create_gpr_table SyntaxError: invalid syntax

[MarieBurel]

Dear Daniel,

Running build_universe --draft downloads first the whole BiGG universe database (I need to do it because not all of bigg's organisms are included in the universal default model of CarveMe). Then it downloads model specific data (not in universal section of BiGG). So good so far. And finally, it creates the Gene-Product-Reaction-Table which is really important thereafter. Unfortunately, it seems to have a problem with SymPy. I get the following error:

Traceback (most recent call last):
  File "create_gpr_table.py", line 33, in <module>
    gpr = parse_gpr_rule(gpr_str)
  File "/home/marie/.local/lib/python3.7/site-packages/framed/io/sbml.py", line 408, in parse_gpr_rule
    expr = parse_expr(rule)
  File "/home/marie/.local/lib/python3.7/site-packages/sympy/parsing/sympy_parser.py", line 1017, in parse_expr
    return eval_expr(code, local_dict, global_dict)
  File "/home/marie/.local/lib/python3.7/site-packages/sympy/parsing/sympy_parser.py", line 904, in eval_expr
    code, global_dict, local_dict)  # take local objects in preference
  File "<string>", line 1
    Integer (5243 )Symbol ('_AT1' )
                        ^
SyntaxError: invalid syntax

Gene_ID from recon1, recon2D, iCHOv1_DG44, iYS1720 and those of the trypanosome seem to be concerned. Thank you for your help!

Issue20 "There were also a few sporadic cases where the download of a particular gene sequence failed, which would explain why the E2348C_RS01240 gene from the iE2348C_1286 is missing." had you encountered this problem too?

[cdanielmachado]

The universe building script needs to be updated as there have been some changes in the BIGG database since I wrote that script. For the moment I would recommend you use the universal model that we already provide.

[MarieBurel]

Thank you. I'll probably have a look. Can't wait for you future updates! (Closing)