senGen

Synopsis: Generate a series of AdvanceSyn Model Specifications from an existing model by multiplying a multiple to the variable in preparation for sensitivity analyses.

Usage: python astools.py senGen [option]

where [option] can be

• modelfile: Name of model specification file in models folder. This assumes that the model file is not in models folder.
• multiple: Multiples to change each variable value. Default = 100 (which will multiple the original parameter value by 100).
• prefix: A prefixing string for the set of new model specification for identification purposes. Default = ''.
• mtype: Type of model specification file. Allowable types are 'ASM' (AdvanceSyn Model Specification). Default = 'ASM'.

For example:

python astools.py senGen \
    --modelfile=models/asm/glycolysis.modelspec \
    --prefix=sen01 --mtype=ASM --multiple=100

Working example:

D:\Dropbox\MyProjects\astoolkit>python astools.py senGen --modelfile=models/asm/glycolysis.modelspec --prefix=sen01 --mtype=ASM --multiple=100
Modified hk.promoter: 1e-07 --> 9.999999999999999e-06
  New ASM model in D:\Dropbox\MyProjects\astoolkit\models\temp\sen01.glycolysis.hk.promoter.modelspec
Modified hk.rbs: 1e-05 --> 0.001
  New ASM model in D:\Dropbox\MyProjects\astoolkit\models\temp\sen01.glycolysis.hk.rbs.modelspec
Modified hk.kcat: 1e-06 --> 9.999999999999999e-05
  New ASM model in D:\Dropbox\MyProjects\astoolkit\models\temp\sen01.glycolysis.hk.kcat.modelspec
Modified hk.km: 1e-06 --> 9.999999999999999e-05
  New ASM model in D:\Dropbox\MyProjects\astoolkit\models\temp\sen01.glycolysis.hk.km.modelspec
Modified pgi.kcat: 1e-06 --> 9.999999999999999e-05
  New ASM model in D:\Dropbox\MyProjects\astoolkit\models\temp\sen01.glycolysis.pgi.kcat.modelspec
Modified pgi.km: 1e-06 --> 9.999999999999999e-05
  New ASM model in D:\Dropbox\MyProjects\astoolkit\models\temp\sen01.glycolysis.pgi.km.modelspec
Modified pfk.kcat: 1e-06 --> 9.999999999999999e-05
  New ASM model in D:\Dropbox\MyProjects\astoolkit\models\temp\sen01.glycolysis.pfk.kcat.modelspec
Modified pfk.km: 1e-06 --> 9.999999999999999e-05
  New ASM model in D:\Dropbox\MyProjects\astoolkit\models\temp\sen01.glycolysis.pfk.km.modelspec
Modified aldo.kcat: 1e-06 --> 9.999999999999999e-05
  New ASM model in D:\Dropbox\MyProjects\astoolkit\models\temp\sen01.glycolysis.aldo.kcat.modelspec
Modified aldo.km: 1e-06 --> 9.999999999999999e-05
  New ASM model in D:\Dropbox\MyProjects\astoolkit\models\temp\sen01.glycolysis.aldo.km.modelspec
Modified tpi.kcat: 1e-06 --> 9.999999999999999e-05
  New ASM model in D:\Dropbox\MyProjects\astoolkit\models\temp\sen01.glycolysis.tpi.kcat.modelspec
Modified tpi.km: 1e-06 --> 9.999999999999999e-05
  New ASM model in D:\Dropbox\MyProjects\astoolkit\models\temp\sen01.glycolysis.tpi.km.modelspec
Modified gapdh.kcat: 1e-06 --> 9.999999999999999e-05
  New ASM model in D:\Dropbox\MyProjects\astoolkit\models\temp\sen01.glycolysis.gapdh.kcat.modelspec
Modified gapdh.km: 1e-06 --> 9.999999999999999e-05
  New ASM model in D:\Dropbox\MyProjects\astoolkit\models\temp\sen01.glycolysis.gapdh.km.modelspec
Modified pkg.kcat: 1e-06 --> 9.999999999999999e-05
  New ASM model in D:\Dropbox\MyProjects\astoolkit\models\temp\sen01.glycolysis.pkg.kcat.modelspec
Modified pkg.km: 1e-06 --> 9.999999999999999e-05
  New ASM model in D:\Dropbox\MyProjects\astoolkit\models\temp\sen01.glycolysis.pkg.km.modelspec
Modified pgm.kcat: 1e-06 --> 9.999999999999999e-05
  New ASM model in D:\Dropbox\MyProjects\astoolkit\models\temp\sen01.glycolysis.pgm.kcat.modelspec
Modified pgm.km: 1e-06 --> 9.999999999999999e-05
  New ASM model in D:\Dropbox\MyProjects\astoolkit\models\temp\sen01.glycolysis.pgm.km.modelspec
Modified eno.kcat: 1e-06 --> 9.999999999999999e-05
  New ASM model in D:\Dropbox\MyProjects\astoolkit\models\temp\sen01.glycolysis.eno.kcat.modelspec
Modified eno.km: 1e-06 --> 9.999999999999999e-05
  New ASM model in D:\Dropbox\MyProjects\astoolkit\models\temp\sen01.glycolysis.eno.km.modelspec
Modified pk.kcat: 1e-06 --> 9.999999999999999e-05
  New ASM model in D:\Dropbox\MyProjects\astoolkit\models\temp\sen01.glycolysis.pk.kcat.modelspec
Modified pk.km: 1e-06 --> 9.999999999999999e-05
  New ASM model in D:\Dropbox\MyProjects\astoolkit\models\temp\sen01.glycolysis.pk.km.modelspec
original:    {"ASM": "D:\\Dropbox\\MyProjects\\astoolkit\\models\\temp\\sen01.glycolysis.original.modelspec", "Change": "None"}
hk.promoter: {"ASM": "D:\\Dropbox\\MyProjects\\astoolkit\\models\\temp\\sen01.glycolysis.hk.promoter.modelspec", "Change": "1e-07 --> 9.999999999999999e-06"}
hk.rbs:      {"ASM": "D:\\Dropbox\\MyProjects\\astoolkit\\models\\temp\\sen01.glycolysis.hk.rbs.modelspec", "Change": "1e-05 --> 0.001"}
hk.kcat:     {"ASM": "D:\\Dropbox\\MyProjects\\astoolkit\\models\\temp\\sen01.glycolysis.hk.kcat.modelspec", "Change": "1e-06 --> 9.999999999999999e-05"}
hk.km:       {"ASM": "D:\\Dropbox\\MyProjects\\astoolkit\\models\\temp\\sen01.glycolysis.hk.km.modelspec", "Change": "1e-06 --> 9.999999999999999e-05"}
pgi.kcat:    {"ASM": "D:\\Dropbox\\MyProjects\\astoolkit\\models\\temp\\sen01.glycolysis.pgi.kcat.modelspec", "Change": "1e-06 --> 9.999999999999999e-05"}
pgi.km:      {"ASM": "D:\\Dropbox\\MyProjects\\astoolkit\\models\\temp\\sen01.glycolysis.pgi.km.modelspec", "Change": "1e-06 --> 9.999999999999999e-05"}
pfk.kcat:    {"ASM": "D:\\Dropbox\\MyProjects\\astoolkit\\models\\temp\\sen01.glycolysis.pfk.kcat.modelspec", "Change": "1e-06 --> 9.999999999999999e-05"}
pfk.km:      {"ASM": "D:\\Dropbox\\MyProjects\\astoolkit\\models\\temp\\sen01.glycolysis.pfk.km.modelspec", "Change": "1e-06 --> 9.999999999999999e-05"}
aldo.kcat:   {"ASM": "D:\\Dropbox\\MyProjects\\astoolkit\\models\\temp\\sen01.glycolysis.aldo.kcat.modelspec", "Change": "1e-06 --> 9.999999999999999e-05"}
aldo.km:     {"ASM": "D:\\Dropbox\\MyProjects\\astoolkit\\models\\temp\\sen01.glycolysis.aldo.km.modelspec", "Change": "1e-06 --> 9.999999999999999e-05"}
tpi.kcat:    {"ASM": "D:\\Dropbox\\MyProjects\\astoolkit\\models\\temp\\sen01.glycolysis.tpi.kcat.modelspec", "Change": "1e-06 --> 9.999999999999999e-05"}
tpi.km:      {"ASM": "D:\\Dropbox\\MyProjects\\astoolkit\\models\\temp\\sen01.glycolysis.tpi.km.modelspec", "Change": "1e-06 --> 9.999999999999999e-05"}
gapdh.kcat:  {"ASM": "D:\\Dropbox\\MyProjects\\astoolkit\\models\\temp\\sen01.glycolysis.gapdh.kcat.modelspec", "Change": "1e-06 --> 9.999999999999999e-05"}
gapdh.km:    {"ASM": "D:\\Dropbox\\MyProjects\\astoolkit\\models\\temp\\sen01.glycolysis.gapdh.km.modelspec", "Change": "1e-06 --> 9.999999999999999e-05"}
pkg.kcat:    {"ASM": "D:\\Dropbox\\MyProjects\\astoolkit\\models\\temp\\sen01.glycolysis.pkg.kcat.modelspec", "Change": "1e-06 --> 9.999999999999999e-05"}
pkg.km:      {"ASM": "D:\\Dropbox\\MyProjects\\astoolkit\\models\\temp\\sen01.glycolysis.pkg.km.modelspec", "Change": "1e-06 --> 9.999999999999999e-05"}
pgm.kcat:    {"ASM": "D:\\Dropbox\\MyProjects\\astoolkit\\models\\temp\\sen01.glycolysis.pgm.kcat.modelspec", "Change": "1e-06 --> 9.999999999999999e-05"}
pgm.km:      {"ASM": "D:\\Dropbox\\MyProjects\\astoolkit\\models\\temp\\sen01.glycolysis.pgm.km.modelspec", "Change": "1e-06 --> 9.999999999999999e-05"}
eno.kcat:    {"ASM": "D:\\Dropbox\\MyProjects\\astoolkit\\models\\temp\\sen01.glycolysis.eno.kcat.modelspec", "Change": "1e-06 --> 9.999999999999999e-05"}
eno.km:      {"ASM": "D:\\Dropbox\\MyProjects\\astoolkit\\models\\temp\\sen01.glycolysis.eno.km.modelspec", "Change": "1e-06 --> 9.999999999999999e-05"}
pk.kcat:     {"ASM": "D:\\Dropbox\\MyProjects\\astoolkit\\models\\temp\\sen01.glycolysis.pk.kcat.modelspec", "Change": "1e-06 --> 9.999999999999999e-05"}
pk.km:       {"ASM": "D:\\Dropbox\\MyProjects\\astoolkit\\models\\temp\\sen01.glycolysis.pk.km.modelspec", "Change": "1e-06 --> 9.999999999999999e-05"}