Refactor-8

Author: niklases

.gitignore

@@ -11,6 +11,8 @@ __pycache__/
 
 
 # Created test/output files
+scripts/Setup/windows/Miniconda3-latest-Windows-x86_64.exe
+scripts/Setup/windows/Miniconda3/*
 scripts/Encoding_low_N/apc.png
 scripts/Encoding_low_N/low_N_avGFP_extrapolation.png
 datasets/ANEH/LS.fasl
@@ -375,3 +377,11 @@ datasets/ANEH/CHAM830104_RIDGE_ML_Model_Performance.png
 datasets/ANEH/CHAM830104_PLS_LOOCV_ML_Model_Performance.png
 datasets/ANEH/37_ANEH_variants_plmc_dca_encoded.csv
 datasets/ANEH/37_ANEH_variants_gremlin_dca_encoded.csv
+scripts/Setup/windows/AVGFP/uref100_avgfp_jhmmer_119.a2m
+scripts/Setup/windows/AVGFP/avGFP.csv
+scripts/Setup/windows/api_encoding_train_test.py
+scripts/Setup/windows/apc.png
+scripts/Setup/linux/AVGFP/uref100_avgfp_jhmmer_119.a2m
+scripts/Setup/linux/AVGFP/avGFP.csv
+scripts/Setup/linux/api_encoding_train_test.py
+scripts/Setup/linux/apc.png

scripts/GREMLIN_numba/gremlin_inference_numba.py

@@ -1,4 +1,7 @@
-# Gremlin in Python
+# GREMLIN in Python using numba
+# 16.08.2023, Niklas Siedhoff
+# Python-port of GREMLIN_CPP; 
+# GREMLIN_CPP is licensed as:
 
 """
 ------------------------------------------------------------

scripts/Setup/linux/conda_install_test.sh

@@ -30,12 +30,12 @@ while true; do
     read -p "Test PyPEF installation (downloads PyPEF example test set files and runs a Python test script, ~ 1 h run time) [Y/N]? " yn
     case $yn in
         [Yy]* ) 
-      mkdir test_dataset_avgfp
+      mkdir -p AVGFP
       wget https://raw.githubusercontent.com/niklases/PyPEF/main/datasets/AVGFP/avGFP.csv
       wget https://raw.githubusercontent.com/niklases/PyPEF/main/datasets/AVGFP/uref100_avgfp_jhmmer_119.a2m
-      wget https://raw.githubusercontent.com/niklases/PyPEF/scripts/Encoding_low_N/api_encoding_train_test.py
-      mv avGFP.csv ./test_dataset_avgfp/avGFP.csv
-      mv uref100_avgfp_jhmmer_119.a2m ./test_dataset_avgfp/uref100_avgfp_jhmmer_119.a2m
+      wget https://raw.githubusercontent.com/niklases/PyPEF/main/scripts/Encoding_low_N/api_encoding_train_test.py
+      mv avGFP.csv ./AVGFP/avGFP.csv
+      mv uref100_avgfp_jhmmer_119.a2m ./AVGFP/uref100_avgfp_jhmmer_119.a2m
       python3 ./api_encoding_train_test.py
       break;;
         [Nn]* ) 

scripts/Setup/windows/download_pypef_test_files.ps1

@@ -1,5 +1,5 @@
 Write-Host "Downloading PyPEF test files..."
-mkdir "test_dataset_avgfp"
-(New-Object Net.WebClient).DownloadFile("https://raw.githubusercontent.com/niklases/PyPEF/main/datasets/AVGFP/avGFP.csv", "test_dataset_avgfp\avGFP.csv")
-(New-Object Net.WebClient).DownloadFile("https://raw.githubusercontent.com/niklases/PyPEF/main/datasets/AVGFP/uref100_avgfp_jhmmer_119.a2m", "test_dataset_avgfp\uref100_avgfp_jhmmer_119.a2m")
-(New-Object Net.WebClient).DownloadFile("https://raw.githubusercontent.com/niklases/PyPEF/scripts/Encoding_low_N/api_encoding_train_test.py", "api_encoding_train_test.py")
+mkdir "AVGFP"
+(New-Object Net.WebClient).DownloadFile("https://raw.githubusercontent.com/niklases/PyPEF/main/datasets/AVGFP/avGFP.csv", "AVGFP\avGFP.csv")
+(New-Object Net.WebClient).DownloadFile("https://raw.githubusercontent.com/niklases/PyPEF/main/datasets/AVGFP/uref100_avgfp_jhmmer_119.a2m", "AVGFP\uref100_avgfp_jhmmer_119.a2m")
+(New-Object Net.WebClient).DownloadFile("https://raw.githubusercontent.com/niklases/PyPEF/main/scripts/Encoding_low_N/api_encoding_train_test.py", "api_encoding_train_test.py")