Mercurial > repos > chrisb > gap_all_glycan_tools

comparison get_data/kegg_glycan/README_KEGG.md @ 0:89592faa2875 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded
author chrisb
date Wed, 23 Mar 2016 14:35:56 -0400
parents
children 0a5e0df17054
comparison
equal deleted inserted replaced
-1:000000000000 0:89592faa2875
1
2 [TOC]
3
4 # 1. findKEGG.py
5 **find entries with matching query keywords or other query data in a given database**
6
7 ## Works with Galaxy?
8 Yes. see [findKEGG.xml](findKEGG.xml)
9
10 ## Command line usage
11 ```
12 ../../virtualpy/bin/activate
13 python findKEGG.py
14 ```
15
16 This will use the default settings for dbname, searchpattern and output
17 To specify these :
18 ```
19 ../../virtualpy/bin/activate
20 findKEGG.py -d $dbname -q $searchpattern -o $output
21 ```
22
23 ## Help
24 ```
25 ../../virtualpy/bin/activate
26 python findKEGG.py -h
27 ```
28
29 ## Unit Testing?
30 Yes. Use test_findKEGG.py
31
32 ```
33 ../../virtualpy/bin/activate
34 python test_findKEGG.py
35 ```
36
37 # 2. getkcfKEGG,py
38 **get – retrieves given database entries _but only for GLYCANS_**
39
40
41 ## Works with Galaxy?
42 Yes. see [getkcfKEGG.xml](getkcfKEGG.xml)
43
44 ## Command line usage
45
46 ```
47 ../../virtualpy/bin/activate
48 cat "G00092" > input
49 python getkcfKEGG.py
50 ```
51
52 This will use the default settings for input, kcfout and dbout
53 To specify these :
54 ```
55 ../../virtualpy/bin/activate
56 getkcfKEGG.py -i $input -k $kcfout -d $dbout
57 ```
58
59 ## Help
60 ```
61 ../../virtualpy/bin/activate
62 python getkcfKEGG.py -h
63 ```
64
65 ## Unit Testing?
66 Yes. Use test_getkcfKEGG.py
67
68 ```
69 ../../virtualpy/bin/activate
70 python test_getkcfKEGG.py
71 ```
72
73 # 3. linkKEGG.py
74 **link – find related entries by using database cross-references**
75
76 ## Works with Galaxy?
77 Yes. see [linkKEGG.xml](linkKEGG.xml)
78
79 ## Command line usage
80 ```
81 ../../virtualpy/bin/activate
82 python linkKEGG.py
83 ```
84
85 This will use the default settings for targetdb, source and output
86 linkKEGG.py -t $targetdb -s $source -o $output
87 To specify these :
88 ```
89 ../../virtualpy/bin/activate
90 linkKEGG.py -t $targetdb -s $source -o $output
91 ```
92
93 ## Help
94 ```
95 ../../virtualpy/bin/activate
96 python linkKEGG.py -h
97 ```
98
99 ## Unit Testing?
100 Yes. Use test_linkKEGG.py
101
102 ```
103 ../../virtualpy/bin/activate
104 python test_linkKEGG.py
105 ```
106