Map mets/rxns in the model to have MNX IDs #167
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Upload the function mapIDsViaMNXref.m and GetMNXID.m which are used for getting the MNX IDs for mapping the KEGGid and CHEBIID to MetaNetX ID. A reference file as MNX.mat was also uploaded, and two mapping lists from yeast7.6MNXmodel also uploaded to the database file.
Run the code: model = loadYeastModel model = GetMNXID(model,'mets',2) to get the met annotation for mets. 2 stands for also include the yeast7.6 MNX model information.
Run the code: model = loadYeastModel model = GetMNXID(model,'rxns',2) to get the met annotation for rxns. 2 stands for also include the yeast7.6 MNX model information.
hongzhonglu
approved these changes
Oct 10, 2018
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Thanks for the PR @feiranl please see my comments in my review for complying with the standard of the repo and making some sections simpler
comply with repo format rewrite the load MNXref data structure part add more annotation to the function remove conflicting part
move these two functions
BenjaSanchez
suggested changes
Oct 16, 2018
fix a bug in function
fix a bug for windows
* corrected matching of slash character in the toolbox path * fixed for loops in the level=1 case * proper indentation of functions * switched RAVEN to master (after 2.0.4 release)
BenjaSanchez
approved these changes
Oct 16, 2018
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I added a couple fixes, including fixing the for loops in the level=1 case. @feiranl note that after the new release of RAVEN you can switch back your branch to master for any new PRs and it should work fine
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Main improvements in this PR:
Adresses issue #154
Yeast7.6MNXRxnMappingList.tsvandYeast7.6MNXMetMappingList.tsvGetMNXID.m.mapIDsViaMNXref.m, which would load MNX database file from RAVEN toolboxI hereby confirm that I have:
develas a target branch (top left drop-down menu)