mergeASM

Synopsis: Read the AdvanceSyn model specification file(s) and merge them into a single AdvanceSyn model specification file.

Usage: python astools.py mergeASM [option]

where [option] can be

• modelfile: Relative path(s) to the model specification file(s), separated by semi-colon.
• outputfile: Relative path to the output ASM model 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 mergeASM \
    --prefix=exp \
    --modelfile=models/asm/glycolysis.modelspec;models/asm/ppp.modelspec \
    --outputfile=models/asm/glycolysis_ppp.modelspec

Working example:

D:\Dropbox\MyProjects\astoolkit>python astools.py mergeASM --prefix=exp --modelfile=models/asm/glycolysis.modelspec;models/asm/ppp.modelspec --outputfile=models/asm/glycolysis_ppp.modelspec
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\ppp.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

Renaming / Renumbering Reactions in Specification 2
  Specification 2: r1 --> exp13

Merge Specifications ...
Numbers of Identifiers = 2, 2
... Total Numbers of Identifiers = 4
Numbers of Objects = 29, 5
... Total Numbers of Objects = 34
Numbers of Initials = 29, 5
... Total Numbers of Initials = 34
Numbers of Variables = 22, 2
... Total Numbers of Variables = 24
Numbers of Reactions = 12, 1
... Total Numbers of Reactions = 13

Output AdvanceSyn Model Specification File: D:\Dropbox\MyProjects\astoolkit\models\asm\glycolysis_ppp.modelspec