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1 # $Id: ScaffoldI.pm,v 1.2 2002/11/11 18:16:30 lapp Exp $
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2 #
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3 # BioPerl module for Bio::Assembly::ScaffoldI
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4 #
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5 # Copyright by Robson F. de Souza
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6 #
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7 # You may distribute this module under the same terms as perl itself
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8 #
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9 # POD documentation - main docs before the code
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10
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11 =head1 NAME
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12
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13 Bio::Assembly::ScaffoldI - Abstract Inteface of Sequence Assemblies
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14
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15 =head1 SYNOPSYS
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16
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17 # get a Bio::Assembly::ScaffoldI object somehow
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18
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19 foreach my $contig ($assembly->all_contigs) {
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20 # do something (see Bio::Assembly::Contig)
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21 }
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22
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23 =head1 DESCRIPTION
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24
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25 This interface defines the basic set of methods an object should have
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26 to manipulate assembly data.
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27
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28 =head1 FEEDBACK
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29
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30 =head2 Mailing Lists
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31
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32 User feedback is an integral part of the evolution of this and other
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33 Bioperl modules. Send your comments and suggestions preferably to the
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34 Bioperl mailing lists Your participation is much appreciated.
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35
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36 bioperl-l@bioperl.org - General discussion
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37 http://bio.perl.org/MailList.html - About the mailing lists
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38
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39 =head2 Reporting Bugs
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40
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41 Report bugs to the Bioperl bug tracking system to help us keep track
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42 the bugs and their resolution. Bug reports can be submitted via email
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43 or the web:
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44
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45 bioperl-bugs@bio.perl.org
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46 http://bugzilla.bioperl.org/
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47
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48 =head1 AUTHOR - Robson Francisco de Souza
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49
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50 Email: rfsouza@citri.iq.usp.br
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51
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52 =head1 APPENDIX
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53
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54 The rest of the documentation details each of the object
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55 methods. Internal methods are usually preceded with a _
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56
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57 =cut
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58
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59 #
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60 # Now, let's code!
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61
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62
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63 package Bio::Assembly::ScaffoldI;
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64
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65 use strict;
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66 use vars qw(@ISA);
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67 use Carp;
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68 use Bio::Root::RootI;
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69
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70 # Inheritance
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71
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72 @ISA = qw(Bio::Root::RootI);
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73
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74 #
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75 # Methods
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76
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77 =head1 Accessing general assembly data
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78
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79 =cut
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80
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81 =head2 get_nof_contigs
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82
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83 Title : get_nof_contigs
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84 Usage : $assembly->get_nof_contigs()
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85 Function: Get the number of contigs included in the assembly
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86 Returns : integer
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87 Args : none
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88
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89 =cut
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90
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91 sub get_nof_contigs {
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92 my $self = shift;
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93
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94 $self->throw_not_implemented();
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95 }
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96
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97 =head2 get_nof_singlets
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98
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99 Title : get_nof_singlets
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100 Usage : $assembly->get_nof_singlets()
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101 Function: Get the number of singlets included in the assembly
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102 Returns : integer
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103 Args : none
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104
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105 =cut
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106
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107 sub get_nof_singlets {
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108 my $self = shift;
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109
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110 $self->throw_not_implemented();
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111 }
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112
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113 =head2 get_contig_ids
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114
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115 Title : get_contig_ids
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116 Usage : $assembly->get_contig_ids()
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117 Function: Access list of contig IDs from assembly
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118 Returns : an array if there are any contigs in the assembly.
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119 undef otherwise
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120 Args : an array of contig IDs
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121
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122 =cut
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123
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124 sub get_contig_ids {
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125 my $self = shift;
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126
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127 $self->throw_not_implemented();
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128 }
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129
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130 =head2 get_singlet_ids
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131
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132 Title : get_singlet_ids
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133 Usage : $assembly->get_singlet_ids()
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134 Function: Access list of singlet IDs from assembly
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135 Returns : an array if there are any singlets in the assembly.
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136 undef otherwise
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137 Args : an array of singlet IDs
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138
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139 =cut
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140
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141 sub get_singlet_ids {
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142 my $self = shift;
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143
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144 $self->throw_not_implemented();
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145 }
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146
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147 =head2 get_contig_by_id
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148
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149 Title : get_contig_by_id
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150 Usage : $assembly->get_contig_by_id($id)
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151 Function: Get a reference for a contig from the assembly
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152 Returns : a Bio::Assembly::Contig object or undef
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153 Args : [string] contig unique identifier (ID)
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154
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155 =cut
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156
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157 sub get_contig_by_id {
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158 my $self = shift;
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159 $self->throw_not_implemented();
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160 }
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161
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162 =head2 get_singlet_by_id
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163
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164 Title : get_singlet_by_id
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165 Usage : $assembly->get_singlet_by_id()
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166 Function: Get a reference for a singlet from the assembly
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167 Returns : Bio::PrimarySeqI object or undef
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168 Args : [string] a singlet ID
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169
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170 =cut
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171
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172 sub get_singlet_by_id {
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173 my $self = shift;
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174 $self->throw_not_implemented();
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175 }
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176
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177 =head1 Modifier methods
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178
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179 Implementation of these methods is optional in the sense that
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180 read-only implementations may not have these. If an object implements
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181 one of them, it should however implement all.
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182
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183 =cut
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184
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185 =head2 add_contig
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186
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187 Title : add_contig
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188 Usage : $assembly->add_contig($contig)
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189 Function: Add another contig to the Bio::Assembly::ScaffoldI object
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190 Returns : 1 on success, 0 otherwise
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191 Args : a Bio::Assembly:Contig object
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192
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193 See Bio::Assembly::Contig for more information
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194
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195 =cut
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196
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197 #---------------------
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198 sub add_contig {
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199 #---------------------
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200 my ($self) = @_;
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201 $self->throw_not_implemented();
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202 }
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203
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204 =head2 add_singlet
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205
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206 Title : add_singlet
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207 Usage : $assembly->add_singlet($seq)
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208 Function: Add another singlet to the Bio::Assembly::ScaffoldI object
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209 Returns : 1 on success, 0 otherwise
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210 Args : a Bio::Align::Singlet object
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211
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212 =cut
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213
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214 #---------------------
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215 sub add_singlet {
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216 #---------------------
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217 my ($self) = @_;
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218 $self->throw_not_implemented();
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219 }
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220
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221 =head2 remove_contigs
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222
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223 Title : remove_contigs
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224 Usage : $assembly->remove_contigs(1..4)
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225 Function: Remove contig from assembly object
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226 Returns : a Bio::Assembly::Contig object
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227 Args : a list of contig IDs
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228
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229 See function get_contig_ids() above
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230
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231 =cut
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232
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233 #---------------------
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234 sub remove_contigs {
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235 #---------------------
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236 my ($self) = @_;
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237 $self->throw_not_implemented();
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238 }
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239
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240 =head2 remove_singlets
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241
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242 Title : remove_singlets
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243 Usage : $assembly->remove_singlets(1..4)
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244 Function: Remove singlet from assembly object
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245 Returns : a Bio::SeqI object
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246 Args : a list of singlet IDs
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247
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248 See function get_singlet_ids() above
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249
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250 =cut
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251
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252 #---------------------
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253 sub remove_singlets {
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254 #---------------------
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255 my ($self) = @_;
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256 $self->throw_not_implemented();
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257 }
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258
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259 =head1 Contig and singlet selection methos
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260
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261 =cut
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262
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263 =head2 select_contigs
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264
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265 Title : select_contig
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266 Usage : $assembly->select_contig
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267 Function: Selects an array of contigs from the assembly
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268 Returns : an array of Bio::Assembly::Contig objects
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269 Args : an array of contig ids
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270
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271 See function get_contig_ids() above
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272
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273 =cut
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274
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275 #---------------------
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276 sub select_contigs {
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277 #---------------------
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278 my ($self) = @_;
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279 $self->throw_not_implemented();
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280 }
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281
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282 =head2 select_singlets
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283
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284 Title : select_singlets
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285 Usage : $assembly->select_singlets(@list)
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286 Function: Selects an array of singlets from the assembly
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287 Returns : an array of Bio::SeqI objects
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288 Args : an array of singlet ids
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289
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290 See function get_singlet_ids() above
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291
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292 =cut
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293
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294 #---------------------
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295 sub select_singlets {
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296 #---------------------
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297 my ($self) = @_;
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298 $self->throw_not_implemented();
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299 }
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300
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301 =head2 all_contigs
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302
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303 Title : all_contigs
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304 Usage : my @contigs = $assembly->all_contigs
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305 Function: Returns a list of all contigs in this assembly.
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306 Contigs are both clusters and alignments of one
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307 or more reads, with an associated consensus
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308 sequence.
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309 Returns : array of Bio::Assembly::Contig
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310 Args : none
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311
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312 =cut
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313
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314 #---------------------
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315 sub all_contigs {
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316 #---------------------
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317 my ($self) = @_;
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318 $self->throw_not_implemented();
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319 }
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320
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321 =head2 all_singlets
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322
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323 Title : all_singlets
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324 Usage : my @singlets = $assembly->all_singlets
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325 Function: Returns a list of all singlets in this assembly.
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326 Singlets are isolated reads, without non-vector
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327 matches to any other read in the assembly.
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328 Returns : array of Bio::Assembly::Contig
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329 Args : none
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330
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331 =cut
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332
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333 #---------------------
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334 sub all_singlets {
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335 #---------------------
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336 my ($self) = @_;
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337 $self->throw_not_implemented();
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338 }
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339
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340 1;
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