[Translation & ProteinDecay & Macromolecular Complexation] Submodel creation for set of protein identifiers

[matthiaskoenig]

Create a submodel for a given set of protein identifiers. This should be a script, so that with a changing set of protein identifiers new submodels can be created for these identifiers.

In case of the multimers the macromolecular complexation group has to provide the submodel for the complexation and extend the list for the translation & ProteinDecay group.

For instance
MG_453_TETRAMER -> MG_453_MONOMER
MG_041_069_429_PENTAMER -> MG_041_MONOMER, MG_069_MONOMER, MG_0429_MONOMER

Example sets:
S1: {MG_061_MONOMER}
S2: {MG_453_TETRAMER, MG_111_DIMER, MG_041_069_429_PENTAMER, MG_053_TRIMER, MG_061_MONOMER}
-- Complexation list extension -->
{MG_453_MONOMER, MG_111_MONOMER, MG_041_MONOMER, MG_069_MONOMER, MG_429_MONOMER, MG_053_MONOMER, MG_061_MONOMER}

• Translation
• Protein Decay
• Macromolecular Complexation

[den2042]

The task is clear in general. But details of the input are not. Let's agree on the input. Mattias, can you please confirm that txt
ProteinIDsubsetExample.txt
file with one long line, IDs separated by commas (attached) would be OK? Or propose another input format

[matthiaskoenig]

Input format is okay.
Proteincomplexation should work with the same inputs & outputs, i.e.
take
MG_453_TETRAMER, MG_111_DIMER, MG_041_069_429_PENTAMER, MG_053_TRIMER, MG_061_MONOMER
create
MG_453_MONOMER, MG_111_MONOMER, MG_041_MONOMER, MG_069_MONOMER, MG_429_MONOMER, MG_053_MONOMER, MG_061_MONOMER

[matthiaskoenig]

In the glycolysis submodel the following proteins are involved

MG_023_DIMER    fructose-1,6-bisphosphate aldolase, class II
MG_041_062_429_PENTAMER PTS system, fructose-specific
MG_041_069_429_PENTAMER PTS system, glucose-specific
MG_061_MONOMER  Mycoplasma MFS transporter
MG_063_DIMER    1-phosphofructokinase, putative
MG_111_DIMER    glucose-6-phosphate isomerase
MG_215_TETRAMER 6-phosphofructokinase
MG_216_TETRAMER pyruvate kinase
MG_300_MONOMER  phosphoglycerate kinase
MG_301_TETRAMER glyceraldehyde-3-phosphate dehydrogenase, type I
MG_407_DIMER    enolase
MG_410_411_412_PENTAMER phosphate ABC transporter
MG_430_MONOMER  2,3-bisphosphoglycerate-independent phosphoglycerate mutase
MG_431_DIMER    triosephosphate isomerase

In input format

MG_023_DIMER, MG_041_062_429_PENTAMER PTS, MG_041_069_429_PENTAMER PTS, MG_061_MONOMER, MG_063_DIMER, MG_111_DIMER, MG_215_TETRAMER, MG_216_TETRAMER, MG_300_MONOMER, MG_301_TETRAMER, MG_407_DIMER, MG_410_411_412_PENTAMER, MG_430_MONOMER, MG_431_DIMER

[den2042]

OK, got it. Working on subset in Translation / Protein Decay

[den2042]

Of note, Translation/Decay operates with monomers only. But the input list is clear

[den2042]

Translation subset xml is located in https://github.com/whole-cell-tutors/whole-cell-reduced/tree/master/Translation/subset
New one can be generated by
python translationSubset.py -subset ProteinIDsubsetExample.txt

[den2042]

Protein decay subset xml is located in https://github.com/whole-cell-tutors/whole-cell-reduced/tree/master/ProteinDecay/subsetDecay
New one can be generated by
python proteindecaySubset.py -species ProteinIDsubsetExample.txt