Closed zzb23 closed 6 years ago
Issue 2 was in fact a problem with the script. The starting environment function was outdated and your correction is what it should be. Thank you for pointing this out (I fixed it in the script). The other issues are related with the version of cobrapy and should be adjusted according to your version, as I believe you are doing.
As for point 5, in fact we published this git to show the computational functions that were used in the study and it's clearly not published as a software suite for the whole analysis process that is needed to successfully use the approach. This goes from generating genome-scale metabolic models, obtaining metagenomics data, etc. I believe the methods in the paper state what is needed. I am happy to help you implement the approach with your data. Please send me an email if you have specific questions. danielriosgarza@gmail.com
When I tried to use the script, I met many problems.
line 26, I think
if (e in reacts and ex in reacts):
should change toif (e in reacts.id and ex in reacts.id):
2.
line 112, I guess this problem may be caused by line 32
starting_reaction_dic[reacts]= (1000.0, -1*numpy.random.uniform ())
. When I change it tostarting_reaction_dic[reacts]= -1*numpy.random.uniform ()
, it works. But I don't know should I change it ??3.
When I use the newest "cobra", line 115 shows no 'solution' object. So I change "list_of_models[i].solution.f" to "list_of_models[i].optimize().objective_value". Is it right ??
4.
The example listed
bte.single_MCMC_run(numpy.random.random_integers(0, len(metabs), models, initial_environment, metabs, relative_abundance, evolution_of_exchange_reactions , i)
has problem, it should be changed tobte.single_MCMC_run(numpy.random.random_integers(0, len(metabs)-1), models, initial_environment, metabs, relative_abundance, evolution_of_exchange_reactions , i)
.5.
I don't know how to use the script to compelet a whole anaysis(for example, I have 16s taxa abundance for several samples, but I don't know how to deal with it to be used in the script), would you mind supplying some usage supplement