Curation/metabolites #74
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The metabolite annotation, including the detailed name, charge, keggID and chebiID was updated based on the latest chebi and kegg databases.
When save the model, the errors occured:
Undefined function or variable 'git'.
Error in saveYeastModel (line 37)
COBRAcommit = git('log -n 1 --format=%H');
Correct some errors and further update the metabolite name information in the model
The duplicated subsystems have been removed. Also the subsystem information is further corrected based on the previous model and kegg database
This reverts commit 4b46e23.
Remove the metabolite annotation infomation in mat format
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@hongzhonglu thanks for the PR. Some changes to address:
Regarding the error you mention, make sure that you have the Git wrapper added to your path |
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@BenjaSanchez I have tried to change the txt format, but not solve it, it may due to mac system. Can you help me change the txt format into the csv separated by comma? Thanks in advance! |
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@hongzhonglu I did it for |
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@BenjaSanchez yeast_uique_metabolites information with correction comment.txt is just similar to metabolite.txt. So we can remove "yeast_uique_metabolites information with correction comment.txt". |
Only the csv format metabolite information was remained and the name of the csv file was also changed ended with date.
This reverts commit 73d0288.
data for only metabolites that changed is saved now
for compatibility in Matlab
csv is no good for fields such as names that already contains commas
all changes from devel applied to model
from metabolite_manual_curation.tsv
from metabolite_manual_curation.tsv
from metabolite_manual_curation.tsv
from metabolite_manual_curation.tsv
…te annotation The remark information has been refined for each update of metabolite annoation to make the results more clear.
mostly mispells or redundant info
@BenjaSanchez @feiranl
The metabolite name, charges, keggID and chebi ID were updated.
When save the model, the errors occured:
Undefined function or variable 'git'.
Error in saveYeastModel (line 37)
COBRAcommit = git('log -n 1 --format=%H');
Can you look into it? Great thanks!