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1 # $Id: Scaffold.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::Scaffold
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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::Scaffold - Perl module to hold and manipulate sequence assembly data.
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14
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15 =head1 SYNOPSYS
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16
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17 # Module loading
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18 use Bio::Assembly::IO;
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19
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20 # Assembly loading methods
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21 my $aio = new Bio::Assembly::IO(-file=>"test.ace.1", -format=>'phrap');
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22 my $assembly = $aio->next_assembly;
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23
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24 foreach my $contig ($assembly->all_contigs) {
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25 # do something... (see Bio::Assembly::Contig)
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26 }
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27
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28 =head1 DESCRIPTION
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29
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30 Bio::Assembly::Scaffold was developed to store and manipulate data
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31 from sequence assembly programs like Phrap. It implements the
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32 ScaffoldI interface and intends to be generic enough to be used by
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33 Bio::Assembly::IO drivers written to programs other than Phrap.
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34
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35 =head1 FEEDBACK
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36
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37 =head2 Mailing Lists
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38
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39 User feedback is an integral part of the evolution of this and other
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40 Bioperl modules. Send your comments and suggestions preferably to the
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41 Bioperl mailing lists Your participation is much appreciated.
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42
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43 bioperl-l@bioperl.org - General discussion
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44 http://bio.perl.org/MailList.html - About the mailing lists
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45
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46 =head2 Reporting Bugs
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47
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48 Report bugs to the Bioperl bug tracking system to help us keep track
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49 the bugs and their resolution. Bug reports can be submitted via email
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50 or the web:
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51
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52 bioperl-bugs@bio.perl.org
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53 http://bugzilla.bioperl.org/
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54
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55 =head1 AUTHOR - Robson Francisco de Souza
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56
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57 rfsouza@citri.iq.usp.br
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58
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59 =head1 APPENDIX
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60
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61 The rest of the documentation details each of the object
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62 methods. Internal methods are usually preceded with a _
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63
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64 =cut
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65
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66 package Bio::Assembly::Scaffold;
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67
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68 use strict;
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69 use vars qw(@ISA $VERSION);
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70
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71 use Bio::Root::Root;
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72 use Bio::Assembly::ScaffoldI;
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73 use Bio::Annotation::Collection;
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74
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75 $VERSION = '0.0.1';
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76 @ISA = qw(Bio::Root::Root Bio::Assembly::ScaffoldI);
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77
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78 =head2 new ()
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79
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80 Title : new
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81 Usage : $assembly = new (-source=>'program_name',
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82 -contigs=>\@contigs,
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83 -id=>"assembly 1");
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84 Function: creates a new assembly object
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85 Returns :
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86 Args :
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87 -source : [string] sequence assembly program
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88 -contigs : reference to array of
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89 Bio::Assembly::Contig objects
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90 -id : [string] assembly name
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91
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92 =cut
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93
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94 sub new {
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95 my($class,@args) = @_;
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96
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97 my $self = $class->SUPER::new(@args);
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98
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99 my ($src,$contigs,$id) = $self->_rearrange([qw(SOURCE CONTIGS ID)], @args);
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100
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101 $self->{'_contigs'} = {};
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102 $self->{'_singlets'} = {};
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103 $self->{'_seqs'} = {};
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104 $self->{'_annotation'} = Bio::Annotation::Collection->new();
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105 $self->{'_id'} = 'NoName';
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106
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107 if (defined $contigs && ref($contigs = 'ARRAY')) {
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108 foreach my $contig (@{$contigs}) {
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109 $self->add_contig($contig);
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110 }
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111 }
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112
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113 $self->{'_id'} = $id if (defined $id);
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114
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115 return $self;
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116 }
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117
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118 =head1 Accessing general assembly data
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119
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120 =cut
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121
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122 =head2 id
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123
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124 Title : id
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125 Usage : $assembly->id()
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126 Function: Get/Set assembly ID
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127 Returns : string or undef
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128 Args : string
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129
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130 =cut
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131
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132 sub id {
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133 my $self = shift;
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134 my $id = shift;
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135
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136 $self->{'_id'} = $id if (defined $id);
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137
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138 return $self->{'_id'};
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139 }
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140
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141 =head2 annotation
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142
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143 Title : annotation
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144 Usage : $assembly->annotation()
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145 Function: Get/Set assembly annotation object
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146 Returns : Bio::Annotation::Collection
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147 Args : none
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148
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149 =cut
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150
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151 sub annotation {
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152 my ($self,$ref) = shift;
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153
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154 $self->{'_annotation'} = $ref if (defined $ref);
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155 return $self->{'_annotation'};
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156 }
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157
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158 =head2 get_nof_contigs
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159
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160 Title : get_nof_contigs
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161 Usage : $assembly->get_nof_contigs()
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162 Function: Get the number of contigs included in the assembly
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163 Returns : integer
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164 Args : none
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165
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166 =cut
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167
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168 sub get_nof_contigs {
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169 my $self = shift;
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170
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171 return scalar( $self->get_contig_ids() );
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172 }
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173
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174 =head2 get_nof_sequences_in_contigs
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175
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176 Title : get_nof_sequences_in_contigs
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177 Usage : $assembly->get_nof_sequences_in_contigs()
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178 Function:
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179
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180 Get the number of sequences included in the
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181 assembly. This number refers only to the sequences used
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182 to build contigs in this assembly. It does not includes
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183 contig consensus sequences or singlets.
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184
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185 Returns : integer
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186 Args : none
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187
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188 =cut
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189
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190 sub get_nof_sequences_in_contigs {
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191 my $self = shift;
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192
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193 my $nof_seqs = 0;
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194 foreach my $contig ($self->all_contigs) {
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195 $nof_seqs += scalar( $contig->get_seq_ids() );
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196 }
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197
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198 return $nof_seqs;
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199 }
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200
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201 =head2 get_nof_singlets
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202
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203 Title : nof_singlets
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204 Usage : $assembly->nof_singlets()
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205 Function: Get the number of singlets included in the assembly
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206 Returns : integer
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207 Args : none
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208
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209 =cut
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210
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211 sub get_nof_singlets {
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212 my $self = shift;
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213
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214 return scalar( $self->get_singlet_ids() );
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215 }
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216
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217 =head2 get_seq_ids
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218
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219 Title : get_seq_ids
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220 Usage : $assembly->get_seq_ids()
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221 Function:
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222
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223 Get the ID of sequences from all contigs. This list
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224 refers only to the aligned sequences in contigs. It does
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225 not includes contig consensus sequences or singlets.
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226
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227 Returns : array of strings
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228 Args : none
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229
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230 =cut
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231
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232 sub get_seq_ids {
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233 my $self = shift;
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234
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235 return keys %{ $self->{'_seqs'} };
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236 }
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237
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238 =head2 get_contig_ids
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239
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240 Title : get_contig_ids
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241 Usage : $assembly->get_contig_ids()
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242 Function: Access list of contig IDs from assembly
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243 Returns : an array, if there are any contigs in the
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244 assembly. An empty array otherwise
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245 Args : none
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246
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247 =cut
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248
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249 sub get_contig_ids {
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250 my $self = shift;
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251
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252 return sort keys %{$self->{'_contigs'}};
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253 }
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254
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255 =head2 get_singlet_ids
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256
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257 Title : get_singlet_ids
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258 Usage : $assembly->get_singlet_ids()
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259 Function: Access list of singlet IDs from assembly
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260 Returns : array of strings if there are any singlets
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261 otherwise an empty array
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262 Args : none
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263
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264 =cut
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265
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266 sub get_singlet_ids {
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267 my $self = shift;
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268
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269 return sort keys %{$self->{'_singlets'}};
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270 }
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271
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272 =head2 get_seq_by_id
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273
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274 Title : get_seq_by_id
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275 Usage : $assembly->get_seq_by_id($id)
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276 Function:
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277
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278 Get a reference for an aligned sequence
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279 This sequence must be part of a contig
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280 in the assembly.
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281
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282 Returns : a Bio::LocatableSeq object
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283 undef if sequence $id is not found
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284 in any contig
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285 Args : [string] sequence identifier (id)
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286
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287 =cut
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288
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289 sub get_seq_by_id {
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290 my $self = shift;
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291 my $seqID = shift;
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292
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293 return undef unless (exists $self->{'_seqs'}{$seqID});
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294
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295 return $self->{'_seqs'}{$seqID}->get_seq_by_name($seqID);
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296 }
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297
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298 =head2 get_contig_by_id
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299
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300 Title : get_contig_by_id
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301 Usage : $assembly->get_contig_by_id($id)
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302 Function: Get a reference for a contig
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303 Returns : a Bio::Assembly::Contig object or undef
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304 Args : [string] contig unique identifier (ID)
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305
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306 =cut
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307
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308 sub get_contig_by_id {
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309 my $self = shift;
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310 my $contigID = shift;
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311
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312 return undef unless (exists $self->{'_contigs'}{$contigID});
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313
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314 return $self->{'_contigs'}{$contigID};
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315 }
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316
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317 =head2 get_singlet_by_id
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318
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319 Title : get_singlet_by_id
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320 Usage : $assembly->get_singlet_by_id()
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321 Function: Get a reference for a singlet
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322 Returns : Bio::PrimarySeqI object or undef
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323 Args : [string] a singlet ID
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324
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325 =cut
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326
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327 sub get_singlet_by_id {
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328 my $self = shift;
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329
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330 my $singletID = shift;
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331
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332 return undef unless (exists $self->{'_singlets'}{$singletID});
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333
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334 return $self->{'_singlets'}{$singletID};
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335 }
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336
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337 =head1 Modifier methods
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338
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339 =cut
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340
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341 =head2 add_contig
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342
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343 Title : add_contig
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344 Usage : $assembly->add_contig($contig)
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345 Function: Add a contig to the assembly
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346 Returns : 1 on success
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347 Args : a Bio::Assembly::Contig object
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348 order (optional)
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349
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350 =cut
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351
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352 sub add_contig {
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353 my $self = shift;
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354 my $contig = shift;
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355
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356 if( !ref $contig || ! $contig->isa('Bio::Assembly::Contig') ) {
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357 $self->throw("Unable to process non Bio::Assembly::Contig object [", ref($contig), "]");
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358 }
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359 my $contigID = $contig->id();
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360 if( !defined $contigID ) {
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361 $contigID = 'Unknown_' . ($self->get_nof_contigs() + 1);
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362 $contig->id($contigID);
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363 $self->warn("Attributing ID $contigID to unidentified Bio::Assembly::Contig object.");
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364 }
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365
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366 $self->warn("Replacing contig $contigID with a new contig object")
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367 if (exists $self->{'_contigs'}{$contigID});
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368 $self->{'_contigs'}{$contigID} = $contig;
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369
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370 foreach my $seqID ($contig->get_seq_ids()) {
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371 if (exists $self->{'_seqs'}{$seqID}) {
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372 $self->warn( "Sequence $seqID already assigned to contig ".
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373 $self->{'_seqs'}{$seqID}->id().". Moving to contig $contigID")
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374 unless ($self->{'_seqs'}{$seqID} eq $contig);
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375 }
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376 $self->{'_seqs'}{$seqID} = $contig;
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377 }
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378
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379 return 1;
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380 }
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381
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382 =head2 add_singlet
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383
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384 Title : add_singlet
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385 Usage : $assembly->add_singlet($seq)
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386 Function: Add a singlet to the assembly
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387 Returns : 1 on success, 0 otherwise
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388 Args : a Bio::PrimarySeqI object
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389 order (optional)
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390
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391 =cut
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392
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393 sub add_singlet {
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394 my $self = shift;
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395 my $singlet = shift;
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396
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397 if( !ref $singlet || ! $singlet->isa('Bio::PrimarySeqI') ) {
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398 $self->warn("Unable to process non Bio::SeqI object [", ref($singlet), "]");
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399 return 0;
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400 }
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401
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402 my $singletID = $singlet->id();
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403 $self->warn("Replacing singlet $singletID wih a new sequence object")
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404 if (exists $self->{'_contigs'}{$singletID});
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405 $self->{'_singlets'}{$singletID} = $singlet;
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406
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407 return 1;
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408 }
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409
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410 =head2 update_seq_list
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411
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412 Title : update_seq_list
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413 Usage : $assembly->update_seq_list()
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414 Function:
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415
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416 Synchronizes the assembly registry for sequences in
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417 contigs and contig actual aligned sequences content. You
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418 probably want to run this after you remove/add a
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419 sequence from/to a contig in the assembly.
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420
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421 Returns : nothing
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422 Args : none
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423
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424 =cut
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425
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426 sub update_seq_list {
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427 my $self = shift;
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428
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429 $self->{'_seqs'} = {};
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430 foreach my $contig ($self->all_contigs) {
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431 foreach my $seqID ($contig->get_seq_ids) {
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432 $self->{'_seqs'}{$seqID} = $contig;
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433 }
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434 }
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435
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436 return 1;
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437 }
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438
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439 =head2 remove_contigs
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440
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441 Title : remove_contigs
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442 Usage : $assembly->remove_contigs(1..4)
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443 Function: Remove contig from assembly object
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444 Returns : an array of removed Bio::Assembly::Contig
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445 objects
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446 Args : an array of contig IDs
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447
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448 See function get_contig_ids() above
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449
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450 =cut
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451
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452 #---------------------
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453 sub remove_contigs {
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454 #---------------------
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455 my ($self,@args) = @_;
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456
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457 my @ret = ();
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458 foreach my $contigID (@args) {
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459 foreach my $seqID ($self->get_contig_by_id($contigID)->get_seq_ids()) {
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460 delete $self->{'_seqs'}{$seqID};
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461 }
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462 push(@ret,$self->{'_contigs'}{$contigID});
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463 delete $self->{'_contigs'}{$contigID};
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464 }
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465
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466 return @ret;
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467 }
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468
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469 =head2 remove_singlets
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470
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471 Title : remove_singlets
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472 Usage : $assembly->remove_singlets(@singlet_ids)
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473 Function: Remove singlet from assembly object
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474 Returns : the Bio::SeqI objects removed
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475 Args : a list of singlet IDs
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476
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477 See function get_singlet_ids() above
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478
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479 =cut
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480
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481 #---------------------
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482 sub remove_singlets {
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483 #---------------------
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484 my ($self,@args) = @_;
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485
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486 my @ret = ();
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487 foreach my $singletID (@args) {
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488 push(@ret,$self->{'_singlets'}{$singletID});
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489 delete $self->{'_singlets'}{$singletID};
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490 }
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491
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492 return @ret;
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493 }
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494
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495 =head1 Contig and singlet selection methos
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496
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497 =cut
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498
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499 =head2 select_contigs
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500
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501 Title : select_contigs
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502 Usage : $assembly->select_contigs(@list)
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503 Function: Select an array of contigs from the assembly
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504 Returns : an array of Bio::Assembly::Contig objects
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505 Args : an array of contig ids
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506
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507 See function get_contig_ids() above
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508
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509 =cut
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510
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511 #---------------------
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512 sub select_contigs {
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513 #---------------------
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514 my ($self,@args) = @_;
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515
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516 my @contigs = ();
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517 foreach my $contig (@args) {
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518 unless (exists $self->{'_contigs'}{$contig}) {
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519 $self->warn("$contig contig not found. Ignoring...");
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520 next;
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521 }
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522 push(@contigs, $self->{'_contigs'}{$contig});
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523 }
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524
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525 return @contigs;
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|
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526 }
|
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527
|
|
|
528 =head2 select_singlets
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529
|
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530 Title : select_singlets
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531 Usage : $assembly->select_singlets(@list)
|
|
|
532 Function: Selects an array of singlets from the assembly
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|
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533 Returns : an array of Bio::SeqI objects
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|
|
534 Args : an array of singlet ids
|
|
|
535
|
|
|
536 See function get_singlet_ids() above
|
|
|
537
|
|
|
538 =cut
|
|
|
539
|
|
|
540 #---------------------
|
|
|
541 sub select_singlets {
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|
|
542 #---------------------
|
|
|
543 my ($self,@args) = @_;
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|
|
544
|
|
|
545 my @singlets = ();
|
|
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546 foreach my $singlet (@args) {
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|
|
547 unless (exists $self->{'_singlets'}{$singlet}) {
|
|
|
548 $self->warn("$singlet singlet not found. Ignoring...");
|
|
|
549 next;
|
|
|
550 }
|
|
|
551 push(@singlets, $self->{'_singlets'}{$singlet});
|
|
|
552 }
|
|
|
553
|
|
|
554 return @singlets;
|
|
|
555 }
|
|
|
556
|
|
|
557 =head2 all_contigs
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|
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558
|
|
|
559 Title : all_contigs
|
|
|
560 Usage : my @contigs = $assembly->all_contigs
|
|
|
561 Function:
|
|
|
562
|
|
|
563 Returns a list of all contigs in this assembly. Contigs
|
|
|
564 are both clusters and alignments of one or more reads,
|
|
|
565 with an associated consensus sequence.
|
|
|
566
|
|
|
567 Returns : array of Bio::Assembly::Contig (in lexical id order)
|
|
|
568 Args : none
|
|
|
569
|
|
|
570 =cut
|
|
|
571
|
|
|
572 #---------------------
|
|
|
573 sub all_contigs {
|
|
|
574 #---------------------
|
|
|
575 my ($self) = @_;
|
|
|
576
|
|
|
577 my @contigs = ();
|
|
|
578 foreach my $contig (sort { $a cmp $b } keys %{ $self->{'_contigs'} }) {
|
|
|
579 push(@contigs, $self->{'_contigs'}{$contig});
|
|
|
580 }
|
|
|
581
|
|
|
582 return @contigs;
|
|
|
583 }
|
|
|
584
|
|
|
585 =head2 all_singlets
|
|
|
586
|
|
|
587 Title : all_singlets
|
|
|
588 Usage : my @singlets = $assembly->all_singlets
|
|
|
589 Function:
|
|
|
590
|
|
|
591 Returns a list of all singlets in this assembly.
|
|
|
592 Singlets are isolated reads, without non-vector
|
|
|
593 matches to any other read in the assembly.
|
|
|
594
|
|
|
595 Returns : array of Bio::SeqI (in lexical order by id)
|
|
|
596 Args : none
|
|
|
597
|
|
|
598 =cut
|
|
|
599
|
|
|
600 #---------------------
|
|
|
601 sub all_singlets {
|
|
|
602 #---------------------
|
|
|
603 my ($self) = @_;
|
|
|
604
|
|
|
605 my @singlets = ();
|
|
|
606 foreach my $singlet (sort { $a cmp $b } keys %{ $self->{'_singlets'} }) {
|
|
|
607 push(@singlets, $self->{'_singlets'}{$singlet});
|
|
|
608 }
|
|
|
609
|
|
|
610 return @singlets;
|
|
|
611 }
|
|
|
612
|
|
|
613 # =head1 Internal Methods
|
|
|
614
|
|
|
615 1;
|
