Bio/Assembly/ScaffoldI.pm

   1 #
   2 #  BioPerl module for Bio::Assembly::ScaffoldI
   3 #
   4 # Copyright by Robson F. de Souza
   5 #
   6 # You may distribute this module under the same terms as perl itself
   7 #
   8 # POD documentation - main docs before the code
   9
  10 =head1 NAME
  11
  12 Bio::Assembly::ScaffoldI - Abstract Inteface of Sequence Assemblies
  13
  14 =head1 SYNOPSIS
  15
  16     # get a Bio::Assembly::ScaffoldI object somehow
  17
  18     foreach my $contig ($assembly->all_contigs) {
  19        # do something (see Bio::Assembly::Contig)
  20     }
  21
  22 =head1 DESCRIPTION
  23
  24 This interface defines the basic set of methods an object should have
  25 to manipulate assembly data.
  26
  27 =head1 FEEDBACK
  28
  29 =head2 Mailing Lists
  30
  31 User feedback is an integral part of the evolution of this and other
  32 Bioperl modules. Send your comments and suggestions preferably to the
  33 Bioperl mailing lists  Your participation is much appreciated.
  34
  35   bioperl-l@bioperl.org                  - General discussion
  36   http://bioperl.org/wiki/Mailing_lists  - About the mailing lists
  37
  38 =head2 Support
  39
  40 Please direct usage questions or support issues to the mailing list:
  41
  42 I<bioperl-l@bioperl.org>
  43
  44 rather than to the module maintainer directly. Many experienced and
  45 reponsive experts will be able look at the problem and quickly
  46 address it. Please include a thorough description of the problem
  47 with code and data examples if at all possible.
  48
  49 =head2 Reporting Bugs
  50
  51 Report bugs to the Bioperl bug tracking system to help us keep track
  52 the bugs and their resolution.  Bug reports can be submitted via the
  53 web:
  54
  55   https://github.com/bioperl/bioperl-live/issues
  56
  57 =head1 AUTHOR - Robson Francisco de Souza
  58
  59 Email: rfsouza@citri.iq.usp.br
  60
  61 =head1 APPENDIX
  62
  63 The rest of the documentation details each of the object
  64 methods. Internal methods are usually preceded with a _
  65
  66 =cut
  67
  68 #
  69 # Now, let's code!
  70
  71
  72 package Bio::Assembly::ScaffoldI;
  73
  74 use strict;
  75 use Carp;
  76
  77 # Inheritance
  78
  79 use base qw(Bio::Root::RootI);
  80
  81 #
  82 # Methods
  83
  84 =head1 Accessing general assembly data
  85
  86 =cut
  87
  88 =head2 get_nof_contigs
  89
  90         Title   : get_nof_contigs
  91         Usage   : $assembly->get_nof_contigs()
  92         Function: Get the number of contigs included in the assembly
  93         Returns : integer
  94         Args    : none
  95
  96 =cut
  97
  98 sub get_nof_contigs {
  99     my $self = shift;
 100
 101     $self->throw_not_implemented();
 102 }
 103
 104 =head2 get_nof_singlets
 105
 106         Title   : get_nof_singlets
 107         Usage   : $assembly->get_nof_singlets()
 108         Function: Get the number of singlets included in the assembly
 109         Returns : integer
 110         Args    : none
 111
 112 =cut
 113
 114 sub get_nof_singlets {
 115     my $self = shift;
 116
 117     $self->throw_not_implemented();
 118 }
 119
 120 =head2 get_contig_ids
 121
 122         Title   : get_contig_ids
 123         Usage   : $assembly->get_contig_ids()
 124         Function: Access list of contig IDs from assembly
 125         Returns : an array if there are any contigs in the assembly.
 126                   undef otherwise
 127         Args    : an array of contig IDs
 128
 129 =cut
 130
 131 sub get_contig_ids {
 132     my $self = shift;
 133
 134     $self->throw_not_implemented();
 135 }
 136
 137 =head2 get_singlet_ids
 138
 139         Title   : get_singlet_ids
 140         Usage   : $assembly->get_singlet_ids()
 141         Function: Access list of singlet IDs from assembly
 142         Returns : an array if there are any singlets in the assembly.
 143                   undef otherwise
 144         Args    : an array of singlet IDs
 145
 146 =cut
 147
 148 sub get_singlet_ids {
 149     my $self = shift;
 150
 151     $self->throw_not_implemented();
 152 }
 153
 154 =head2 get_contig_by_id
 155
 156     Title   : get_contig_by_id
 157     Usage   : $assembly->get_contig_by_id($id)
 158     Function: Get a reference for a contig from the assembly
 159     Returns : a Bio::Assembly::Contig object or undef
 160     Args    : [string] contig unique identifier (ID)
 161
 162 =cut
 163
 164 sub get_contig_by_id {
 165     my $self = shift;
 166     $self->throw_not_implemented();
 167 }
 168
 169 =head2 get_singlet_by_id
 170
 171     Title   : get_singlet_by_id
 172     Usage   : $assembly->get_singlet_by_id()
 173     Function: Get a reference for a singlet from the assembly
 174     Returns : Bio::Assembly::Singlet object or undef
 175     Args    : [string] a singlet ID
 176
 177 =cut
 178
 179 sub get_singlet_by_id {
 180     my $self = shift;
 181     $self->throw_not_implemented();
 182 }
 183
 184 =head1 Modifier methods
 185
 186 Implementation of these methods is optional in the sense that
 187 read-only implementations may not have these. If an object implements
 188 one of them, it should however implement all.
 189
 190 =cut
 191
 192 =head2 add_contig
 193
 194         Title   : add_contig
 195         Usage   : $assembly->add_contig($contig)
 196         Function: Add another contig to the Bio::Assembly::ScaffoldI object
 197         Returns : 1 on success, 0 otherwise
 198         Args    : a Bio::Assembly:Contig object
 199
 200     See Bio::Assembly::Contig for more information
 201
 202 =cut
 203
 204 #---------------------
 205 sub add_contig {
 206 #---------------------
 207         my ($self) = @_;
 208         $self->throw_not_implemented();
 209 }
 210
 211 =head2 add_singlet
 212
 213         Title   : add_singlet
 214         Usage   : $assembly->add_singlet($seq)
 215         Function: Add another singlet to the Bio::Assembly::ScaffoldI object
 216         Returns : 1 on success, 0 otherwise
 217         Args    : a Bio::Assembly::Singlet object
 218
 219 =cut
 220
 221 #---------------------
 222 sub add_singlet {
 223 #---------------------
 224         my ($self) = @_;
 225         $self->throw_not_implemented();
 226 }
 227
 228 =head2 remove_contigs
 229
 230         Title   : remove_contigs
 231         Usage   : $assembly->remove_contigs(1..4)
 232         Function: Remove contig from assembly object
 233         Returns : a Bio::Assembly::Contig object
 234         Args    : a list of contig IDs
 235
 236     See function get_contig_ids() above
 237
 238 =cut
 239
 240 #---------------------
 241 sub remove_contigs {
 242 #---------------------
 243         my ($self) = @_;
 244         $self->throw_not_implemented();
 245 }
 246
 247 =head2 remove_singlets
 248
 249         Title   : remove_singlets
 250         Usage   : $assembly->remove_singlets(1..4)
 251         Function: Remove singlets from assembly object
 252         Returns : an array of Bio::Assembly::Singlet objects
 253         Args    : an array of singlet IDs
 254
 255     See function get_singlet_ids() above
 256
 257 =cut
 258
 259 #---------------------
 260 sub remove_singlets {
 261 #---------------------
 262         my ($self) = @_;
 263         $self->throw_not_implemented();
 264 }
 265
 266 =head1 Contig and singlet selection methos
 267
 268 =cut
 269
 270 =head2 select_contigs
 271
 272         Title   : select_contig
 273         Usage   : $assembly->select_contig
 274         Function: Selects an array of contigs from the assembly
 275         Returns : an array of Bio::Assembly::Contig objects
 276         Args    : an array of contig ids
 277
 278     See function get_contig_ids() above
 279
 280 =cut
 281
 282 #---------------------
 283 sub select_contigs {
 284 #---------------------
 285         my ($self) = @_;
 286         $self->throw_not_implemented();
 287 }
 288
 289 =head2 select_singlets
 290
 291         Title   : select_singlets
 292         Usage   : $assembly->select_singlets(@list)
 293         Function: Selects an array of singlets from the assembly
 294         Returns : an array of Bio::Assembly::Singlet objects
 295         Args    : an array of singlet ids
 296
 297     See function get_singlet_ids() above
 298
 299 =cut
 300
 301 #---------------------
 302 sub select_singlets {
 303 #---------------------
 304         my ($self) = @_;
 305         $self->throw_not_implemented();
 306 }
 307
 308 =head2 all_contigs
 309
 310         Title   : all_contigs
 311         Usage   : my @contigs = $assembly->all_contigs
 312         Function: Returns a list of all contigs in this assembly.
 313                   Contigs are both clusters and alignments of one
 314                   or more reads, with an associated consensus
 315                   sequence.
 316         Returns : array of Bio::Assembly::Contig
 317         Args    : none
 318
 319 =cut
 320
 321 #---------------------
 322 sub all_contigs {
 323 #---------------------
 324         my ($self) = @_;
 325         $self->throw_not_implemented();
 326 }
 327
 328 =head2 all_singlets
 329
 330     Title   : all_singlets
 331     Usage   : my @singlets = $assembly->all_singlets
 332     Function: Returns a list of all singlets in this assembly.
 333               Singlets are isolated reads, without non-vector
 334               matches to any other read in the assembly.
 335     Returns : array of Bio::Assembly::Singlet objects
 336     Args    : none
 337
 338 =cut
 339
 340 #---------------------
 341 sub all_singlets {
 342 #---------------------
 343         my ($self) = @_;
 344         $self->throw_not_implemented();
 345 }
 346
 347 1;