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Problem converting RECON1 to core/standard model #563
Comments
Hello! |
Note to self: add RECON to tests. |
Anyway it seems that we didn't consider underscores as valid gene names in the GRR formulas so far; a very quick evening fix is available in branch |
Thanks! Note: I think the other human BiGG models like iAB_RBC_283.json and Recon3D contain underscores because I got similar GRR errors that disappeared when I used this test branch. |
I kinda guessed the problem from the error message-- do I read correctly that the fix worked? 😀 If all is OK now, I'll add some QA&tests and send this to release. Thanks again for reporting! |
Yup everything is working great and thanks for the quick reply! Please close the issue at your convenience. |
Great, thanks for confirming! This is now then fixed and tested (so hopefully should not break again :D ), the fix is in development branch, will be released in the next version. 🚀 |
Minimal code example to reproduce the problem
Expected result
Convert BiGG model to
CoreModel
and/orStandardModel
. Not sure if this is an error with COBREXA or the RECON1 json input file.Actual behavior
Optional: Environment
julia>
(@v1.6) pkg> status
Status
~/.julia/environments/v1.6/Project.toml
[c7e460c6] ArgParse v1.1.4
[6e4b80f9] BenchmarkTools v1.2.2
[babc4406] COBREXA v1.2.1
[336ed68f] CSV v0.10.2
[479239e8] Catalyst v10.4.0
[a93c6f00] DataFrames v1.3.2
[0c46a032] DifferentialEquations v7.1.0
[31c24e10] Distributions v0.25.41
[8cc96de1] Escher v0.5.0
[60bf3e95] GLPK v0.14.14
[28b8d3ca] GR v0.62.1
[2e9cd046] Gurobi v0.9.14
[f67ccb44] HDF5 v0.15.7
[42fd0dbc] IterativeSolvers v0.9.2
[4076af6c] JuMP v0.21.10
[b8f27783] MathOptInterface v0.9.22
[961ee093] ModelingToolkit v8.3.2
[c020b1a1] NaturalSort v1.0.0
[bac558e1] OrderedCollections v1.4.1
[14b8a8f1] PkgTemplates v0.7.26
[91a5bcdd] Plots v1.24.3
[93e0c654] Reduce v1.2.12
[295af30f] Revise v3.3.1
[8bb1440f] DelimitedFiles
[9a3f8284] Random
[10745b16] Statistics
[8dfed614] Test
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