Thank you! Your answer is helpful for another step that I will need (i.e. elementary mode analysis). I'm in the process of manually recreating the model file in the correct format but it's difficult b/c arbitrary names were used, not KEGG IDs or some other standard.
Tool to convert METATOOLS model file to SBML or .psc format
Is there any way to convert a METATOOLS model file to either SBML or .psc format? I am devising a way to parse it (kind of weird since there aren't standards for the pathway abbreviations...going to use KEGG pathways eventually). I was just wondering if anyone knows of any packages or tools online to convert these model files. This is an example of the METATOOLS model file.
-ENZREV
GG2r GG5r GG6r GG7r GG8r GG9r GG10r PPP4r
-ENZIRREV
GG1 GG3 GG4 GG11
-METINT
PEP G6P PYR F6P
-METEXT
O2_ext ETOH_ext ACE_ext NH3_ext
-CAT
GG1 : GLC_ext + PEP = G6P + PYR .
GG2r : G6P = F6P .
GG3 : F6P + ATP = F16BP + ADP .
GG4 : F16BP = F6P .
GG5r : F16BP = DHAP + GA3P .
1 answer
This is not a complete answer, but I know that PySCeS has an interface to METATOOL - see http://pysces.sourceforge.net/docs/modules_doc.html and search for "metatool". PySCeS only seems to use METATOOL for certain calculations, but the fact that it can interface to it at all may mean that internally, PySCeS has some capability to convert the formats. Those capabilities may not be exposed (unless there's more there than what is listed in the docs I linked to), but they may be there under the hood and perhaps you could either use that as a starting point or else contact PySCeS's author (Brett Olivier) and ask him for help with this.
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