Mercurial > repos > cpt > cpt_psm_prep

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planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
author cpt
date Mon, 05 Jun 2023 02:50:07 +0000
parents
children
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cpt
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1 package CPT::BioData;
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2 use Moose;
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3 use strict;
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4 use warnings;
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5 use autodie;
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6
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7 has 'dummy_var' => (isa => 'Str', is => 'ro');
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8
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9 my %genbank_feature_tags = (
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10 "locus_tag" => 1,
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11 "gene" => 1,
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12 "product" => 1,
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13 "allele" => 1,
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14 "anticodon" => 1,
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15 "artificial_location" => 1,
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16 "bio_material" => 1,
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17 "bound_moiety" => 1,
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18 "cell_line" => 1,
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19 "cell_type" => 1,
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20 "chromosome" => 1,
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21 "citation" => 1,
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22 "clone" => 1,
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23 "clone_lib" => 1,
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24 "codon_start" => 1,
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25 "collected_by" => 1,
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26 "collection_date" => 1,
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27 "compare" => 1,
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28 "country" => 1,
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29 "cultivar" => 1,
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30 "culture_collection" => 1,
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31 "db_xref" => 1,
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32 "dev_stage" => 1,
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33 "direction" => 1,
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34 "EC_number" => 1,
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35 "ecotype" => 1,
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36 "environmental_sample" => 1,
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37 "estimated_length" => 1,
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38 "exception" => 1,
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39 "experiment" => 1,
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40 "focus" => 1,
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41 "frequency" => 1,
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42 "function" => 1,
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43 "gap_type" => 1,
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44 "gene_synonym" => 1,
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45 "germline" => 1,
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46 "haplogroup" => 1,
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47 "haplotype" => 1,
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48 "host" => 1,
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49 "identified_by" => 1,
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50 "inference" => 1,
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51 "isolate" => 1,
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52 "isolation_source" => 1,
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53 "lab_host" => 1,
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54 "lat_lon" => 1,
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55 "linkage_evidence" => 1,
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56 "macronuclear" => 1,
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57 "map" => 1,
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58 "mating_type" => 1,
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59 "mobile_element_type" => 1,
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60 "mod_base" => 1,
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61 "mol_type" => 1,
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62 "ncRNA_class" => 1,
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63 "note" => 1,
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64 "number" => 1,
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65 "old_locus_tag" => 1,
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66 "operon" => 1,
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67 "organelle" => 1,
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68 "organism" => 1,
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69 "partial" => 1,
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70 "PCR_conditions" => 1,
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71 "PCR_primers" => 1,
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72 "phenotype" => 1,
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73 "plasmid" => 1,
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74 "pop_variant" => 1,
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75 "protein_id" => 1,
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76 "proviral" => 1,
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77 "pseudo" => 1,
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78 "rearranged" => 1,
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79 "replace" => 1,
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80 "ribosomal_slippage" => 1,
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81 "rpt_family" => 1,
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82 "rpt_type" => 1,
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83 "rpt_unit_range" => 1,
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84 "rpt_unit_seq" => 1,
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85 "satellite" => 1,
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86 "segment" => 1,
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87 "serotype" => 1,
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88 "serovar" => 1,
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89 "sex" => 1,
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90 "specimen_voucher" => 1,
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91 "standard_name" => 1,
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92 "strain" => 1,
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93 "sub_clone" => 1,
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94 "sub_species" => 1,
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95 "sub_strain" => 1,
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96 "tag_peptide" => 1,
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97 "tissue_lib" => 1,
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98 "tissue_type" => 1,
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99 "transgenic" => 1,
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100 "translation" => 1,
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101 "transl_except" => 1,
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102 "transl_table" => 1,
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103 "trans_splicing" => 1,
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104 "variety" => 1,
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105 );
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106 my %artemis_colours = (
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107 0 => 'rgb(255,255,255)',
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108 1 => 'rgb(100,100,100)',
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109 2 => 'rgb(255,0,0)',
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110 3 => 'rgb(0,255,0)',
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111 4 => 'rgb(0,0,255)',
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112 5 => 'rgb(0,255,255)',
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113 6 => 'rgb(255,0,255)',
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114 7 => 'rgb(255,255,0)',
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115 8 => 'rgb(152,251,152)',
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116 9 => 'rgb(135,206,250)',
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117 10 => 'rgb(255,165,0)',
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118 11 => 'rgb(200,150,100)',
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119 12 => 'rgb(255,200,200)',
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120 13 => 'rgb(170,170,170)',
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121 14 => 'rgb(0,0,0)',
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122 15 => 'rgb(255,63,63)',
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123 16 => 'rgb(255,127,127)',
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124 17 => 'rgb(255,191,191)',
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125 );
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126
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127 sub artemis_colour_decode{
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128 my ($self, $idx) = @_;
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129 return $artemis_colours{$idx};
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130 }
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131
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132 my %table321 = (
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133 'Gly' => 'G', 'Pro' => 'P',
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134 'Ala' => 'A',
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135 'Val' => 'V',
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136 'Leu' => 'L',
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137 'Ile' => 'I',
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138 'Met' => 'M',
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139 'Cys' => 'C',
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140 'Phe' => 'F',
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141 'Tyr' => 'Y',
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142 'Trp' => 'W',
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143 'His' => 'H',
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144 'Lys' => 'K',
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145 'Arg' => 'R',
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146 'Gln' => 'Q',
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147 'Asn' => 'N',
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148 'Glu' => 'E',
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149 'Asp' => 'D',
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150 'Ser' => 'S',
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151 'Thr' => 'T',
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152 'XXX' => 'X',
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153 'End' => '*',
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154 'Stop' => '*'
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155 );
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156
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157 sub decode321{
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158 my ($self, $three) = @_;
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159 return $table321{$three};
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160 }
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161
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162
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163 sub get321Table {
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164 my ($self) = @_;
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165 return \%table321;
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166 }
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167
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168
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169 sub getTranslationTable {
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170 my ($self, $table_id) = @_;
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171 require Bio::Tools::CodonTable;
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172 my $table = Bio::Tools::CodonTable->new( -id => (defined $table_id? $table_id: 1) );
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173 my %result;
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174 my @codons = qw(A C T G);
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175 foreach my $i (@codons) {
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176 foreach my $j (@codons) {
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177 foreach my $k (@codons) {
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178 $result{"$i$j$k"} = $table->translate("$i$j$k");
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179 }
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180 }
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181 }
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182 if(defined($table_id) && $table_id == 11){
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183 $result{TGA} = '*';
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184 $result{TAA} = '#';
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185 $result{TAG} = '+';
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186 }
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187 return \%result;
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188 }
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189
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190
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191
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192 sub isValidTag {
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193 my ( $self, $tag ) = @_;
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194 return $genbank_feature_tags{$tag};
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195 }
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196
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197 no Moose;
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198 1;
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199
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200 __END__
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201
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202 =pod
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203
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204 =encoding UTF-8
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205
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206 =head1 NAME
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207
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208 CPT::BioData
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209
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210 =head1 VERSION
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211
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212 version 1.99.4
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213
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214 =head2 get321Table
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215
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216 $bio->get321Table();
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217
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218 Convenience function which returns a codon translation table (3 letter ID to 1 letter code)
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219
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220 =head2 getTranslationTable
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221
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222 $bio->getTranslationTable();
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223
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224 Convenience function which returns a hash translated according to Bio::Tools::CodonTable
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225
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226 This is done for speed reasons. CodonTable is very slow and we require better performance
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227
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228 =head2 isValidTag
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229
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230 if($cptbio->isValidTag('locus_tag')) { ... }
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231
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232 Will validate a GBK feature tag
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233
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234 =head1 AUTHOR
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235
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236 Eric Rasche <rasche.eric@yandex.ru>
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237
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238 =head1 COPYRIGHT AND LICENSE
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239
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240 This software is Copyright (c) 2014 by Eric Rasche.
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241
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242 This is free software, licensed under:
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243
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244 The GNU General Public License, Version 3, June 2007
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245
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246 =cut