The subModel structure generated by this function does not include a rxnNames field. O

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extractSubNetwork doesn't return rxnNames about cobratoolbox HOT 4 CLOSED

bheavner commented on June 14, 2024

extractSubNetwork doesn't return rxnNames

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Comments (4)

rmtfleming commented on June 14, 2024

pls make pull request

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laurentheirendt commented on June 14, 2024

@bheavner , you seem to have a good idea on how to solve this issue. Could you please open a pull-request (PR) with the suggested changes in the code?

Guidelines on how to contribute are here.

Please let me know if you are running into any issues.

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stefaniamagg commented on June 14, 2024

@laurentheirendt This issue has already been fixed by Srikiran C on 7/15/14. From src\extractSubNetwork.m:

%extractSubNetwork Extract subnetwork model
%
% subModel = extractSubNetwork(model,rxnList,metList)
%
%INPUTS
% model     COBRA model structure
% rxnList  Reaction list for the subnetwork to be extracted
%
%OPTIONAL INPUTS
% metNames  Metabolite list for the subnetwork to be extracted
%
%OUTPUT
% subModel  COBRA model of subnetwork
%
% Markus Herrgard 12/11/06
%
% Srikiran C 7/15/14
% - Replaced rxnNames with rxnList as model.rxnNames is different from
% model.rxns, and model.rxns is used to select the subnetwork.
% - Replaced metNames with metList, to avoid similar confusion.
% - Added the fields - rxnNames, rules and metCharge to subModel.

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laurentheirendt commented on June 14, 2024

Thank you @stefaniamagg . Closing now.

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