Hi all,
I have come across an issue with my model improperly defining my exchange reactions. I am trying to use the cobra.medium.minimal_medium() function, but since it is only recognizing my exchange reactions as boundary and not exchanges, my results are incorrect.
I've pasted how the model defines my reactions here: boundary and exchange reactions
I used the following code to obtain the definitions:
As you can see, it recognizes a couple of the exchanges, but the majority are defined as
Can anyone help me get my model to recognize the exchange reactions (the reactions named with "_exch")?
Thanks,
Adam
model = load_cobra("models/iSMUv01_CDM_LOO.xml")
print("############## BOUNDARY ##############")
for rxn in model.boundary:
print(rxn)
print("\n\n")
print("############## EXCHANGE ##############")
for rxn in model.exchanges:
print(rxn)
print("\n\n")
print("############## SINKS ##############")
for rxn in model.sinks:
print(rxn)
print("\n\n")
print("############## DEMANDS ##############")
for rxn in model.demands:
print(rxn)
[e] (which seems correct) but maybe there is a difference to the exchange reactions that are being recognized?
@Midnighter Thanks for the reply.
- Just to double check, you're able to see everything in my pastebin code output?-- if so, then you're seeing everything I intended to paste.
- As for compartments, I only have {'c': 'c', 'e': 'e'} set up.
- Yes, maybe the reactions are set up wrong. But, the way I understand exchange reactions is that they just need a product/reactant in an external compartment, with the other side of the reaction being null--which is how the unrecognized reactions are set up--am I incorrect in that definition?
The strangest behavior that I'm confused by is that many of my reactions (most of the ones named with "_exch") do not show up as sink, demand, or exchange; yet, they show up in the boundary reaction set. I thought that boundary was a superset of only sink, demand, and exchange sets, but many reactions only appear in the superset and none of the subsets.
Thanks,
Adam
DM_* which usually denotes demand reactions. This the names like _CDM_exch are annotated as not being exchanges. This should only match the beginning of the ID. I'll put in a PR.
add_boundary() when you define the exchange reactions? I always try to get rid of the prefixes and suffixes (so only the metabolite id), since cobrapy will add them again when you define a boundary (I have had some trouble with exchange reactions myself).
add_boundary(), I’ve been letting cobrapy automatically define the boundary reactions. But I’ll look into it, thanks!
Yeah this is is big here. What trips up C brapy is that it has some standardized I'd notations that are usually used to annotate reaction types. One if the is
DM_*which usually denotes demand reactions. This the names like_CDM_exchare annotated as not being exchanges. This should only match the beginning of the ID. I'll put in a PR.
Too much phone autocorrect here ;) Should be "Yeah this is a bug here. What trips up cobrapy is that it has some standardized ID notations that are usually used to annotate reaction types. One of them is DM_* which usually denotes demand reactions. Thus, the names like _CDM_exch are annotated as not being exchanges. This should only match the beginning of the ID. I'll put in a PR."
M_OCTADEC__9__ENE__118__DIOIC__ACID (for example). Of course, not all of them are like this. This stems from a function which converts MetaCyc ID's so the resulting ID does not contain hyphens. The error that is raised is ValueError: Names cannot contain whitespace characters. "OCTADEC ENEvDIOIC__ACID" contains whitespace character " ". I believe that the sbml parser somehow converts things like __9__ into tabs? What would the ID's have to look like or is there any other workaround for this? Any help is greatly appreciated.
@josePereiro the usage of the padmet utilities to convert from one sbml version to another is as follows:
sbml_to_padmet.py --sbml=FILE --padmetSpec=FILE
sbmlGenerator.py --padmet=FILE --output=FILE --sbml_lvl=STR
# thus e.g.
python3.5 sbml_to_padmet.py --sbml=infile.xml --padmetSpec=padmetFile.xml.tmp
python3.5 sbmlGenerator.py --padmet=padmetFile.xml.tmp --output=outfile.xml --sbml_lvl="2"there was an issue with the python version in the past, I do not know if it is fixed. That is why it says python3.5 .
What the above does is convert to the padmet format, which is generalized, and then with the .tmp file as input to the sbml version you want.
Could not find a version that satisfies the requirement matplotlib==3.1.1 (from padmet) I have tried using python 3.5.8 and 3.5.3 . How exactly do you set up the environment to make it work?Thanks in advance :)
@josePereiro the usage of the padmet utilities to convert from one sbml version to another is as follows:
sbml_to_padmet.py --sbml=FILE --padmetSpec=FILE sbmlGenerator.py --padmet=FILE --output=FILE --sbml_lvl=STR # thus e.g. python3.5 sbml_to_padmet.py --sbml=infile.xml --padmetSpec=padmetFile.xml.tmp python3.5 sbmlGenerator.py --padmet=padmetFile.xml.tmp --output=outfile.xml --sbml_lvl="2"there was an issue with the python version in the past, I do not know if it is fixed. That is why it says python3.5 .
What the above does is convert to the padmet format, which is generalized, and then with the .tmp file as input to the sbml version you want.
Worked perfectly for python 3.7.5.
Thanks again!!!
Hi everybody, I have a silly situation. I have a GEM sbml file that in the related publication sais to have 3975 metabolites and 4555 reactions but once I loaded it has different dimensions.
>>> len(model.metabolites)
5427
>>> len(model.reactions)
4555I downloaded from https://www.metabolicatlas.org/gems/repository and this situation is happening with others models too. I don't know if this is normal, but if it is, how can I fix it.
Thanks :)
boundarCondition=true at the same time (not allowed by SBML spec).
@cdanielmachado https://github.com/opencobra/cobrapy/releases/tag/0.6.0
Gapfilling
The SMILEY and growMatch implementations were refactored to a
single new function cobra.flux_analysis.gapfilling.gapfill which
handles both use-cases.
@Midnighter
Here an example: I download the model xml file from U-251 MG, and the associated publication is nature. In the table1 of the publication (last row) says that the model has 5320 reactions and 4209 metabolites, but once I loaded (using Python 3.7.5, cobra 0.14.0) I get:
>>> model = cobra.io.read_sbml_model('models/U-251 MG.xml');
>>> len(model.reactions)
5320
>>> len(model.metabolites)
6157As I can find more models with the same behavior I must be the one who is missing something!!!
{'C_c': 1588, 'C_r': 460, 'C_s': 2531, 'C_m': 636, 'C_p': 330, 'C_l': 316, 'C_g': 197, 'C_n': 99, 'C_x': 246}