Bio/Map/Contig.pm

   1 # $Id$
   2 #
   3 # BioPerl module for Bio::Map::Contig
   4 #
   5 # Cared for by Sendu Bala <bix@sendu.me.uk>
   6 #
   7 # Copyright Gaurav Gupta
   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::Map::Contig - A MapI implementation handling the contigs of a
  16 Physical Map (such as FPC)
  17
  18 =head1 SYNOPSIS
  19
  20     # get the contig object of $contig from the Bio::Map::Physical
  21     my $ctgobj = $physical->get_contigobj($contig);
  22
  23     # acquire all the markers that lie in this contig
  24     foreach my $marker ($ctgobj->each_markerid()) {
  25         print "   +++$marker\n";
  26     }
  27
  28     # find the group of this contig
  29     print "Group: ",$ctgobj->group(),"\n";
  30
  31     # find the range of this contig
  32     print "RANGE: start:",$ctgobj->range()->start(),"\tend: ",
  33            $ctgobj->range()->end(),"\n";
  34
  35     # find the position of this contig in $group (chromosome)
  36     print "Position in Group $group"," = ",$ctgobj->position($group),"\n";
  37
  38
  39 =head1 DESCRIPTION
  40
  41 This is an implementation of Bio::Map::MapI.  It handles the
  42 essential storage of name, species, type, and units as well as in
  43 memory representation of the elements of a map.
  44
  45 Bio::Map::Contig has been tailored to work for FPC physical maps, but
  46 could probably be used for others as well (with the appropriate MapIO
  47 module).
  48
  49 =head1 FEEDBACK
  50
  51 =head2 Mailing Lists
  52
  53 User feedback is an integral part of the evolution of this and other
  54 Bioperl modules. Send your comments and suggestions preferably to
  55 the Bioperl mailing list.  Your participation is much appreciated.
  56
  57   bioperl-l@bioperl.org                  - General discussion
  58   http://bioperl.org/wiki/Mailing_lists  - About the mailing lists
  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::Contig;
 102 use vars qw($MAPCOUNT);
 103 use strict;
 104
 105 # Object preamble - inherits from Bio::Root::Root
 106
 107 use Bio::Range;
 108
 109 use base qw(Bio::Map::SimpleMap);
 110 BEGIN { $MAPCOUNT = 1; }
 111
 112 =head2 new
 113
 114  Title   : new
 115  Usage   : my $clone = Bio::Map::Contig->new
 116                       (
 117                        -name    => $name,
 118                        -chr_remark   => $cremark,
 119                        -user_remark  => $uremark,
 120                        -trace_remark => $tremark,
 121                        -group   => $group,
 122                        -subgroup=> $subgroup,
 123                        -anchor  => $anchor,
 124                        -markers => \%markers,
 125                        -clones  => \%clones,
 126                        -position => $pos
 127                        -range    => Bio::Range->new(-start =>$s,-end=>$e),
 128                        );
 129
 130  Function: Initialize a new Bio::Map::Contig object
 131            Most people will not use this directly but get Markers
 132            through L<Bio::MapIO::fpc>
 133  Returns : L<Bio::Map::Contig> object
 134  Args    : ( -name    => name string,
 135              -chr_remark   => chr remark string,
 136              -user_remark  => userremark string,
 137              -trace_remark => tremark string,
 138              -group   => group string,
 139              -subgroup=> subgroup string,
 140              -anchor  => boolean if this is anchored or not,
 141              -markers => hashref of contained markers,
 142              -clones  => hashref of contained clones,
 143              -position => position
 144              -range    => L<Bio::Range>
 145
 146 =cut
 147
 148 sub new {
 149    my ($class,@args) = @_;
 150    my $self = $class->SUPER::new(@args);
 151
 152    my ($name,$cremark,$uremark,$tremark,
 153        $group,$subgroup, $anchor,$markers, $clones,
 154        $position,$range) = $self->_rearrange([qw(NAME CHR_REMARK USER_REMARK
 155                                                  TRACE_REMARK GROUP SUBGROUP
 156                                                  ANCHOR MARKERS CLONES
 157                                                  POSITION RANGE)],@args);
 158
 159    $self->name($name)                  if defined $name;
 160    $self->chr_remark($cremark)         if defined $cremark;
 161    $self->user_remark($uremark)        if defined $uremark;
 162    $self->trace_remark($tremark)       if defined $tremark;
 163    $self->group($group)                if defined $group;
 164    $self->subgroup($group)             if defined $subgroup;
 165    $self->anchor($anchor)              if defined $anchor;
 166
 167    $self->set_markers($markers)        if defined $markers;
 168    $self->set_clones($clones)          if defined $clones;
 169    $self->range($range)                if defined $range;
 170    $self->position($position)          if defined $position;
 171
 172    return $self;
 173 }
 174
 175 =head2 Modifier methods
 176
 177 All methods present in L<Bio::Map::SimpleMap> are implemented by this class.
 178 Most of the methods are inherited from SimpleMap.  The following methods
 179 have been modified to reflect the needs of physical maps.
 180
 181 =head2 chr_remark
 182
 183  Title   : chr_remark
 184  Usage   : my $chrremark = $contigobj->chr_remark();
 185  Function: Get/set the group remark for this contig
 186  Returns : scalar representing the current group_remark of this contig
 187  Args    : none to get, OR string to set
 188
 189 =cut
 190
 191 sub chr_remark {
 192     my ($self) = shift;
 193     $self->{'_cremark'} = shift if @_;
 194     return defined $self->{'_cremark'} ? $self->{'_cremark'} : '';
 195 }
 196
 197 =head2 user_remark
 198
 199  Title   : user_remark
 200  Usage   : my $userremark = $contigobj->user_remark();
 201  Function: Get/set the user remark for this contig
 202  Returns : scalar representing the current user_remark of this contig
 203  Args    : none to get, OR string to set
 204
 205 =cut
 206
 207 sub user_remark {
 208     my ($self) = shift;
 209     $self->{'_uremark'} = shift if @_;
 210     return defined $self->{'_uremark'} ? $self->{'_uremark'} : '';
 211 }
 212
 213 =head2 trace_remark
 214
 215  Title   : trace_remark
 216  Usage   : my $traceremark = $contigobj->trace_remark();
 217  Function: Get/set the trace remark for this contig
 218  Returns : scalar representing the current trace_remark of this contig
 219  Args    : none to get, OR string to set
 220
 221 =cut
 222
 223 sub trace_remark {
 224     my ($self) = shift;
 225     $self->{'_tremark'} = shift if @_;
 226     return defined $self->{'_tremark'} ? $self->{'_tremark'} : '';
 227 }
 228
 229 =head2 range
 230
 231  Title   : range
 232  Usage   : my $range = $contigobj->range();
 233  Function: Get/set the range for this Contig
 234  Returns : Bio::Range representing the current range of this contig,
 235            start and end of the contig can be thus found using:
 236            my $start = $contigobj->range()->start();
 237            my $end   = $contigobj->range()->end();
 238  Args    : none to get, OR Bio::Range to set
 239
 240 =cut
 241
 242 sub range {
 243     my ($self) = shift;
 244     return $self->{'_range'} = shift if @_;
 245     return $self->{'_range'};
 246 }
 247
 248 =head2 position
 249
 250  Title   : position
 251  Usage   : $ctgpos = $contigobj->position();
 252  Function: Get/set the position of the contig in the group
 253  Returns : scalar representing the position of the contig in the group
 254  Args    : none to get, OR string to set
 255
 256 =cut
 257
 258 sub position {
 259     my ($self) = shift;
 260     $self->{'_position'} = shift if @_;
 261     return $self->{'_position'} || 0;
 262 }
 263
 264 =head2 anchor
 265
 266  Title   : anchor
 267  Usage   : $ctganchor = $contig->anchor();
 268  Function: Get/set the anchor value for this Contig (True | False)
 269  Returns : scalar representing the anchor (1 | 0) for this contig
 270  Args    : none to get, OR string to set
 271
 272 =cut
 273
 274 sub anchor {
 275     my ($self) = shift;
 276     return $self->{'_anchor'} = shift if @_;
 277     return $self->{'_anchor'};
 278 }
 279
 280 =head2 group
 281
 282  Title   : group
 283  Usage   : $groupno = $contigobj->group();
 284  Function: Get/set the group number for this contig.
 285            This is a generic term, used for Linkage-Groups as well as for
 286            Chromosomes.
 287  Returns : scalar representing the group number of this contig
 288  Args    : none
 289
 290 =cut
 291
 292 sub group {
 293     my ($self) = shift;
 294     $self->{'_group'} = shift if @_;
 295     return $self->{'_group'} || 0;
 296 }
 297
 298 =head2 subgroup
 299
 300  Title   : subgroup
 301  Usage   : $subgroup = $contig->subgroup();
 302  Function: Get/set the subgroup for this contig. This is a generic term:
 303            subgroup here could represent subgroup of a Chromosome or of a
 304            Linkage Group. The user must take care of which subgroup he/she is
 305            querying for.
 306  Returns : A scalar representing the subgroup of this contig
 307  Args    : none
 308
 309 =cut
 310
 311 sub subgroup {
 312     my ($self) = @_;
 313     return $self->{'_subgroup'} = shift if @_;
 314     return $self->{'_subgroup'} || 0;
 315 }
 316
 317 =head2 each_cloneid
 318
 319  Title   : each_cloneid
 320  Usage   : my @clones  = $map->each_cloneid();
 321  Function: retrieves all the clone ids in a map unordered
 322  Returns : list of strings (ids)
 323  Args    : none
 324
 325  *** This only supplies the ids set with the set_clones method ***
 326  *** It has nothing to do with actual Bio::Map::MappableI objects ***
 327
 328 =cut
 329
 330 sub each_cloneid {
 331     my ($self) = @_;
 332     return $self->_each_element('clones');
 333 }
 334
 335 =head2 each_markerid
 336
 337  Title   : each_markerid
 338  Usage   : my @markers = $map->each_markerid();
 339  Function: retrieves all the marker ids in a map unordered
 340  Returns : list of strings (ids)
 341  Args    : none
 342
 343  *** This only supplies the ids set with the set_markers method ***
 344  *** It has nothing to do with actual Bio::Map::MarkerI objects ***
 345
 346 =cut
 347
 348 sub each_markerid {
 349     my ($self) = @_;
 350     return $self->_each_element('markers');
 351 }
 352
 353 sub _each_element {
 354     my ($self, $type) = @_;
 355     $type = 'clones' if (!defined($type));
 356     $type = lc("_$type");
 357     return keys %{$self->{$type} || {}};
 358 }
 359
 360 =head2 set_clones
 361
 362  Title   : set_clones
 363  Usage   : $marker->set_clones(\%clones)
 364  Function: Set the clones hashref
 365  Returns : None
 366  Args    : Hashref of clone ids
 367
 368  *** This only sets a hash of ids ***
 369  *** It has nothing to do with actual Bio::Map::MappableI objects ***
 370
 371 =cut
 372
 373 sub set_clones {
 374    my ($self,$clones) = @_;
 375    if( defined $clones && ref($clones) =~ /HASH/ ) {
 376        $self->{'_clones'} = $clones;
 377    }
 378 }
 379
 380 =head2 set_markers
 381
 382  Title   : markers
 383  Usage   : $obj->set_markers($newval)
 384  Function: Set list of Markers (hashref)
 385  Returns : None
 386  Args    : Hashref of marker ids
 387
 388  *** This only sets a hash of ids ***
 389  *** It has nothing to do with actual Bio::Map::MarkerI objects ***
 390
 391 =cut
 392
 393 sub set_markers {
 394     my ($self,$markers) = @_;
 395     if( defined $markers && ref($markers) =~ /HASH/ ) {
 396         $self->{'_markers'} = $markers;
 397     }
 398 }
 399
 400 1;