Traceback (most recent call last):
File "/opt/conda/envs/science/bin/seed2lp", line 6, in <module>
sys.exit(main())
File "/opt/conda/envs/science/lib/python3.10/site-packages/seed2lp/__main__.py", line 873, in main
run_seed2lp(cfg, args.cmd, log_dir)
File "/opt/conda/envs/science/lib/python3.10/site-packages/seed2lp/__main__.py", line 456, in run_seed2lp
network = Network(args['infile'], run_mode, args['targets_as_seeds'],
File "/opt/conda/envs/science/lib/python3.10/site-packages/seed2lp/network.py", line 1385, in __init__
self.get_network(self.name, to_print, write_sbml)
File "/opt/conda/envs/science/lib/python3.10/site-packages/seed2lp/network.py", line 427, in get_network
reaction.lbound, reaction.ubound = self.get_boundaries(r,species)
File "/opt/conda/envs/science/lib/python3.10/site-packages/seed2lp/network.py", line 183, in get_boundaries
lower_bound = self.parameters[species][reaction.attrib.get('{'+self.fbc[species]+'}lowerFluxBound')] \
KeyError: None
Please could you catch this error and inform the user that they are working with a metabolic network that does not comply with seed2lp requirements (metabolic network version 3.X)?
Information: To upgrade the SBML version, users could use cobrapy.
I tried to run the
seed2lp targetcommand on a metabolic network whose SBML version is older than 3.X, and got the following error:Please could you catch this error and inform the user that they are working with a metabolic network that does not comply with
seed2lprequirements (metabolic network version 3.X)?Information: To upgrade the SBML version, users could use cobrapy.