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1 <tool id="Extract genomic DNA 1" name="Extract Genomic DNA" version="3.0.0">
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2 <description>using coordinates from assembled/unassembled genomes</description>
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1
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3 <requirements>
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10
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4 <requirement type="package" version="0.7.1">bx-python</requirement>
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1
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5 <requirement type="package" version="35x1">faToTwoBit</requirement>
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6 </requirements>
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0
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7 <command>
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8 <![CDATA[
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9 #set genome = $input.metadata.dbkey
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10 #set datatype = $input.datatype
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11 mkdir -p output_dir &&
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12 python $__tool_directory__/extract_genomic_dna.py
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13 --input "$input"
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14 --genome "$genome"
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12
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15 #if $input.is_of_type("gff"):
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16 --input_format "gff"
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17 --columns "1,4,5,7"
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18 --interpret_features $interpret_features
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19 #else:
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20 --input_format "interval"
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21 --columns "${input.metadata.chromCol},${input.metadata.startCol},${input.metadata.endCol},${input.metadata.strandCol},${input.metadata.nameCol}"
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22 #end if
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23 --reference_genome_source $reference_genome_cond.reference_genome_source
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24 #if str($reference_genome_cond.reference_genome_source) == "cached"
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25 --reference_genome $reference_genome_cond.reference_genome.fields.path
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26 #else:
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27 --reference_genome $reference_genome_cond.reference_genome
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28 #end if
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29 --output_format $output_format
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30 --output $output
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31 ]]>
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32 </command>
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33 <inputs>
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34 <param name="input" type="data" format="gff,interval" label="Fetch sequences for intervals in">
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35 <validator type="unspecified_build" />
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36 </param>
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37 <param name="interpret_features" type="select" label="Interpret features when possible" help="Applicable only when input dataset format is in the gff family">
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38 <option value="yes">Yes</option>
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39 <option value="no">No</option>
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40 </param>
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41 <conditional name="reference_genome_cond">
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42 <param name="reference_genome_source" type="select" label="Choose the source for the reference genome">
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43 <option value="cached">locally cached</option>
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44 <option value="history">from history</option>
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45 </param>
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46 <when value="cached">
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47 <param name="reference_genome" type="select" label="Using reference genome">
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48 <options from_data_table="twobit">
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49 <filter type="data_meta" key="dbkey" ref="input" column="0"/>
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50 </options>
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51 <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file"/>
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52 </param>
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53 </when>
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54 <when value="history">
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55 <param name="reference_genome" type="data" format="fasta" label="Using reference genome">
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56 <options>
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1
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57 <filter type="data_meta" key="dbkey" ref="input"/>
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58 </options>
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59 <validator type="no_options" message="The current history does not include a fasta dataset with the build associated with the selected input file"/>
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60 </param>
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61 </when>
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62 </conditional>
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63 <param name="output_format" type="select" label="Select output format">
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64 <option value="fasta" selected="True">fasta</option>
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65 <option value="gff">gff</option>
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66 <option value="interval">interval</option>
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67 </param>
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68 </inputs>
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69 <outputs>
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70 <data name="output" format="fasta">
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71 <change_format>
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72 <when input="output_format" value="gff" format="gff" />
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73 <when input="output_format" value="interval" format="interval" />
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74 </change_format>
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75 </data>
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76 </outputs>
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77 <tests>
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78 <test>
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79 <param name="input" value="1.bed" dbkey="hg17" ftype="bed" />
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80 <param name="interpret_features" value="yes"/>
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81 <param name="index_source" value="cached"/>
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82 <param name="out_format" value="fasta"/>
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83 <output name="out_file1" file="extract_genomic_dna_out1.fasta" compare="contains" />
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84 </test>
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85 <test>
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86 <param name="input" value="droPer1.bed" dbkey="droPer1" ftype="bed" />
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87 <param name="interpret_features" value="yes"/>
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88 <param name="index_source" value="cached"/>
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89 <param name="out_format" value="fasta"/>
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90 <output name="out_file1" file="extract_genomic_dna_out2.fasta" compare="contains" />
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91 </test>
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92 <test>
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93 <param name="input" value="1.bed" dbkey="hg17" ftype="bed" />
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94 <param name="interpret_features" value="yes"/>
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95 <param name="index_source" value="cached"/>
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96 <param name="out_format" value="interval"/>
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97 <output name="out_file1" file="extract_genomic_dna_out3.interval" compare="contains" />
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98 </test>
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99 <!-- Test GFF file support. -->
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100 <test>
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101 <param name="input" value="gff_filter_by_attribute_out1.gff" dbkey="mm9" ftype="gff" />
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102 <param name="interpret_features" value="no"/>
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103 <param name="index_source" value="cached"/>
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104 <param name="out_format" value="interval"/>
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105 <output name="out_file1" file="extract_genomic_dna_out4.gff" compare="contains" />
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0
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106 </test>
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107 <test>
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108 <param name="input" value="gff_filter_by_attribute_out1.gff" dbkey="mm9" ftype="gff" />
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109 <param name="interpret_features" value="no"/>
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110 <param name="out_format" value="fasta"/>
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111 <param name="index_source" value="cached"/>
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7
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112 <output name="out_file1" file="extract_genomic_dna_out5.fasta" compare="contains" />
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113 </test>
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114 <!-- Test custom sequences support and GFF feature interpretation. -->
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115 <test>
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116 <param name="input" value="cufflinks_out1.gtf" dbkey="mm9" ftype="gff" />
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117 <param name="interpret_features" value="no"/>
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118 <param name="index_source" value="history"/>
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119 <param name="ref_file" value="tophat_in1.fasta"/>
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120 <param name="out_format" value="fasta"/>
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121 <output name="out_file1" file="extract_genomic_dna_out6.fasta" compare="contains" />
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122 </test>
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123 <test>
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124 <param name="input" value="cufflinks_out1.gtf" dbkey="mm9" ftype="gff" />
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125 <param name="interpret_features" value="yes"/>
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126 <param name="index_source" value="history"/>
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127 <param name="ref_file" value="tophat_in1.fasta"/>
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128 <param name="out_format" value="fasta"/>
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129 <output name="out_file1" file="extract_genomic_dna_out7.fasta" compare="contains" />
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130 </test>
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131 </tests>
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132 <help>
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133
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134 .. class:: warningmark
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135
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136 This tool requires interval or gff (special tabular formatted data). If your data is not TAB delimited, first use *Text Manipulation->Convert*.
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137
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138 .. class:: warningmark
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139
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140 Make sure that the genome build is specified for the dataset from which you are extracting sequences (click the pencil icon in the history item if it is not specified).
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141
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142 .. class:: warningmark
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143
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144 All of the following will cause a line from the input dataset to be skipped and a warning generated. The number of warnings and skipped lines is documented in the resulting history item.
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145 - Any lines that do not contain at least 3 columns, a chromosome and numerical start and end coordinates.
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146 - Sequences that fall outside of the range of a line's start and end coordinates.
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147 - Chromosome, start or end coordinates that are invalid for the specified build.
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148 - Any lines whose data columns are not separated by a **TAB** character ( other white-space characters are invalid ).
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149
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150 .. class:: infomark
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151
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152 **Extract genomic DNA using coordinates from ASSEMBLED genomes and UNassembled genomes** previously were achieved by two separate tools.
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153
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154 -----
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155
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156 **What it does**
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157
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158 This tool uses coordinate, strand, and build information to fetch genomic DNAs in FASTA or interval format.
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159
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160 If strand is not defined, the default value is "+".
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161
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162 -----
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163
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164 **Example**
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165
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166 If the input dataset is::
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167
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168 chr7 127475281 127475310 NM_000230 0 +
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169 chr7 127485994 127486166 NM_000230 0 +
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170 chr7 127486011 127486166 D49487 0 +
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171
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172 Extracting sequences with **FASTA** output data type returns::
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173
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174 >hg17_chr7_127475281_127475310_+ NM_000230
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175 GTAGGAATCGCAGCGCCAGCGGTTGCAAG
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176 >hg17_chr7_127485994_127486166_+ NM_000230
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177 GCCCAAGAAGCCCATCCTGGGAAGGAAAATGCATTGGGGAACCCTGTGCG
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178 GATTCTTGTGGCTTTGGCCCTATCTTTTCTATGTCCAAGCTGTGCCCATC
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179 CAAAAAGTCCAAGATGACACCAAAACCCTCATCAAGACAATTGTCACCAG
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180 GATCAATGACATTTCACACACG
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181 >hg17_chr7_127486011_127486166_+ D49487
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182 TGGGAAGGAAAATGCATTGGGGAACCCTGTGCGGATTCTTGTGGCTTTGG
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183 CCCTATCTTTTCTATGTCCAAGCTGTGCCCATCCAAAAAGTCCAAGATGA
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184 CACCAAAACCCTCATCAAGACAATTGTCACCAGGATCAATGACATTTCAC
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185 ACACG
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186
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187 Extracting sequences with **Interval** output data type returns::
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188
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189 chr7 127475281 127475310 NM_000230 0 + GTAGGAATCGCAGCGCCAGCGGTTGCAAG
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190 chr7 127485994 127486166 NM_000230 0 + GCCCAAGAAGCCCATCCTGGGAAGGAAAATGCATTGGGGAACCCTGTGCGGATTCTTGTGGCTTTGGCCCTATCTTTTCTATGTCCAAGCTGTGCCCATCCAAAAAGTCCAAGATGACACCAAAACCCTCATCAAGACAATTGTCACCAGGATCAATGACATTTCACACACG
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191 chr7 127486011 127486166 D49487 0 + TGGGAAGGAAAATGCATTGGGGAACCCTGTGCGGATTCTTGTGGCTTTGGCCCTATCTTTTCTATGTCCAAGCTGTGCCCATCCAAAAAGTCCAAGATGACACCAAAACCCTCATCAAGACAATTGTCACCAGGATCAATGACATTTCACACACG
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192
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193 </help>
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194 <citations>
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195 <citation type="bibtex">
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196 @unpublished{None,
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197 author = {Guru Ananda,Greg Von Kuster},
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198 title = {None},
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199 year = {None},
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200 eprint = {None},
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201 url = {http://www.bx.psu.edu/~anton/labSite/}
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202 }</citation>
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203 </citations>
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204 </tool>
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