Mercurial > repos > mbernt > fasta_regex_finder

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bioinformatics-cafe commit c318cd3f894f89c13d7eb257678673da70f72212
author iuc
date Wed, 25 Jan 2023 14:03:52 +0000
parents 269c627ae9f4
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9a811adb714f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bioinformatics-cafe commit c318cd3f894f89c13d7eb257678673da70f72212
iuc
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1 <tool id="fasta_regex_finder" name="Fasta regular expression finder" version="0.1.0">
0
269c627ae9f4 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/fasta_regex_finder commit 8e118a4d24047e2c62912b962e854f789d6ff559
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2 <description>
269c627ae9f4 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/fasta_regex_finder commit 8e118a4d24047e2c62912b962e854f789d6ff559
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3 Search in fasta for regexp match
269c627ae9f4 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/fasta_regex_finder commit 8e118a4d24047e2c62912b962e854f789d6ff559
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4 </description>
269c627ae9f4 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/fasta_regex_finder commit 8e118a4d24047e2c62912b962e854f789d6ff559
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5 <requirements>
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9a811adb714f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bioinformatics-cafe commit c318cd3f894f89c13d7eb257678673da70f72212
iuc
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6 <requirement type="package" version="3.8">python</requirement>
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269c627ae9f4 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/fasta_regex_finder commit 8e118a4d24047e2c62912b962e854f789d6ff559
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7 </requirements>
1
9a811adb714f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bioinformatics-cafe commit c318cd3f894f89c13d7eb257678673da70f72212
iuc
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8 <version_command>python '$__tool_directory__/fastaregexfinder.py' --version</version_command>
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269c627ae9f4 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/fasta_regex_finder commit 8e118a4d24047e2c62912b962e854f789d6ff559
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9 <command detect_errors="exit_code"><![CDATA[
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9a811adb714f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bioinformatics-cafe commit c318cd3f894f89c13d7eb257678673da70f72212
iuc
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10 python '$__tool_directory__/fastaregexfinder.py'
9a811adb714f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bioinformatics-cafe commit c318cd3f894f89c13d7eb257678673da70f72212
iuc
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11 --fasta '$input'
9a811adb714f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bioinformatics-cafe commit c318cd3f894f89c13d7eb257678673da70f72212
iuc
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12 --regex '$regex'
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13 #if $settings.advanced == "advanced"
269c627ae9f4 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/fasta_regex_finder commit 8e118a4d24047e2c62912b962e854f789d6ff559
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14 $settings.matchcase
269c627ae9f4 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/fasta_regex_finder commit 8e118a4d24047e2c62912b962e854f789d6ff559
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15 $settings.noreverse
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16 --maxstr $settings.maxstr
269c627ae9f4 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/fasta_regex_finder commit 8e118a4d24047e2c62912b962e854f789d6ff559
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17 #if $settings.seqnames != ""
269c627ae9f4 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/fasta_regex_finder commit 8e118a4d24047e2c62912b962e854f789d6ff559
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18 --seqnames $settings.seqnames
269c627ae9f4 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/fasta_regex_finder commit 8e118a4d24047e2c62912b962e854f789d6ff559
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19 #end if
269c627ae9f4 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/fasta_regex_finder commit 8e118a4d24047e2c62912b962e854f789d6ff559
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20 #end if
269c627ae9f4 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/fasta_regex_finder commit 8e118a4d24047e2c62912b962e854f789d6ff559
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21 --quiet
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22 > '$output'
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23 ]]></command>
269c627ae9f4 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/fasta_regex_finder commit 8e118a4d24047e2c62912b962e854f789d6ff559
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24 <inputs>
269c627ae9f4 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/fasta_regex_finder commit 8e118a4d24047e2c62912b962e854f789d6ff559
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25 <param type="data" name="input" format="fasta" />
269c627ae9f4 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/fasta_regex_finder commit 8e118a4d24047e2c62912b962e854f789d6ff559
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26 <param name="regex" size="30" type="text" value="([gG]{3,}\w{1,7}){3,}[gG]{3,}" label="Regular expression" help="(--regex)">
269c627ae9f4 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/fasta_regex_finder commit 8e118a4d24047e2c62912b962e854f789d6ff559
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27 <sanitizer>
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28 <valid initial="string.printable">
269c627ae9f4 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/fasta_regex_finder commit 8e118a4d24047e2c62912b962e854f789d6ff559
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29 <remove value="&apos;"/>
269c627ae9f4 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/fasta_regex_finder commit 8e118a4d24047e2c62912b962e854f789d6ff559
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30 </valid>
269c627ae9f4 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/fasta_regex_finder commit 8e118a4d24047e2c62912b962e854f789d6ff559
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31 <mapping initial="none">
269c627ae9f4 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/fasta_regex_finder commit 8e118a4d24047e2c62912b962e854f789d6ff559
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32 <add source="&apos;" target="__sq__"/>
269c627ae9f4 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/fasta_regex_finder commit 8e118a4d24047e2c62912b962e854f789d6ff559
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33 </mapping>
269c627ae9f4 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/fasta_regex_finder commit 8e118a4d24047e2c62912b962e854f789d6ff559
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34 </sanitizer>
269c627ae9f4 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/fasta_regex_finder commit 8e118a4d24047e2c62912b962e854f789d6ff559
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35 </param>
269c627ae9f4 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/fasta_regex_finder commit 8e118a4d24047e2c62912b962e854f789d6ff559
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36 <conditional name="settings">
269c627ae9f4 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/fasta_regex_finder commit 8e118a4d24047e2c62912b962e854f789d6ff559
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37 <param name="advanced" type="select" label="Specify advanced parameters">
269c627ae9f4 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/fasta_regex_finder commit 8e118a4d24047e2c62912b962e854f789d6ff559
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38 <option value="simple" selected="true">No, use program defaults.</option>
269c627ae9f4 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/fasta_regex_finder commit 8e118a4d24047e2c62912b962e854f789d6ff559
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39 <option value="advanced">Yes, see full parameter list.</option>
269c627ae9f4 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/fasta_regex_finder commit 8e118a4d24047e2c62912b962e854f789d6ff559
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40 </param>
269c627ae9f4 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/fasta_regex_finder commit 8e118a4d24047e2c62912b962e854f789d6ff559
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41 <when value="simple">
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42 </when>
269c627ae9f4 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/fasta_regex_finder commit 8e118a4d24047e2c62912b962e854f789d6ff559
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43 <when value="advanced">
269c627ae9f4 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/fasta_regex_finder commit 8e118a4d24047e2c62912b962e854f789d6ff559
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44 <param name="matchcase" type="boolean" label="Match case" truevalue="--matchcase" falsevalue="" help="(--matchcase)" />
269c627ae9f4 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/fasta_regex_finder commit 8e118a4d24047e2c62912b962e854f789d6ff559
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45 <param name="noreverse" type="boolean" label="Do not search the reverse complement" truevalue="--noreverse" falsevalue="" help="(--noreverse)" />
269c627ae9f4 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/fasta_regex_finder commit 8e118a4d24047e2c62912b962e854f789d6ff559
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46 <param name="maxstr" type="integer" label="Maximum length of the match to report" value="10000" min="1" help="(--maxstr)" />
269c627ae9f4 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/fasta_regex_finder commit 8e118a4d24047e2c62912b962e854f789d6ff559
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47 <param name="seqnames" size="30" type="text" value="" label="Space separated list of fasta sequences to search" help="--seqnames"/>
269c627ae9f4 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/fasta_regex_finder commit 8e118a4d24047e2c62912b962e854f789d6ff559
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48 </when>
269c627ae9f4 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/fasta_regex_finder commit 8e118a4d24047e2c62912b962e854f789d6ff559
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49 </conditional>
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50 </inputs>
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51 <outputs>
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52 <data name="output" format="bed" from_work_dir="TestSeqGroup-G4.bed" />
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53 </outputs>
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54 <tests>
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55 <test>
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56 <param name="input" value="TestSeqGroup-G4.fasta"/>
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57 <output name="output" file="TestSeqGroup-G4.bed"/>
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58 </test>
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59 <test>
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60 <param name="input" value="test.fas"/>
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61 <param name="regex" value="ACTG"/>
269c627ae9f4 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/fasta_regex_finder commit 8e118a4d24047e2c62912b962e854f789d6ff559
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62 <output name="output" file="test-1.bed"/>
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63 </test>
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64 <test>
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65 <param name="input" value="test.fas"/>
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66 <param name="regex" value="ACTG"/>
269c627ae9f4 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/fasta_regex_finder commit 8e118a4d24047e2c62912b962e854f789d6ff559
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67 <param name="advanced" value="advanced"/>
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68 <param name="matchcase" value="--matchcase"/>
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69 <output name="output" file="test-2.bed"/>
269c627ae9f4 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/fasta_regex_finder commit 8e118a4d24047e2c62912b962e854f789d6ff559
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70 </test>
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71 <test>
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72 <param name="input" value="test.fas"/>
269c627ae9f4 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/fasta_regex_finder commit 8e118a4d24047e2c62912b962e854f789d6ff559
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73 <param name="regex" value="ACTG"/>
269c627ae9f4 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/fasta_regex_finder commit 8e118a4d24047e2c62912b962e854f789d6ff559
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74 <param name="advanced" value="advanced"/>
269c627ae9f4 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/fasta_regex_finder commit 8e118a4d24047e2c62912b962e854f789d6ff559
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75 <param name="noreverse" value="--noreverse"/>
269c627ae9f4 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/fasta_regex_finder commit 8e118a4d24047e2c62912b962e854f789d6ff559
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76 <output name="output" file="test-3.bed"/>
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77 </test>
269c627ae9f4 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/fasta_regex_finder commit 8e118a4d24047e2c62912b962e854f789d6ff559
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78 <test>
269c627ae9f4 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/fasta_regex_finder commit 8e118a4d24047e2c62912b962e854f789d6ff559
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79 <param name="input" value="test.fas"/>
269c627ae9f4 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/fasta_regex_finder commit 8e118a4d24047e2c62912b962e854f789d6ff559
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80 <param name="regex" value="ACTG"/>
269c627ae9f4 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/fasta_regex_finder commit 8e118a4d24047e2c62912b962e854f789d6ff559
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81 <param name="advanced" value="advanced"/>
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82 <param name="maxstr" value="3"/>
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83 <output name="output" file="test-4.bed"/>
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84 </test>
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85 <test>
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86 <param name="input" value="TestSeqGroup-G4.fasta"/>
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87 <param name="advanced" value="advanced"/>
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88 <param name="seqnames" value="HJ24-Shp2_oncogenicProtein2 HJ24-Shp2_oncogenicProtein"/>
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89 <output name="output" file="TestSeqGroup-G4-sub.bed"/>
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90 </test>
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91 </tests>
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92 <help><![CDATA[
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93 DESCRIPTION
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94
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95 Search a fasta file for matches to a regular expression and return a bed file with the
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96 coordinates of the match and the matched sequence itself.
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97
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98 Output bed file has columns:
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99
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100 1. Name of fasta sequence (e.g. chromosome)
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101 2. Start of the match
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102 3. End of the match
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103 4. ID of the match
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104 5. Length of the match
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105 6. Strand
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106 7. Matched sequence as it appears on the forward strand
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107
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108 For matches on the reverse strand it is reported the start and end position on the
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109 forward strand and the matched string on the forward strand (so the G4 'GGGAGGGT'
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110 present on the reverse strand is reported as ACCCTCCC).
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111
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112
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113 Note: Fasta sequences (chroms) are read in memory one at a time along with the
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114 matches for that chromosome.
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115 The order of the output is: chroms as they are found in the inut fasta, matches
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116 sorted within chroms by positions.
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117
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118 ARGUMENTS:
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119
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120 - regex Regex to be searched in the fasta input. Matches to the reverse complement will have - strand. The default regex is '([gG]{3,}\w{1,7}){3,}[gG]{3,}' which searches for G-quadruplexes.
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121 - matchcase Match case while searching for matches. Default is to ignore case (I.e. 'ACTG' will match 'actg').
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122 - noreverse Do not search the reverse complement of the input fasta. Use this flag to search protein sequences.
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123 - maxstr Maximum length of the match to report in the 7th column of the output. Default is to report up to 10000nt. Truncated matches are reported as <ACTG...ACTG>[<maxstr>,<tot length>]
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124 - seqnames List of fasta sequences in the input to search. E.g. use --seqnames chr1 chr2 chrM to search only these crhomosomes. Default is to search all the sequences in input.
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125
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126 EXAMPLE:
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127
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128 Test data::
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129 >mychr
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130 ACTGnACTGnACTGnTGAC
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131
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132 Example1 regex=ACTG::
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133
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134 mychr 0 4 mychr_0_4_for 4 + ACTG
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135 mychr 5 9 mychr_5_9_for 4 + ACTG
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136 mychr 10 14 mychr_10_14_for 4 + ACTG
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137
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138 Example2 regex=ACTG maxstr=3::
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139
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140 mychr 0 4 mychr_0_4_for 4 + ACT[3,4]
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141 mychr 5 9 mychr_5_9_for 4 + ACT[3,4]
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142 mychr 10 14 mychr_10_14_for 4 + ACT[3,4]
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143
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144 Example3 regex=A\w\wG::
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145
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146 mychr 0 5 mychr_0_5_for 5 + ACTGn
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147 mychr 5 10 mychr_5_10_for 5 + ACTGn
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148 mychr 10 15 mychr_10_15_for 5 + ACTGn
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149
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150 ]]></help>
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151 <citations>
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152 <citation type="bibtex">
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153 @misc{githubfastaRegexFinder,
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154 author = {Dario Beraldi},
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155 year = {2017},
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156 title = {fastaRegexFinder},
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157 publisher = {GitHub},
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158 journal = {GitHub repository},
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159 url = {https://github.com/dariober/bioinformatics-cafe/tree/master/fastaRegexFinder},
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160 }</citation>
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161 </citations>
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162 </tool>