) =~ /HASH/ ) {
 435        $self->{'_positions'} = $pos;
 436    }
 437 }
 438
 439 1;