Fix/export functions #81
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Update fix/export_functions with latest changes from devel branch
reads a RAVEN model and creates the corresponding yaml
wrapper was leaving behind a final white space for each metabolite name
-applied MATLAB smart indent (EDITOR -> EDIT -> Indent -> Smart) -removed unecessary semicolons (end;) -reformatted comments
* remove constructYaml, superseded by writeYaml * remove Yaml export as function from exportModel, superseded by writeYaml * remove Yaml libraries
applied MATLAB smart indent (EDITOR -> EDIT -> Indent -> Smart)
>feat: -removed the obsolete addNull parameter -retained backwards compatibility with other RAVEN functions -the function now is capable to extract all the information from miriam field. The output is literally the same as in previous version, just the different miriam names are saved in different columns >refactor: -got rid of some redundant function parts >style: -updated the function annotation and comments
added second output variable, which provides miriam names for extracted miriams
>feat: -removed the hard-coded fields for several miriams (metCHEBI, metKEGG, rxnKEGG). Now the exporter identifies all the possible miriam names in the given miriam field and exports this information to YAML file -added support for geneMiriams and compMiriams >style: -applied MATLAB smart indent (EDITOR -> EDIT -> Indent -> Smart)
removed the unecessary change to the code in previous commit
ravenCobraWrapper will try to find pmids in the field rxnNotes, and if found will place them in rxnMiriams. If not, it will leave it in rxnNotes
deletes middle names for compatibility with writeYaml
ordered dictionary for compartments
BenjaSanchez
added
the
feature
added 2 commits
April 16, 2018 09:40
fixed typo in the description
added the execution permission in the command line (chmod a+x writeYaml.m)
simas232
approved these changes
Apr 16, 2018
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Problem this branch addreses:
Refer to issue #77. The functionality of RAVEN for saving a model as
.ymlhas been fixed; now the.ymlfile is created with a simpler standard, and all associated functions have been adapted accordingly.