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Fix Duplicate Stearoyl-CoA Beta-Oxidation Reactions #820
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…weren't appropriate
…eactions.tsv and moved MAR00776 to deprecatedReactions.tsv
…46 in reactions.tsv and moved MAR00778 to deprecatedReactions.tsv
it would be easier to figure out what went wrong with the metabolic tasks if the test indicated which tasks failed rather than just saying that the test as a whole failed (if this information is in the output somewhere and I'm just not seeing it, let me know) |
@JHL-452b Could you help check this? |
Yeah. In the current code, it would exit the matlab program directly if the task failed without any feedback. This suggestion should be incorporated into plans for subsequent improvements. However, in this bug, I tested on my own computer and finded that the task of |
Actually, the failed task seems to have nothing to do with the modification of this PR due to same problem occured when I re-run the task for I tried changing the solver to >> taskType = 'essential';
>> setRavenSolver('glpk')
>> status = testMetabolicTasks(taskType)
Boundary metabolites were added to 1660 reactions.
New (boundary) versions of 1660 metabolites were added to the model.
FAIL: [GR] Growth on Ham's media (biomass production)
status =
0
>> setRavenSolver('gurobi')
>> status = testMetabolicTasks(taskType)
Boundary metabolites were added to 1660 reactions.
New (boundary) versions of 1660 metabolites were added to the model.
Suceeded with essential tasks.
status =
1 I don't know why RAVEN cannot automatically change the solver to |
See #821 (comment) for consideration regarding gurobi/glpk. |
# Conflicts: # data/testResults/README.md
This PR has been automatically tested with GH Actions. Here is the output of the MACAW test: Starting dead-end test... This and a more detailed output from MACAW are also committed to
|
@Devlin-Moyer @edkerk Is this PR ready to be merged? |
Yes, but I'd like to merge-in |
# Conflicts: # data/testResults/README.md
This PR has been automatically tested with GH Actions. Here is the output of the gene essentiality test: cellLine TP TN FP FN accuracy sensitivity specificity F1 MCC
|
Main improvements in this PR:
As proposed in #802:
MAR00776
for being a duplicate ofMAR03115
+MAR03116
+MAR03117
+MAR03118
MAR00778
for being a duplicate ofMAR03116
+MAR03117
+MAR03118
+MAR03121
+MAR03122
+MAR03123
+MAR03125
+MAR03128
+MAR03129
+MAR03130
+MAR03132
+MAR03135
+MAR03136
+MAR03137
+MAR03139
+MAR03142
+MAR03143
+MAR03144
+MAR03146
I noticed that
MAR00776
had references associated with it butMAR03115
,MAR03116
,MAR03117
, andMAR03118
didn't, but the two references associated withMAR00776
were about ACADS and ACADM, neither of which can actually catalyze the first round of beta-oxidation of stearoyl-CoA (at 18 carbons, it's too long), so I instead associated those four reactions withPMID:20490924
, a review of mitochondrial beta-oxidation.MAR03121
onwards all had several references already associated with them, so I left those alone.I hereby confirm that I have:
develop
as a target branch