Recreate model creation/gap filling using ModelSEEDpy

hgscott commented 4 months ago

Want to get away from using the KBase interface, and just use the ModelSEED tools in python directly.

hgscott commented 3 months ago

I got ModelSEEDpy installed (was not super easy) in a new conda environment called gem-reconstruction. I had to make sure I used python=3.8, I got a lot of errors for both 3.9 and 3.7.

hgscott commented 3 months ago

I drafted up a script for generating a model (https://github.com/C-CoMP-STC/GEM-mit1002/blob/a0d9046ae8e41c3e84a243dbe7496c5ce7a46466/make_model.py) based on an example from the ModelSEEDpy documentation (https://github.com/ModelSEED/ModelSEEDpy/blob/dev/examples/Model%20Reconstruction/genome_scale_build_model.ipynb).

hgscott commented 3 months ago

I decided to use the MIT1002_anvio_prot_seqs.fa file that Zac sent me on 2023-11-15 as my genome.

hgscott commented 3 months ago

When I try to run the script, I get an error about numpy:

The version of numpy in my environment is 1.24.4:

So I will try to downgrade my numpy version to 1.20.0 or earlier.

hgscott commented 3 months ago

I uninstalled numpy.

I tried to install v.1.19, but that caused other clashes:

So I installed v.1.20 instead. That still has clashes:

That clash means that COBRApy cannot load:

So I installed v.1.20.3 specifically:

And with that I was able to get passed the get_classifier() line!

hgscott commented 3 months ago

I got an error when running get_template().

hgscott commented 3 months ago

That was a simple mistake- I left "template" out of the name- I just had to compare to what what they did in the tutorial notebook.

I added "template" to the names and that worked.

hgscott commented 3 months ago

With that change I was able to run the rest of the script, and make a model: https://github.com/C-CoMP-STC/GEM-mit1002/blob/11b302485abfef371126ba7530b0b08e2f3c3717/modelseedpy_model.xml

hgscott commented 3 months ago

Now, I want to see how this model differs from my other model.

hgscott commented 3 months ago

I was able to run the MEMOTE diff function to get report comparing the two models: https://github.com/C-CoMP-STC/GEM-mit1002/blob/625824886a7480bdd9b39fcc0ad108a7329a0c0f/index.html

Some interesting differences:

There are no metabolite annotations:
There are only SEED reaction annotations
It's missing a lot of the SBO terms- but I'm not really sure what those were doing in the first place:
I am not getting the same number of genes/metabolites/reactions:

hgscott commented 3 months ago

I also looked at which reactions are specifically unique to each model.

Here are the reactions unique to the KBase model:

rxn03239_c0
rxn12008_c0
rxn02316_c0
rxn00890_c0
rxn08275_c0
rxn03436_c0
rxn05324_c0
rxn02315_c0
rxn01894_c0
rxn02798_c0
rxn05030_c0
rxn06777_c0
rxn05327_c0
rxn05296_c0
rxn05322_c0
rxn02317_c0
rxn00868_c0
rxn00360_c0
rxn00977_c0
rxn03244_c0
rxn05619_c0
rxn05325_c0
rxn14334_c0
rxn05294_c0
rxn14040_c0
rxn04954_c0
rxn05328_c0
rxn05323_c0
rxn03242_c0
rxn00819_c0
rxn02276_c0
rxn05295_c0
rxn05326_c0
rxn02093_c0
rxn01757_c0
rxn14333_c0
rxn03246_c0
rxn14011_c0
rxn15021_c0
rxn15249_c0
rxn05121_c0
rxn39978_c0
rxn39979_c0
rxn14422_c0
rxn14419_c0
rxn14426_c0
rxn14412_c0
rxn14418_c0
rxn14421_c0
rxn14425_c0
rxn14420_c0
rxn14415_c0
rxn15121_c0
rxn17275_c0
rxn23850_c0
rxn40368_c0
rxn15230_c0
rxn20583_c0
rxn15467_c0
rxn27318_c0
rxn16824_c0
rxn39964_c0
rxn16806_c0
rxn14061_c0
rxn13957_c0
rxn09304_c0
rxn08722_c0
rxn08062_c0
rxn21863_c0
rxn21859_c0
rxn15750_c0
rxn19704_c0
rxn41965_c0
rxn43657_c0
rxn45692_c0
rxn05469_c0
rxn05730_c0
rxn05129_c0
rxn05488_c0
rxn05559_c0
rxn00064_c0
rxn02666_c0
rxn08428_c0
rxn08032_c0
rxn09008_c0
rxn08691_c0
rxn08350_c0
rxn08689_c0
rxn09260_c0
rxn09330_c0
rxn00062_c0
bio1_biomass
EX_cpd00268_e0
EX_cpd00363_e0
EX_cpd00081_e0
EX_cpd00239_e0
EX_cpd00227_e0
EX_cpd00029_e0
EX_cpd00071_e0
EX_cpd00020_e0
EX_cpd00221_e0
EX_cpd11574_e0
EX_cpd00047_e0
EX_cpd00161_e0
EX_cpd00418_e0
EX_cpd01414_e0
EX_cpd11640_e0
DM_cpd11416_c0
DM_cpd02701_c0
DM_cpd15302_c0

And here are the reactions unique to the ModelSEEDpy model:

rxn13783_c0
rxn05459_c0
rxn02380_c0
rxn06937_c0
rxn10113_c0
rxn13784_c0
rxn00058_c0
rxn01132_c0
rxn06445_c0
rxn13782_c0
rxn08287_c0
rxn10043_c0
rxn05206_c0
rxn05937_c0
rxn06591_c0
rxn03194_c0
rxn45425_c0
rxn08924_c0
EX_cpd00254_e0
bio1
SK_cpd02701_c0
SK_cpd11416_c0
SK_cpd15302_c0
bio2

C-CoMP-STC / GEM-mit1002

Recreate model creation/gap filling using ModelSEEDpy #58