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2 <tool id="removeFastaSubSequence" name="Remove Fasta Substring Sequence" version="1.0.0">
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3 <description>Removes sequences from query fasta file that are present in a reference Fasta File.</description>
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4 <requirements>
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5 <requirement type="package" version="1.70">biopython</requirement>
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6 </requirements>
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7 <command interpreter="python"><![CDATA[removeFastaSubSequence.py $ref_fastafile $query_fastafile $output]]></command>
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8 <inputs>
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9 <param name="ref_fastafile" type="data" format="fasta">
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10 <label>Input Reference Fasta File</label>
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11 </param>
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12 <param name="query_fastafile" type="data" format="fasta">
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13 <label>Input Query Fasta File</label>
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14 </param>
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15 </inputs>
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16
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17 <outputs>
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18 <data format="fasta" name="output" label="uniqSeq_${query_fastafile.name.rsplit('.',1)[0]}.fasta" />
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19 </outputs>
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20
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21 <tests>
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22 <test>
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23 <param name="ref_fastafile" value="test_ref.fasta" />
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24 <param name="query_fastafile" value="test_query.fasta" />
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25 <output name="output" file="uniqSeq_test_query.fasta">
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26 <assert_contents>
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27 <has_text text="ENSMUST00000193003" />
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28 </assert_contents>
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29 </output>
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30 </test>
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31 </tests>
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32
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33
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34 <help>
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35 This program removes the sequences from the query fasta file that are present in a reference fasta file (removes even those query sequences that are present as substring in reference fasta file).
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36
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37 EXAMPLE:
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38
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39 ----
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40
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41 Ref sequences:
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42
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43 >reference_seq_1
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44
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45 TSLDKDHLELCCTLSLPFSWACSWVLVLRLSINGQLPRSRLWAAHCLWGVP
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46
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47 >reference_seq_2
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48
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49 RGLCISGLEKEVQVQSRQAEGPVHLWLRKGSTSAE
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50
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51 ----
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52
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53 Query Sequences:
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54
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55 >query_seq_1
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56
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57 TKTILNYAVLSPCLSPGHVLGC
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58
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59
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60 >query_seq_2
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61
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62 LDKDHLELCCTLSLPFSWACSWVLVL
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63
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64
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65 >query_seq_3
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66
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67 LWGVPRGLCISG
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68
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69 ----
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70
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71 Output Sequences:
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72
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73 >query_seq_1
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74
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75 TKTILNYAVLSPCLSPGHVLGC
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76
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77
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78 >query_seq_3
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79
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80 LWGVPRGLCISG
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81
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82 ----
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83
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84 Output Sequence file will have only query_seq_1 and query_seq_3. query_seq_2 is removed because query_seq_2's sequence "LDKDHLELCCTLSLPFSWACSWVLVL" is
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85 present as substring in reference_seq_1's sequence "TSLDKDHLELCCTLSLPFSWACSWVLVLRLSINGQLPRSRLWAAHCLWGVP".
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86
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87 </help>
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88 </tool>
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