Closed cheng-yu-zhang closed 2 years ago
You should make new feature branches of a recent devel
branch, this one is derived from a devel
commit from last December.
In addition, please do not modify existing curation files, but make new file/folders in code/modelCuration
and data/modelCuration
. This prevents confusion on what are new curations and old curations.
I have rebased this onto the most recent devel
branch and refactored the datafiles to be contained in their own folder.
Metric | yeast-GEM 8.6.0 | this PR |
---|---|---|
Number of genes | 1151 | 1153 |
Accuracy | 0.8801 | 0.8810 |
TP | 923 | 923 |
TN | 61 | 62 |
FP | 98 | 97 |
FN | 36 | 36 |
FYI, I'm "hijacking" this PR to demonstrate how to consolidate curation from a particular model version towards the next release. For the moment I've also already merged #305 and #306 to hear, to combine all three curations in one consolidated script.
@edkerk When I run "/code/modelCuration/v8_6_0.m", I find that there is a extra parameter "grRatioMuts" in line 44 of the "essentialGenes.m", which may cause some issues.
[genes, fluxes, originalGenes, details, grRatioMuts]=findGeneDeletions(model,'sgd','fba');
[genes, fluxes, originalGenes, details]=findGeneDeletions(model,testType,analysisType,refModel,oeFactor)
Apart from that, this pipeline works well.
When I run "/code/modelCuration/v8_6_0.m", I find that there is a extra parameter "grRatioMuts" in line 44 of the "essentialGenes.m", which may cause some issues.
[genes, fluxes, originalGenes, details, grRatioMuts]=findGeneDeletions(model,'sgd','fba');
[genes, fluxes, originalGenes, details]=findGeneDeletions(model,testType,analysisType,refModel,oeFactor)
Apart from that, this pipeline works well.
Great, this behaviour of essentialGenes
is expected as long as https://github.com/SysBioChalmers/RAVEN/pull/421 is not merged.
Main improvements in this PR:
Add 19 new GPR accoording to SGD and uniprot.
This PR is used to demonstrate consolidation of multiple curations in one script, that can convert a previous model release to the next version.
I hereby confirm that I have:
develop
as a target branch (top left drop-down menu)