Mercurial > repos > chrisb > gap_all_glycan_tools
diff 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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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/get_data/cfg_array/README_CFG_array.md Wed Mar 23 14:35:56 2016 -0400 @@ -0,0 +1,46 @@ +[TOC] + +# 1. cfg_get_glycan_array_data.py + +Retrieve glycan array data from the CFG. + +With focus on retrieving the xls data and also pull the metadata. + +## Works with Galaxy? + +Not properly tested yet!! The xml in this directory is not correct. + +## Command line usage + +**NOT RECOMMENDED** This will download all xls and will take a while. +``` +../../virtualpy/bin/activate +python cfg_get_glycan_array_data.py +``` + +**RECOMMENDED** This will get all metadata and not download xls +``` +../../virtualpy/bin/activate +python cfg_get_glycan_array_data.py -d +``` + +This metadata can be viewed using the [CFG glycan array explorer](https://bitbucket.org/rxncor/cfg-data-chart) + +## Help +``` +../../virtualpy/bin/activate +python cfg_get_glycan_from_cells.py -h +``` + +## Unit Testing? +Not yet! Although some testing has been done using *.html in ./info and ./templates +Also passed json metadata to [CFG glycan array explorer](https://bitbucket.org/rxncor/cfg-data-chart) + +In principle: + +``` +../../virtualpy/bin/activate +python test_cfg_get_glycan_from_cells.py + +``` +