IndexError: list index out of range about mergem HOT 5 CLOSED

Hi, thank you for reporting the error. There was indeed a bug in the code. It is fixed now and a new version of mergem was pushed to pypi (0.21.5).

I tried your test with those two models from the CarveMe repo and it worked.

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Yes, the results can be different depending on the order of the merge. Notice that the output model always contains all the metabolites and reactions of the first model, and the rest are merged into this one as much as possible. This is important in the case of a model containing synonymous metabolites (such as NH2 and NH3). In this case, both metabolites will be preserved if that model is the first, but one of those metabolites will be lost if the first model does not contain both metabolites. These differences can result in different number of reactions.

If your computer cannot handle 200 models at once, you could try merging them one at a time in a for loop, starting with your best base model:

# A list with your 200 models
models = ["test/Abiotrophia_defectiva_ATCC_49176.xml", "test/Acidaminococcus_fermentans_DSM_20731.xml", ...] 

merged_model = mergem.load_model(models[0])

for model_index in range(1, len(models)):
   merged_model = mergem.merge([merged_model, models[model_index]], 1)

from mergem.

That parameter only affects the objective function. What I wrote is true for all the metabolites, and hence reactions in the model. Either parameter would work, depending on what you want.

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I had another question, my device crashed when I worked on 200 models at once, so I though to merge each 50 together then the 4 result files i'll merge to one..

I tested on smaller file
1_merge => 3 models
2_merge => 3 models
and this was the result of merging (1_merge + 2_merge)

but when i merged the 6 models at once, I git this result, which the number of reactions is more than above

so I was wondering if there's any mistake in this techniqe about merging the outcome of the merge

from mergem.

but isn't this in case i put the -obj as 1?
am using => -obj merge,, which means will merge all _ which i want to get _ ?

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