Mercurial > repos > chrisb > gap_all_glycan_tools
comparison get_data/cfg_array/README_CFG_array.md @ 0:89592faa2875 draft
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| author | chrisb |
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| date | Wed, 23 Mar 2016 14:35:56 -0400 |
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| -1:000000000000 | 0:89592faa2875 |
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| 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 |