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2 [TOC]
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3
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4 # 1. findKEGG.py
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5 **find entries with matching query keywords or other query data in a given database**
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6
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7 ## Works with Galaxy?
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8 Yes. see [findKEGG.xml](findKEGG.xml)
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9
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10 ## Command line usage
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11 ```
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12 ../../virtualpy/bin/activate
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13 python findKEGG.py
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14 ```
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15
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16 This will use the default settings for dbname, searchpattern and output
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17 To specify these :
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18 ```
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19 ../../virtualpy/bin/activate
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20 findKEGG.py -d $dbname -q $searchpattern -o $output
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21 ```
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22
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23 ## Known Issues
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24 Yes, the and/or functionality of the KEGG rest API (Release 78.0+/05-05, May 16 ) does not always function as expected. This has been resolved in the code. More details, [KEGGnotes.md ](KEGGnotes.md)
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25
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26 ## Help
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27 ```
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28 ../../virtualpy/bin/activate
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29 python findKEGG.py -h
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30 ```
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31
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32 ## Unit Testing?
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33 Yes. Use test_findKEGG.py
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34
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35 ```
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36 ../../virtualpy/bin/activate
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37 nosetests test_findKEGG.py
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38 ```
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39
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40 # 2. getkcfKEGG,py
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41 **get – retrieves given database entries _but only for GLYCANS_**
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42
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43
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44 ## Works with Galaxy?
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45 Yes. see [getkcfKEGG.xml](getkcfKEGG.xml)
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46
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47 ## Command line usage
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48
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49 ```
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50 ../../virtualpy/bin/activate
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51 cat "G00092" > input
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52 python getkcfKEGG.py
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53 ```
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54
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55 This will use the default settings for input, kcfout and dbout
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56 To specify these :
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57 ```
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58 ../../virtualpy/bin/activate
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59 getkcfKEGG.py -i $input -k $kcfout -d $dbout
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60 ```
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61
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62 ## Help
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63 ```
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64 ../../virtualpy/bin/activate
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65 python getkcfKEGG.py -h
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66 ```
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67
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68 ## Unit Testing?
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69 Yes. Use test_getkcfKEGG.py
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70
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71 ```
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72 ../../virtualpy/bin/activate
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73 nosetests test_getkcfKEGG.py
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74 ```
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75
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76 # 3. linkKEGG.py
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77 **link – find related entries by using database cross-references**
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78
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79 ## Works with Galaxy?
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80 Yes. see [linkKEGG.xml](linkKEGG.xml)
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81
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82 ## Command line usage
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83 ```
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84 ../../virtualpy/bin/activate
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85 python linkKEGG.py
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86 ```
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87
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88 This will use the default settings for targetdb, source and output
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89 linkKEGG.py -t $targetdb -s $source -o $output
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90 To specify these :
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91 ```
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92 ../../virtualpy/bin/activate
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93 linkKEGG.py -t $targetdb -s $source -o $output
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94 ```
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95
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96 ## Help
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97 ```
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98 ../../virtualpy/bin/activate
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99 python linkKEGG.py -h
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100 ```
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101
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102 ## Unit Testing?
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103 Yes. Use test_linkKEGG.py
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104
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105 ```
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106 ../../virtualpy/bin/activate
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107 nosetests test_linkKEGG.py
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108 ```
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109
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