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comparison get_data/kegg_glycan/README_KEGG.md @ 1:0a5e0df17054 draft default tip

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author chrisb
date Fri, 06 May 2016 08:05:48 -0400
parents 89592faa2875
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0:89592faa2875 1:0a5e0df17054
18 ``` 18 ```
19 ../../virtualpy/bin/activate 19 ../../virtualpy/bin/activate
20 findKEGG.py -d $dbname -q $searchpattern -o $output 20 findKEGG.py -d $dbname -q $searchpattern -o $output
21 ``` 21 ```
22 22
23 ## Known Issues
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)
25
23 ## Help 26 ## Help
24 ``` 27 ```
25 ../../virtualpy/bin/activate 28 ../../virtualpy/bin/activate
26 python findKEGG.py -h 29 python findKEGG.py -h
27 ``` 30 ```
29 ## Unit Testing? 32 ## Unit Testing?
30 Yes. Use test_findKEGG.py 33 Yes. Use test_findKEGG.py
31 34
32 ``` 35 ```
33 ../../virtualpy/bin/activate 36 ../../virtualpy/bin/activate
34 python test_findKEGG.py 37 nosetests test_findKEGG.py
35 ``` 38 ```
36 39
37 # 2. getkcfKEGG,py 40 # 2. getkcfKEGG,py
38 **get – retrieves given database entries _but only for GLYCANS_** 41 **get – retrieves given database entries _but only for GLYCANS_**
39 42
65 ## Unit Testing? 68 ## Unit Testing?
66 Yes. Use test_getkcfKEGG.py 69 Yes. Use test_getkcfKEGG.py
67 70
68 ``` 71 ```
69 ../../virtualpy/bin/activate 72 ../../virtualpy/bin/activate
70 python test_getkcfKEGG.py 73 nosetests test_getkcfKEGG.py
71 ``` 74 ```
72 75
73 # 3. linkKEGG.py 76 # 3. linkKEGG.py
74 **link – find related entries by using database cross-references** 77 **link – find related entries by using database cross-references**
75 78
99 ## Unit Testing? 102 ## Unit Testing?
100 Yes. Use test_linkKEGG.py 103 Yes. Use test_linkKEGG.py
101 104
102 ``` 105 ```
103 ../../virtualpy/bin/activate 106 ../../virtualpy/bin/activate
104 python test_linkKEGG.py 107 nosetests test_linkKEGG.py
105 ``` 108 ```
106 109