cdanielmachado / embl_gems Goto Github PK

Hi,

I've downloaded Pseudomonas_aeruginosa_PAO1.xml.gz and tried to read it into COBRA

from cobra.io.sbml import create_cobra_model_from_sbml_file
model = create_cobra_model_from_sbml_file('Pseudomonas_aeruginosa_PAO1.xml')

However, it give me this error:
Traceback (most recent call last):
File "D:\Dropbox\Briefcase\BSU_GSM\iBsu1103.py", line 7, in
model = create_cobra_model_from_sbml_file('Pseudomonas_aeruginosa_PAO1.xml')
File "C:\Python36\lib\site-packages\cobra\io\sbml.py", line 284, in create_cobra_model_from_sbml_file
reaction.upper_bound = parameter_dict['upper_bound']
File "C:\Python36\lib\site-packages\cobra\util\context.py", line 69, in wrapper
f(self, new_value)
File "C:\Python36\lib\site-packages\cobra\core\reaction.py", line 232, in upper_bound
update_forward_and_reverse_bounds(self, 'upper')
File "C:\Python36\lib\site-packages\cobra\core\reaction.py", line 1115, in update_forward_and_reverse_bounds
separate_forward_and_reverse_bounds(*reaction.bounds)
File "C:\Python36\lib\site-packages\cobra\core\reaction.py", line 1093, in separate_forward_and_reverse_bounds
assert lower_bound <= upper_bound, "lower bound is greater than upper"
AssertionError: lower bound is greater than upper

Is there anything that I can do?

Are the models gapfilled for any particular media?