Mercurial > repos > chrisb > gap_all_glycan_tools
comparison get_data/cfg_array/README_CFG_array.md @ 0:89592faa2875 draft
Uploaded
author | chrisb |
---|---|
date | Wed, 23 Mar 2016 14:35:56 -0400 |
parents | |
children |
comparison
equal
deleted
inserted
replaced
-1:000000000000 | 0:89592faa2875 |
---|---|
1 [TOC] | |
2 | |
3 # 1. cfg_get_glycan_array_data.py | |
4 | |
5 Retrieve glycan array data from the CFG. | |
6 | |
7 With focus on retrieving the xls data and also pull the metadata. | |
8 | |
9 ## Works with Galaxy? | |
10 | |
11 Not properly tested yet!! The xml in this directory is not correct. | |
12 | |
13 ## Command line usage | |
14 | |
15 **NOT RECOMMENDED** This will download all xls and will take a while. | |
16 ``` | |
17 ../../virtualpy/bin/activate | |
18 python cfg_get_glycan_array_data.py | |
19 ``` | |
20 | |
21 **RECOMMENDED** This will get all metadata and not download xls | |
22 ``` | |
23 ../../virtualpy/bin/activate | |
24 python cfg_get_glycan_array_data.py -d | |
25 ``` | |
26 | |
27 This metadata can be viewed using the [CFG glycan array explorer](https://bitbucket.org/rxncor/cfg-data-chart) | |
28 | |
29 ## Help | |
30 ``` | |
31 ../../virtualpy/bin/activate | |
32 python cfg_get_glycan_from_cells.py -h | |
33 ``` | |
34 | |
35 ## Unit Testing? | |
36 Not yet! Although some testing has been done using *.html in ./info and ./templates | |
37 Also passed json metadata to [CFG glycan array explorer](https://bitbucket.org/rxncor/cfg-data-chart) | |
38 | |
39 In principle: | |
40 | |
41 ``` | |
42 ../../virtualpy/bin/activate | |
43 python test_cfg_get_glycan_from_cells.py | |
44 | |
45 ``` | |
46 |