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1 <tool id="complete_immunerepertoire_igg" name="Immune Repertoire pipeline" version="1.0">
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2 <description> </description>
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3 <command interpreter="bash">
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4 complete.sh "
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5 #for $i, $f in enumerate($patients)
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6 "${f.id}"
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7 #for $j, $g in enumerate($f.samples)
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8 ${g.sample}
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9 #end for
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10 #end for
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11 " $out_file $out_file.files_path "$clonaltype"
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12 #if $gene_selection.source == "imgtdb"
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13 "${gene_selection.species}" "${gene_selection.locus}" $filterproductive ${clonality_method}
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14 #else
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15 "custom" "${gene_selection.vgenes};${gene_selection.dgenes};${gene_selection.jgenes}" $filterproductive $clonality_method
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16 #end if
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17 </command>
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18 <inputs>
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19 <repeat name="patients" title="Donor" min="1" default="1">
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20 <repeat name="samples" title="Sample" min="1" default="1">
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21 <param name="sample" type="data" label="Sample to Process" />
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22 </repeat>
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23 <param name="id" type="text" label="ID" />
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24 </repeat>
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25 <param name="clonaltype" type="select" label="Clonal Type Definition">
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26 <option value="none">Don't remove duplicates based on clonaltype</option>
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27 <option value="Top.V.Gene,CDR3.Seq">Top.V.Gene, CDR3 (AA)</option>
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28 <option value="Top.V.Gene,CDR3.Seq.DNA">Top.V.Gene, CDR3 (nt)</option>
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29 <option value="Top.V.Gene,Top.J.Gene,CDR3.Seq">Top.V.Gene, Top.J.Gene, CDR3 (AA)</option>
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30 <option value="Top.V.Gene,Top.J.Gene,CDR3.Seq.DNA">Top.V.Gene, Top.J.Gene, CDR3 (nt)</option>
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31 <option value="Top.V.Gene,Top.D.Gene,Top.J.Gene,CDR3.Seq.DNA">Top.V.Gene, Top.D.Gene, Top.J.Gene, CDR3 (nt)</option>
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32 </param>
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33
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34 <conditional name="gene_selection" >
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35 <param name="source" type="select" label="Order of V(D)J genes in graphs" help="" >
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36 <option value="imgtdb" selected="true">IMGT-DB</option>
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37 <option value="custom">User defined</option>
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38 </param>
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39 <when value="imgtdb">
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40 <param name="species" type="select" label="Species">
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41 <option value="Homo sapiens functional">Homo sapiens functional</option>
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42 <option value="Homo sapiens">Homo sapiens</option>
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43 <option value="Homo sapiens non-functional">Homo sapiens non-functional</option>
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44 <option value="Bos taurus">Bos taurus</option>
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45 <option value="Bos taurus functional">Bos taurus functional</option>
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46 <option value="Bos taurus non-functional">Bos taurus non-functional</option>
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47 <option value="Camelus dromedarius">Camelus dromedarius</option>
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48 <option value="Camelus dromedarius functional">Camelus dromedarius functional</option>
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49 <option value="Camelus dromedarius non-functional">Camelus dromedarius non-functional</option>
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50 <option value="Canis lupus familiaris">Canis lupus familiaris</option>
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51 <option value="Canis lupus familiaris functional">Canis lupus familiaris functional</option>
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52 <option value="Canis lupus familiaris non-functional">Canis lupus familiaris non-functional</option>
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53 <option value="Danio rerio">Danio rerio</option>
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54 <option value="Danio rerio functional">Danio rerio functional</option>
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55 <option value="Danio rerio non-functional">Danio rerio non-functional</option>
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56 <option value="Macaca mulatta">Macaca mulatta</option>
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57 <option value="Macaca mulatta functional">Macaca mulatta functional</option>
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58 <option value="Macaca mulatta non-functional">Macaca mulatta non-functional</option>
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59 <option value="Mus musculus">Mus musculus</option>
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60 <option value="Mus musculus functional">Mus musculus functional</option>
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61 <option value="Mus musculus non-functional">Mus musculus non-functional</option>
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62 <option value="Mus spretus">Mus spretus</option>
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63 <option value="Mus spretus functional">Mus spretus functional</option>
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64 <option value="Mus spretus non-functional">Mus spretus non-functional</option>
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65 <option value="Oncorhynchus mykiss">Oncorhynchus mykiss</option>
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66 <option value="Oncorhynchus mykiss functional">Oncorhynchus mykiss functional</option>
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67 <option value="Oncorhynchus mykiss non-functional">Oncorhynchus mykiss non-functional</option>
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68 <option value="Ornithorhynchus anatinus">Ornithorhynchus anatinus</option>
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69 <option value="Ornithorhynchus anatinus functional">Ornithorhynchus anatinus functional</option>
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70 <option value="Ornithorhynchus anatinus non-functional">Ornithorhynchus anatinus non-functional</option>
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71 <option value="Oryctolagus cuniculus">Oryctolagus cuniculus</option>
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72 <option value="Oryctolagus cuniculus functional">Oryctolagus cuniculus functional</option>
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73 <option value="Oryctolagus cuniculus non-functional">Oryctolagus cuniculus non-functional</option>
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74 <option value="Rattus norvegicus">Rattus norvegicus</option>
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75 <option value="Rattus norvegicus functional">Rattus norvegicus functional</option>
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76 <option value="Rattus norvegicus non-functional">Rattus norvegicus non-functional</option>
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77 <option value="Sus scrofa">Sus scrofa</option>
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78 <option value="Sus scrofa functional">Sus scrofa functional</option>
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79 <option value="Sus scrofa non-functional">Sus scrofa non-functional</option>
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80 </param>
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81
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82 <param name="locus" type="select" label="Locus">
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83 <option value="TRA">TRA</option>
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84 <option value="TRD">TRD</option>
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85 <option value="TRG">TRG</option>
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86 <option value="TRB">TRB</option>
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87 <option value="IGH">IGH</option>
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88 <option value="IGI">IGI</option>
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89 <option value="IGK">IGK</option>
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90 <option value="IGL">IGL</option>
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91 </param>
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92 </when>
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93 <when value="custom">
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94 <param name="species" type="hidden" value="custom" size="50" />
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95 <param name="vgenes" type="text" label="V Genes, add the custom genes comma seperated, no spaces" size="100" />
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96 <param name="dgenes" type="text" label="D Genes" size="100" />
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97 <param name="jgenes" type="text" label="J Genes" size="100" />
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98 </when>
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99 </conditional>
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100
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101 <param name="filterproductive" type="select" label="Remove the unproductive sequences from graphs ">
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102 <option value="yes">Yes</option>
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103 <option value="no">No</option>
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104 </param>
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105
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106 <param name="clonality_method" type="select" label="Old clonality algorithm or the newer R package">
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107 <option value="old">Old</option>
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108 <option value="boyd">R Package (needs 3 replicate minimum)</option>
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109 </param>
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110 </inputs>
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111 <outputs>
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112 <data format="html" name="out_file" />
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113 </outputs>
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114 <requirements>
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115 <requirement type="package" version="0.6">igblastwrp</requirement>
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116 <requirement type="package" version="3.3">weblogo</requirement>
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117 <!--<requirement type="package" version="0.20">circostools</requirement>-->
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118 </requirements>
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119 <help>
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120 The entire Immune Repertoire pipeline as a single tool, input several FASTA files or IMGT zip/txz files, give them an ID and it will BLAST/parse, merge and plot them.
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121
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122 .. class:: warningmark
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123
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124 Custom gene ordering based on position on genome:
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125
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126 **Human**
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127
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128 IGH::
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129
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130 V:
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131 IGHV7-81,IGHV3-74,IGHV3-73,IGHV3-72,IGHV3-71,IGHV2-70,IGHV1-69,IGHV3-66,IGHV3-64,IGHV4-61,IGHV4-59,IGHV1-58,IGHV3-53,IGHV3-52,IGHV5-a,IGHV5-51,IGHV3-49,IGHV3-48,IGHV3-47,IGHV1-46,IGHV1-45,IGHV3-43,IGHV4-39,IGHV3-35,IGHV4-34,IGHV3-33,IGHV4-31,IGHV4-30-4,IGHV4-30-2,IGHV3-30-3,IGHV3-30,IGHV4-28,IGHV2-26,IGHV1-24,IGHV3-23,IGHV3-22,IGHV3-21,IGHV3-20,IGHV3-19,IGHV1-18,IGHV3-15,IGHV3-13,IGHV3-11,IGHV3-9,IGHV1-8,IGHV3-7,IGHV2-5,IGHV7-4-1,IGHV4-4,IGHV4-b,IGHV1-3,IGHV1-2,IGHV6-1
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132 D:
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133 IGHD1-1,IGHD2-2,IGHD3-3,IGHD6-6,IGHD1-7,IGHD2-8,IGHD3-9,IGHD3-10,IGHD4-11,IGHD5-12,IGHD6-13,IGHD1-14,IGHD2-15,IGHD3-16,IGHD4-17,IGHD5-18,IGHD6-19,IGHD1-20,IGHD2-21,IGHD3-22,IGHD4-23,IGHD5-24,IGHD6-25,IGHD1-26,IGHD7-27
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134 J:
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135 IGHJ1,IGHJ2,IGHJ3,IGHJ4,IGHJ5,IGHJ6
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136
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137
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138 IGK::
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139
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140 V:
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141 IGKV3D-7,IGKV1D-8,IGKV1D-43,IGKV3D-11,IGKV1D-12,IGKV1D-13,IGKV3D-15,IGKV1D-16,IGKV1D-17,IGKV3D-20,IGKV2D-26,IGKV2D-28,IGKV2D-29,IGKV2D-30,IGKV1D-33,IGKV1D-39,IGKV2D-40,IGKV2-40,IGKV1-39,IGKV1-33,IGKV2-30,IGKV2-29,IGKV2-28,IGKV1-27,IGKV2-24,IGKV3-20,IGKV1-17,IGKV1-16,IGKV3-15,IGKV1-13,IGKV1-12,IGKV3-11,IGKV1-9,IGKV1-8,IGKV1-6,IGKV1-5,IGKV5-2,IGKV4-1
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142 J:
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143 IGKJ1,IGKJ2,IGKJ3,IGKJ4,IGKJ5
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144
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145
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146 IGL::
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147
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148 V:
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149 IGLV4-69,IGLV8-61,IGLV4-60,IGLV6-57,IGLV5-52,IGLV1-51,IGLV9-49,IGLV1-47,IGLV7-46,IGLV5-45,IGLV1-44,IGLV7-43,IGLV1-41,IGLV1-40,IGLV5-39,IGLV5-37,IGLV1-36,IGLV3-27,IGLV3-25,IGLV2-23,IGLV3-22,IGLV3-21,IGLV3-19,IGLV2-18,IGLV3-16,IGLV2-14,IGLV3-12,IGLV2-11,IGLV3-10,IGLV3-9,IGLV2-8,IGLV4-3,IGLV3-1
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150 J:
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151 IGLJ1,IGLJ2,IGLJ3,IGLJ6,IGLJ7
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152
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153
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154 TRB::
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155
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156 V:
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157 TRBV2,TRBV3-1,TRBV4-1,TRBV5-1,TRBV6-1,TRBV4-2,TRBV6-2,TRBV4-3,TRBV6-3,TRBV7-2,TRBV6-4,TRBV7-3,TRBV9,TRBV10-1,TRBV11-1,TRBV10-2,TRBV11-2,TRBV6-5,TRBV7-4,TRBV5-4,TRBV6-6,TRBV5-5,TRBV7-6,TRBV5-6,TRBV6-8,TRBV7-7,TRBV6-9,TRBV7-8,TRBV5-8,TRBV7-9,TRBV13,TRBV10-3,TRBV11-3,TRBV12-3,TRBV12-4,TRBV12-5,TRBV14,TRBV15,TRBV16,TRBV18,TRBV19,TRBV20-1,TRBV24-1,TRBV25-1,TRBV27,TRBV28,TRBV29-1,TRBV30
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158 D:
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159 TRBD1,TRBD2
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160 J:
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161 TRBJ1-1,TRBJ1-2,TRBJ1-3,TRBJ1-4,TRBJ1-5,TRBJ1-6,TRBJ2-1,TRBJ2-2,TRBJ2-3,TRBJ2-4,TRBJ2-5,TRBJ2-6,TRBJ2-7
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162
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163
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164 TRA::
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165
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166 V:
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167 TRAV1-1,TRAV1-2,TRAV2,TRAV3,TRAV4,TRAV5,TRAV6,TRAV7,TRAV8-1,TRAV9-1,TRAV10,TRAV12-1,TRAV8-2,TRAV8-3,TRAV13-1,TRAV12-2,TRAV8-4,TRAV13-2,TRAV14/DV4,TRAV9-2,TRAV12-3,TRAV8-6,TRAV16,TRAV17,TRAV18,TRAV19,TRAV20,TRAV21,TRAV22,TRAV23/DV6,TRAV24,TRAV25,TRAV26-1,TRAV27,TRAV29/DV5,TRAV30,TRAV26-2,TRAV34,TRAV35,TRAV36/DV7,TRAV38-1,TRAV38-2/DV8,TRAV39,TRAV40,TRAV41
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168 J:
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169 TRAJ57,TRAJ56,TRAJ54,TRAJ53,TRAJ52,TRAJ50,TRAJ49,TRAJ48,TRAJ47,TRAJ46,TRAJ45,TRAJ44,TRAJ43,TRAJ42,TRAJ41,TRAJ40,TRAJ39,TRAJ38,TRAJ37,TRAJ36,TRAJ34,TRAJ33,TRAJ32,TRAJ31,TRAJ30,TRAJ29,TRAJ28,TRAJ27,TRAJ26,TRAJ24,TRAJ23,TRAJ22,TRAJ21,TRAJ20,TRAJ18,TRAJ17,TRAJ16,TRAJ15,TRAJ14,TRAJ13,TRAJ12,TRAJ11,TRAJ10,TRAJ9,TRAJ8,TRAJ7,TRAJ6,TRAJ5,TRAJ4,TRAJ3
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170
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171
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172 TRG::
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173
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174 V:
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175 TRGV9,TRGV8,TRGV5,TRGV4,TRGV3,TRGV2
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176 J:
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177 TRGJ2,TRGJP2,TRGJ1,TRGJP1
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178
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179
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180 TRD::
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181
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182 V:
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183 TRDV1,TRDV2,TRDV3
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184 D:
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185 TRDD1,TRDD2,TRDD3
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186 J:
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187 TRDJ1,TRDJ4,TRDJ2,TRDJ3
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188
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189
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190 **Mouse**
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191
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192 TRB::
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193
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194 V:
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195 TRBV1,TRBV2,TRBV3,TRBV4,TRBV5,TRBV12-1,TRBV13-1,TRBV12-2,TRBV13-2,TRBV13-3,TRBV14,TRBV15,TRBV16,TRBV17,TRBV19,TRBV20,TRBV23,TRBV24,TRBV26,TRBV29,TRBV30,TRBV31
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196 D:
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197 TRBD1,TRBD2
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198 J:
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199 TRBJ1-1,TRBJ1-2,TRBJ1-3,TRBJ1-4,TRBJ1-5,TRBJ2-1,TRBJ2-2,TRBJ2-3,TRBJ2-4,TRBJ2-5,TRBJ2-6,TRBJ2-7
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200
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201 </help>
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202
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203 </tool>
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