Skip to content

Commit

Permalink
Merge pull request #8 from niklases/dev
Browse files Browse the repository at this point in the history
v0.3.6 merge 'dev' to 'main'
  • Loading branch information
niklases authored Sep 21, 2024
2 parents 90e113b + 02c9dad commit 8ab8a48
Show file tree
Hide file tree
Showing 33 changed files with 550 additions and 675 deletions.
Binary file added .github/imgs/multi_point_mut_performance.png
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
Binary file added .github/imgs/single_point_mut_performance.png
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
2 changes: 1 addition & 1 deletion .github/workflows/build.yml
Original file line number Diff line number Diff line change
Expand Up @@ -14,7 +14,7 @@ jobs:
runs-on: [ubuntu-latest]
strategy:
matrix:
python-version: ["3.9", "3.10", "3.11"]
python-version: ["3.9", "3.10", "3.11", "3.12"]

steps:
- uses: actions/checkout@v4
Expand Down
3 changes: 3 additions & 0 deletions .gitignore
Original file line number Diff line number Diff line change
Expand Up @@ -388,3 +388,6 @@ avGFP_shortened_dca_encoded.csv
datasets/AVGFP/avGFP_shortened.csv
avGFP_dca_encoded.csv
scripts/Runtime_tests/runtimes.png
datasets/AVGFP/Recomb_Double_Split/Predictions_Hybrid_TopRecomb_Double_Split.txt
scripts/ProteinGym_runs/single_point_mut_performance_violin.png
scripts/ProteinGym_runs/multi_point_mut_performance_violin.png
93 changes: 81 additions & 12 deletions .vscode/launch.json
Original file line number Diff line number Diff line change
Expand Up @@ -6,7 +6,7 @@
"configurations": [
{
"name": "Python: PyPEF Help",
"type": "python",
"type": "debugpy",
"request": "launch",
"env": {"PYTHONPATH": "${workspaceFolder}"},
"program": "${workspaceFolder}/pypef/main.py",
Expand All @@ -19,7 +19,7 @@

{
"name": "Python: PyPEF MKLSTS ANEH",
"type": "python",
"type": "debugpy",
"request": "launch",
"env": {"PYTHONPATH": "${workspaceFolder}"},
"program": "${workspaceFolder}/pypef/main.py",
Expand All @@ -35,7 +35,7 @@

{
"name": "Python: PyPEF MKLSTS avGFP",
"type": "python",
"type": "debugpy",
"request": "launch",
"env": {"PYTHONPATH": "${workspaceFolder}"},
"program": "${workspaceFolder}/pypef/main.py",
Expand All @@ -49,9 +49,26 @@
]
},

{
"name": "Python: PyPEF MKPS avGFP drecomb",
"type": "debugpy",
"request": "launch",
"env": {"PYTHONPATH": "${workspaceFolder}"},
"program": "${workspaceFolder}/pypef/main.py",
"console": "integratedTerminal",
"justMyCode": true,
"cwd": "${workspaceFolder}/datasets/AVGFP/",
"args": [
"mkps",
"--wt", "P42212_F64L.fasta",
"--input", "avGFP.csv",
"--drecomb"
]
},

{
"name": "Python: PyPEF ml -e onehot pls_loocv",
"type": "python",
"type": "debugpy",
"request": "launch",
"env": {"PYTHONPATH": "${workspaceFolder}"},
"program": "${workspaceFolder}/pypef/main.py",
Expand All @@ -73,7 +90,7 @@
// or
// 2. $pypef hybrid -m GREMLIN -t TS.fasl --params GREMLIN
"name": "Python: PyPEF save GREMLIN avGFP model",
"type": "python",
"type": "debugpy",
"request": "launch",
"env": {"PYTHONPATH": "${workspaceFolder}"},
"program": "${workspaceFolder}/pypef/main.py",
Expand All @@ -87,9 +104,27 @@
]
},

{
"name": "Python: PyPEF hybrid LS-TS GREMLIN-DCA avGFP",
"type": "debugpy",
"request": "launch",
"env": {"PYTHONPATH": "${workspaceFolder}"},
"program": "${workspaceFolder}/pypef/main.py",
"console": "integratedTerminal",
"justMyCode": true,
"cwd": "${workspaceFolder}/datasets/AVGFP/",
"args": [
"hybrid",
//"-m", "GREMLIN", // optional, not required
"--ls", "LS.fasl",
"--ts", "TS.fasl",
"--params", "GREMLIN"
]
},

{
"name": "Python: PyPEF hybrid/only-TS-zero-shot GREMLIN-DCA avGFP",
"type": "python",
"type": "debugpy",
"request": "launch",
"env": {"PYTHONPATH": "${workspaceFolder}"},
"program": "${workspaceFolder}/pypef/main.py",
Expand All @@ -106,7 +141,7 @@

{
"name": "Python: PyPEF hybrid/only-PS-zero-shot GREMLIN-DCA avGFP",
"type": "python",
"type": "debugpy",
"request": "launch",
"env": {"PYTHONPATH": "${workspaceFolder}"},
"program": "${workspaceFolder}/pypef/main.py",
Expand All @@ -121,11 +156,45 @@
]
},

{
"name": "Python: PyPEF hybrid/only-PS-zero-shot GREMLIN-DCA avGFP drecomb II",
"type": "debugpy",
"request": "launch",
"env": {"PYTHONPATH": "${workspaceFolder}"},
"program": "${workspaceFolder}/pypef/main.py",
"console": "integratedTerminal",
"justMyCode": true,
"cwd": "${workspaceFolder}/datasets/AVGFP/",
"args": [
"hybrid",
"-m", "HYBRIDgremlin",
"--pmult", "--drecomb",
"--params", "GREMLIN"
]
},

{
"name": "Python: PyPEF hybrid/only-PS-zero-shot GREMLIN-DCA avGFP drecomb",
"type": "debugpy",
"request": "launch",
"env": {"PYTHONPATH": "${workspaceFolder}"},
"program": "${workspaceFolder}/pypef/main.py",
"console": "integratedTerminal",
"justMyCode": true,
"cwd": "${workspaceFolder}/datasets/AVGFP/",
"args": [
"hybrid",
"-m", "GREMLIN",
"--pmult", "--drecomb",
"--params", "GREMLIN"
]
},

{ // PLMC zero-shot steps:
// 1. $pypef param_inference --params uref100_avgfp_jhmmer_119_plmc_42.6.params
// 2. $pypef hybrid -t TS.fasl --params PLMC
"name": "Python: PyPEF save PLMC avGFP model",
"type": "python",
"type": "debugpy",
"request": "launch",
"env": {"PYTHONPATH": "${workspaceFolder}"},
"program": "${workspaceFolder}/pypef/main.py",
Expand All @@ -140,7 +209,7 @@

{
"name": "Python: PyPEF hybrid/only-TS-zero-shot PLMC-DCA avGFP",
"type": "python",
"type": "debugpy",
"request": "launch",
"env": {"PYTHONPATH": "${workspaceFolder}"},
"program": "${workspaceFolder}/pypef/main.py",
Expand All @@ -157,7 +226,7 @@

{
"name": "Python: PyPEF hybrid/only-PS-zero-shot PLMC-DCA avGFP",
"type": "python",
"type": "debugpy",
"request": "launch",
"env": {"PYTHONPATH": "${workspaceFolder}"},
"program": "${workspaceFolder}/pypef/main.py",
Expand All @@ -175,7 +244,7 @@

{
"name": "Python: PyPEF hybrid/only-PS-zero-shot PLMC-DCA variant 2 avGFP",
"type": "python",
"type": "debugpy",
"request": "launch",
"env": {"PYTHONPATH": "${workspaceFolder}"},
"program": "${workspaceFolder}/pypef/main.py",
Expand All @@ -193,7 +262,7 @@

{
"name": "Python: PyPEF !wrong! MSA input format (STO)",
"type": "python",
"type": "debugpy",
"request": "launch",
"env": {"PYTHONPATH": "${workspaceFolder}"},
"program": "${workspaceFolder}/pypef/main.py",
Expand Down
Loading

0 comments on commit 8ab8a48

Please sign in to comment.