genMO

Synopsis: Read the AdvanceSyn model specification file(s) and generate a file consisting of the internal model objects.

Usage: python astools.py genMO [option]

where [option] can be

• modelfile: Relative path to the model specification file.
• outputfile: Relative path to the output model objects file.
• prefix: Prefix for new reaction IDs. This prefix cannot be any existing prefixes in any of the model specifications to be merged. Default = 'exp'.

For example:

python astools.py readflux --mtype=ASM --modelfile=models/asm/glycolysis.modelspec

Working example #1: Model Objects From 1 Model Specification File:

D:\Dropbox\MyProjects\astoolkit>python astools.py genMO --prefix=exp --modelfile=models/asm/glycolysis.modelspec --outputfile=models/mo/glycolysis.mo
Input Model File(s) ...
ASM Model File 1: D:\Dropbox\MyProjects\astoolkit\models\asm\glycolysis.modelspec

Renaming / Renumbering Reactions in Specification 1
  Specification 1: e1.rna --> exp1
  Specification 1: e1 --> exp2
  Specification 1: r1 --> exp3
  Specification 1: r2 --> exp4
  Specification 1: r3 --> exp5
  Specification 1: r4 --> exp6
  Specification 1: r5 --> exp7
  Specification 1: r6 --> exp8
  Specification 1: r7 --> exp9
  Specification 1: r8 --> exp10
  Specification 1: r9 --> exp11
  Specification 1: r10 --> exp12

  Number of Model Objects in Specification 1: 29

  Object Name / Description 1: glucose | D-glucose

    Outflux r1 --> exp3

  Object Name / Description 2: atp | adenosine-triphosphate

    Influx r7 --> exp9
    Influx r10 --> exp12
    Outflux r1 --> exp3
    Outflux r3 --> exp5

  Object Name / Description 3: adp | adenosine-diphosphate

    Influx r1 --> exp3
    Influx r3 --> exp5
    Outflux r7 --> exp9
    Outflux r10 --> exp12

  Object Name / Description 4: proton | proton

    Influx r1 --> exp3
    Influx r3 --> exp5
    Influx r6 --> exp8
    Outflux r10 --> exp12

  Object Name / Description 5: nad | NAD

    Outflux r6 --> exp8

  Object Name / Description 6: pi | phosphate

    Outflux r6 --> exp8

  Object Name / Description 7: nadh | NADH

    Influx r6 --> exp8

  Object Name / Description 8: water | water

    Influx r9 --> exp11

  Object Name / Description 9: g6p | a-D-Glucose-6-phosphate

    Influx r1 --> exp3
    Outflux r2 --> exp4

  Object Name / Description 10: f6p | b-D-Fructose-6-phosphate

    Influx r2 --> exp4
    Outflux r3 --> exp5

  Object Name / Description 11: f16p | b-D-Fructose-1,6-phosphate

    Influx r3 --> exp5
    Outflux r4 --> exp6

  Object Name / Description 12: gadp | D-glyceraldehyde 3-phosphate

    Influx r4 --> exp6
    Influx r5 --> exp7
    Outflux r6 --> exp8

  Object Name / Description 13: dhap | Dihydroxyacetone phosphate

    Influx r4 --> exp6
    Outflux r5 --> exp7

  Object Name / Description 14: bpg13 | D-1,3-bisphosphoglycerate

    Influx r6 --> exp8
    Outflux r7 --> exp9

  Object Name / Description 15: pg3 | 3-phosphoglycerate

    Influx r7 --> exp9
    Outflux r8 --> exp10

  Object Name / Description 16: pg2 | 2-phosphoglycerate

    Influx r8 --> exp10
    Outflux r9 --> exp11

  Object Name / Description 17: pep | phosphoenolpyruvate

    Influx r9 --> exp11
    Outflux r10 --> exp12

  Object Name / Description 18: pyr | pyruvate

    Influx r10 --> exp12

  Object Name / Description 19: hk.rna | hexokinase

    Influx e1.rna --> exp1

  Object Name / Description 20: hk | hexokinase

    Influx e1 --> exp2

  Object Name / Description 21: pgi | Phosphoglucose isomerase


  Object Name / Description 22: pfk | phosphofructokinase


  Object Name / Description 23: aldo | fructose-bisphosphate aldolase


  Object Name / Description 24: tpi | triosephosphate isomerase


  Object Name / Description 25: gapdh | glyceraldehyde phosphate dehydrogenase


  Object Name / Description 26: pkg | phosphoglycerate kinase


  Object Name / Description 27: pgm | phosphoglycerate mutase


  Object Name / Description 28: eno | enolase


  Object Name / Description 29: pk | pyruvate kinase


Merge Specifications ...
Numbers of Identifiers = 2
... Total Numbers of Identifiers = 2
Numbers of Objects = 29
... Total Numbers of Objects = 29
Numbers of Initials = 29
... Total Numbers of Initials = 29
Numbers of Variables = 22
... Total Numbers of Variables = 22
Numbers of Reactions = 12
... Total Numbers of Reactions = 12

Merging Model Objects ...
Number of Model Objects: 29
... Total Numbers of Model Objects = 29

  Names of Model Objects from Specification 1: glucose | atp | adp | proton | nad | pi | nadh | water | g6p | f6p | f16p | gadp | dhap | bpg13 | pg3 | pg2 | pep | pyr | hk.rna | hk | pgi | pfk | aldo | tpi | gapdh | pkg | pgm | eno | pk

  Number of Merged Model Objects: 29
  Current Names of Merged Model Objects: glucose | atp | adp | proton | nad | pi | nadh | water | g6p | f6p | f16p | gadp | dhap | bpg13 | pg3 | pg2 | pep | pyr | hk.rna | hk | pgi | pfk | aldo | tpi | gapdh | pkg | pgm | eno | pk

Output Model Objects File: D:\Dropbox\MyProjects\astoolkit\models\mo\glycolysis.mo

Working example #2: Model Objects After Merging 2 Model Specification Files:

D:\Dropbox\MyProjects\astoolkit>python astools.py genMO --prefix=exp --modelfile=models/asm/glycolysis.modelspec;models/asm/RFPproduction.modelspec --outputfile=models/mo/glycolysis.mo
Input Model File(s) ...
ASM Model File 1: D:\Dropbox\MyProjects\astoolkit\models\asm\glycolysis.modelspec
ASM Model File 2: D:\Dropbox\MyProjects\astoolkit\models\asm\RFPproduction.modelspec

Renaming / Renumbering Reactions in Specification 1
  Specification 1: e1.rna --> exp1
  Specification 1: e1 --> exp2
  Specification 1: r1 --> exp3
  Specification 1: r2 --> exp4
  Specification 1: r3 --> exp5
  Specification 1: r4 --> exp6
  Specification 1: r5 --> exp7
  Specification 1: r6 --> exp8
  Specification 1: r7 --> exp9
  Specification 1: r8 --> exp10
  Specification 1: r9 --> exp11
  Specification 1: r10 --> exp12

  Number of Model Objects in Specification 1: 29

  Object Name / Description 1: glucose | D-glucose

    Outflux r1 --> exp3

  Object Name / Description 2: atp | adenosine-triphosphate

    Influx r7 --> exp9
    Influx r10 --> exp12
    Outflux r1 --> exp3
    Outflux r3 --> exp5

  Object Name / Description 3: adp | adenosine-diphosphate

    Influx r1 --> exp3
    Influx r3 --> exp5
    Outflux r7 --> exp9
    Outflux r10 --> exp12

  Object Name / Description 4: proton | proton

    Influx r1 --> exp3
    Influx r3 --> exp5
    Influx r6 --> exp8
    Outflux r10 --> exp12

  Object Name / Description 5: nad | NAD

    Outflux r6 --> exp8

  Object Name / Description 6: pi | phosphate

    Outflux r6 --> exp8

  Object Name / Description 7: nadh | NADH

    Influx r6 --> exp8

  Object Name / Description 8: water | water

    Influx r9 --> exp11

  Object Name / Description 9: g6p | a-D-Glucose-6-phosphate

    Influx r1 --> exp3
    Outflux r2 --> exp4

  Object Name / Description 10: f6p | b-D-Fructose-6-phosphate

    Influx r2 --> exp4
    Outflux r3 --> exp5

  Object Name / Description 11: f16p | b-D-Fructose-1,6-phosphate

    Influx r3 --> exp5
    Outflux r4 --> exp6

  Object Name / Description 12: gadp | D-glyceraldehyde 3-phosphate

    Influx r4 --> exp6
    Influx r5 --> exp7
    Outflux r6 --> exp8

  Object Name / Description 13: dhap | Dihydroxyacetone phosphate

    Influx r4 --> exp6
    Outflux r5 --> exp7

  Object Name / Description 14: bpg13 | D-1,3-bisphosphoglycerate

    Influx r6 --> exp8
    Outflux r7 --> exp9

  Object Name / Description 15: pg3 | 3-phosphoglycerate

    Influx r7 --> exp9
    Outflux r8 --> exp10

  Object Name / Description 16: pg2 | 2-phosphoglycerate

    Influx r8 --> exp10
    Outflux r9 --> exp11

  Object Name / Description 17: pep | phosphoenolpyruvate

    Influx r9 --> exp11
    Outflux r10 --> exp12

  Object Name / Description 18: pyr | pyruvate

    Influx r10 --> exp12

  Object Name / Description 19: hk.rna | hexokinase

    Influx e1.rna --> exp1

  Object Name / Description 20: hk | hexokinase

    Influx e1 --> exp2

  Object Name / Description 21: pgi | Phosphoglucose isomerase


  Object Name / Description 22: pfk | phosphofructokinase


  Object Name / Description 23: aldo | fructose-bisphosphate aldolase


  Object Name / Description 24: tpi | triosephosphate isomerase


  Object Name / Description 25: gapdh | glyceraldehyde phosphate dehydrogenase


  Object Name / Description 26: pkg | phosphoglycerate kinase


  Object Name / Description 27: pgm | phosphoglycerate mutase


  Object Name / Description 28: eno | enolase


  Object Name / Description 29: pk | pyruvate kinase


Renaming / Renumbering Reactions in Specification 2
  Specification 2: r1 --> exp13
  Specification 2: r2 --> exp14
  Specification 2: r3 --> exp15

  Number of Model Objects in Specification 2: 4

  Object Name / Description 1: EL2 | EL222

    Influx r1 --> exp13

  Object Name / Description 2: mRFP | mRNA of RFP

    Influx r2 --> exp14

  Object Name / Description 3: RFP | Red Fluoro Protein

    Influx r3 --> exp15

  Object Name / Description 4: blue | blue light


Merge Specifications ...
Numbers of Identifiers = 2, 2
... Total Numbers of Identifiers = 4
Numbers of Objects = 29, 4
... Total Numbers of Objects = 33
Numbers of Initials = 29, 4
... Total Numbers of Initials = 33
Numbers of Variables = 22, 8
... Total Numbers of Variables = 30
Numbers of Reactions = 12, 3
... Total Numbers of Reactions = 15

Merging Model Objects ...
Number of Model Objects: 29, 4
... Total Numbers of Model Objects = 33

  Names of Model Objects from Specification 1: glucose | atp | adp | proton | nad | pi | nadh | water | g6p | f6p | f16p | gadp | dhap | bpg13 | pg3 | pg2 | pep | pyr | hk.rna | hk | pgi | pfk | aldo | tpi | gapdh | pkg | pgm | eno | pk

  Number of Merged Model Objects: 29
  Current Names of Merged Model Objects: glucose | atp | adp | proton | nad | pi | nadh | water | g6p | f6p | f16p | gadp | dhap | bpg13 | pg3 | pg2 | pep | pyr | hk.rna | hk | pgi | pfk | aldo | tpi | gapdh | pkg | pgm | eno | pk

  Names of Model Objects from Specification 2: EL2 | mRFP | RFP | blue

    EL2 object is not in current merged list - full model object merge
    mRFP object is not in current merged list - full model object merge
    RFP object is not in current merged list - full model object merge
    blue object is not in current merged list - full model object merge

  Number of Merged Model Objects: 33
  Current Names of Merged Model Objects: glucose | atp | adp | proton | nad | pi | nadh | water | g6p | f6p | f16p | gadp | dhap | bpg13 | pg3 | pg2 | pep | pyr | hk.rna | hk | pgi | pfk | aldo | tpi | gapdh | pkg | pgm | eno | pk | EL2 | mRFP | RFP | blue

Output Model Objects File: D:\Dropbox\MyProjects\astoolkit\models\mo\glycolysis.mo