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1 # BioPerl module for Bio::Seq::TraceI
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2 #
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3 # Cared for by Chad Matsalla <bioinformatics@dieselwurks.com
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4 #
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5 # Copyright Chad Matsalla
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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::Seq::TraceI - Interface definition for a Bio::Seq::Trace
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14
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15 =head1 SYNOPSIS
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16
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17 # get a Bio::Seq::Qual compliant object somehow
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18 $st = &get_object_somehow();
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19
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20 # to test this is a seq object
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21 $st->isa("Bio::Seq::TraceI")
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22 || $obj->throw("$obj does not implement the Bio::Seq::TraceI interface");
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23
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24 # set the trace for T to be @trace_points
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25 my $arrayref = $st->trace("T",\@trace_points);
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26 # get the trace points for "C"
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27 my $arrayref = $st->trace("C");
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28 # get a subtrace for "G" from 10 to 100
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29 $arrayref = $st->subtrace("G",10,100);
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30 # what is the trace value for "A" at position 355?
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31 my $trace_calue = $st->traceat("A",355);
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32 # create a false trace for "A" with $accuracy
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33 $arrayref = $st->false_trace("A",Bio::Seq::SeqWithQuality, $accuracy);
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34 # does this trace have entries for each base?
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35 $bool = $st->is_complete();
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36 # how many entries are there in this trace?
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37 $length = $st->length();
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38
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39
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40
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41 =head1 DESCRIPTION
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42
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43 This object defines an abstract interface to basic trace information. This
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44 information may have come from an ABI- or scf- formatted file or may have been
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45 made up.
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46
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47 =head1 FEEDBACK
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48
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49 =head2 Mailing Lists
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50
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51 User feedback is an integral part of the evolution of this and other
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52 Bioperl modules. Send your comments and suggestions preferably to one
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53 of the Bioperl mailing lists. Your participation is much appreciated.
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54
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55 bioperl-l@bioperl.org - General discussion
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56 http://bio.perl.org/MailList.html - About the mailing lists
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57
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58 =head2 Reporting Bugs
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59
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60 Report bugs to the Bioperl bug tracking system to help us keep track
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61 the bugs and their resolution. Bug reports can be submitted via email
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62 or the web:
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63
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64 bioperl-bugs@bio.perl.org
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65 http://bugzilla.bioperl.org/
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66
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67 =head1 AUTHOR - Chad Matsalla
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68
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69 Email bioinformatics@dieselwurks.com
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70
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71 =head1 APPENDIX
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72
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73 The rest of the documentation details each of the object methods.
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74 Internal methods are usually preceded with a _
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75
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76 =cut
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77
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78
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79 # Let the code begin...
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80
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81
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82 package Bio::Seq::TraceI;
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83 use vars qw(@ISA);
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84 use strict;
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85 use Carp;
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86 use Dumpvalue;
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87
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88 =head1 Implementation Specific Functions
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89
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90 These functions are the ones that a specific implementation must
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91 define.
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92
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93 =head2 trace($base,\@new_values)
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94
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95 Title : trace($base,\@new_values)
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96 Usage : @trace_Values = @{$obj->trace($base,\@new_values)};
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97 Function: Returns the trace values as a reference to an array containing the
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98 trace values. The individual elements of the trace array are not validated
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99 and can be any numeric value.
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100 Returns : A reference to an array.
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101 Status :
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102 Arguments: $base : which color channel would you like the trace values for?
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103 - $base must be one of "A","T","G","C"
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104 \@new_values : a reference to an array of values containing trace
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105 data for this base
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106
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107 =cut
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108
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109 sub trace {
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110 my ($self) = @_;
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111 if( $self->can('throw') ) {
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112 $self->throw("Bio::Seq::TraceI definition of trace - implementing class did not provide this method");
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113 } else {
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114 confess("Bio::Seq::TraceI definition of trace - implementing class did not provide this method");
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115 }
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116 }
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117
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118 =head2 subtrace($base,$start,$end)
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119
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120 Title : subtrace($base,$start,$end)
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121 Usage : @subset_of_traces = @{$obj->subtrace("A",10,40)};
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122 Function: returns the trace values from $start to $end, where the
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123 first value is 1 and the number is inclusive, ie 1-2 are the first
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124 two trace values of this base. Start cannot be larger than end but can
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125 be equal.
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126 Returns : A reference to an array.
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127 Args : $base: "A","T","G" or "C"
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128 $start: a start position
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129 $end : an end position
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130
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131 =cut
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132
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133 sub subtrace {
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134 my ($self) = @_;
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135
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136 if( $self->can('throw') ) {
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137 $self->throw("Bio::Seq::TraceI definition of subtrace - implementing class did not provide this method");
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138 } else {
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139 confess("Bio::Seq::TraceI definition of subtrace - implementing class did not provide this method");
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140 }
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141
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142 }
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143
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144 =head2 can_call_new()
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145
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146 Title : can_call_new()
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147 Usage : if( $obj->can_call_new ) {
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148 $newobj = $obj->new( %param );
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149 }
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150 Function: can_call_new returns 1 or 0 depending on whether an
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151 implementation allows new constructor to be called. If a new
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152 constructor is allowed, then it should take the followed hashed
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153 constructor list.
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154 $myobject->new( -qual => $quality_as_string,
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155 -display_id => $id,
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156 -accession_number => $accession,
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157 );
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158 Example :
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159 Returns : 1 or 0
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160 Args :
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161
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162
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163 =cut
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164
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165 sub can_call_new{
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166 my ($self,@args) = @_;
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167 # we default to 0 here
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168 return 0;
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169 }
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170
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171 =head2 traceat($channel,$position)
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172
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173 Title : qualat($channel,$position)
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174 Usage : $trace = $obj->traceat(500);
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175 Function: Return the trace value at the given location, where the
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176 first value is 1 and the number is inclusive, ie 1-2 are the first
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177 two bases of the sequence. Start cannot be larger than end but can
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178 be equal.
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179 Returns : A scalar.
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180 Args : A base and a position.
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181
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182 =cut
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183
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184 sub traceat {
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185 my ($self,$value) = @_;
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186 if( $self->can('warn') ) {
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187 $self->warn("Bio::Seq::TraceI definition of traceat - implementing class did not provide this method");
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188 } else {
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189 warn("Bio::Seq::TraceI definition of traceat - implementing class did not provide this method");
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190 }
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191 return '';
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192 }
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193
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194 =head2 length()
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195
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196 Title : length()
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197 Usage : $length = $obj->length("A");
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198 Function: Return the length of the array holding the trace values for the "A"
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199 channel. A check should be done to make sure that this Trace object
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200 is_complete() before doing this to prevent hazardous results.
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201 Returns : A scalar (the number of elements in the quality array).
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202 Args : If used, get the traces from that channel. Default to "A"
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203
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204 =cut
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205
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206 sub length {
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207 my ($self)= @_;
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208 if( $self->can('throw') ) {
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209 $self->throw("Bio::Seq::TraceI definition of length - implementing class did not provide this method");
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210 } else {
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211 confess("Bio::Seq::TraceI definition of length - implementing class did not provide this method");
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212 }
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213 }
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214
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215 =head2 trace_indices($new_indices)
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216
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217 Title : trace_indices($new_indices)
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218 Usage : $indices = $obj->trace_indices($new_indices);
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219 Function: Return the trace iindex points for this object.
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220 Returns : A scalar
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221 Args : If used, the trace indices will be set to the provided value.
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222
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223 =cut
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224
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225 sub trace_indices {
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226 my ($self)= @_;
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227 if( $self->can('throw') ) {
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228 $self->throw("Bio::Seq::TraceI definition of trace_indices - implementing class did not provide this method");
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229 } else {
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230 confess("Bio::Seq::TraceI definition of trace_indices - implementing class did not provide this method");
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231 }
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232 }
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233
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234
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235
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236
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237 1;
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