Bio/Map/Contig.pm

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