Merge pull request #82 from Jumitti/beta

Beta

TFinder-v1.py

@@ -130,10 +130,11 @@ def load_lottiefile(filepath: str):
 
 if 'LOCAL' not in st.session_state:
     local_test = platform.processor()
-    print("Platform:", local_test)
+
     if local_test == "":
         st.session_state["LOCAL"] = 'False'
     else:
+        print("Platform:", local_test)
         st.session_state["LOCAL"] = 'True'
 
 if st.session_state["LOCAL"] == 'False':

TFinder_standalone_win.bat

@@ -0,0 +1,122 @@
+@echo off
+:: Colors
+for /f "delims=" %%i in ('echo prompt $E^|cmd') do set "ESC=%%i"
+set "COLOR_RESET=%ESC%[0m"
+set "COLOR_GREEN=%ESC%[32m"
+set "COLOR_RED=%ESC%[31m"
+set "COLOR_YELLOW=%ESC%[33m"
+set "COLOR_BLUE=%ESC%[34m"
+set "COLOR_CYAN=%ESC%[36m"
+set "COLOR_BOLD=%ESC%[1m"
+
+:: Welcome
+echo %COLOR_GREEN%======================================================================================================%COLOR_RESET%
+echo %COLOR_GREEN%!%COLOR_RESET%                                        %COLOR_BOLD%%COLOR_BLUE%Welcome to TFinder%COLOR_RESET%                                         %COLOR_GREEN%!%COLOR_RESET%
+echo %COLOR_GREEN%======================================================================================================%COLOR_RESET%
+echo %COLOR_CYAN%TFinder%COLOR_RESET% is a %COLOR_BOLD%%COLOR_GREEN%Python easy-to-use web tool%COLOR_RESET% for identifying Transcription Factor Binding Sites (TFBS) and
+echo Individual Motif (IM). Using the %COLOR_BOLD%NCBI API%COLOR_RESET%, it can easily extract either the promoter or terminal regions of a gene 
+echo through a simple query of NCBI gene name or ID. It enables simultaneous analysis across five different species 
+echo for an unlimited number of genes. The tool searches for TFBS and IM in different formats, including IUPAC codes
+echo and JASPAR entries. Moreover, %COLOR_CYAN%TFinder%COLOR_RESET% also allows the generation and use of a %COLOR_BOLD%Position Weight Matrix (PWM)%COLOR_RESET%. 
+echo Finally, the data may be recovered in a tabular form and a graph showing the relevance of the TFBSs and IMs as 
+echo well as its location relative to the Transcription Start Site (TSS) or gene end. The results may be sent by email 
+echo to the user facilitating the ulterior analysis and data sharing.
+echo %COLOR_GREEN%======================================================================================================%COLOR_RESET%
+echo %COLOR_YELLOW%Created by Minniti Julien%COLOR_RESET% - %COLOR_BLUE%GitHub(%COLOR_RESET%https://github.com/Jumitti/TFinder%COLOR_BLUE%)%COLOR_RESET%
+echo %COLOR_YELLOW%MIT Licence%COLOR_RESET% - %COLOR_BLUE%https://github.com/Jumitti/TFinder/blob/main/LICENSE%COLOR_RESET%
+echo %COLOR_GREEN%======================================================================================================%COLOR_RESET%
+
+:: Check if Python >= 3.10 is installed
+echo %COLOR_CYAN%Checking for Python version higher or equal to 3.10...%COLOR_RESET%
+for /f "usebackq tokens=2 delims= " %%v in (`python --version`) do set PYTHON_VERSION=%%v
+
+:: Extract major and minor version numbers
+for /f "tokens=1,2 delims=." %%a in ("%PYTHON_VERSION%") do (
+    set MAJOR=%%a
+    set MINOR=%%b
+)
+
+:: Check if version is >= 3.10
+if not defined MAJOR (
+    echo %COLOR_RED%Python is not installed.%COLOR_RESET%
+    goto install_python
+)
+
+if %MAJOR% lss 3 (
+    echo %COLOR_RED%Python version is less than 3.10.%COLOR_RESET%
+    goto install_python
+) else if %MAJOR% equ 3 if %MINOR% lss 10 (
+    echo %COLOR_RED%Python version is less than 3.10.%COLOR_RESET%
+    goto install_python
+)
+
+echo %COLOR_GREEN%Python version %PYTHON_VERSION% is sufficient.%COLOR_RESET%
+goto continue
+
+:install_python
+echo %COLOR_YELLOW%Installing Python 3.11.9 from https://www.python.org/ftp/python/3.11.9/python-3.11.9-amd64.exe...%COLOR_RESET%
+powershell -Command "Invoke-WebRequest -Uri https://www.python.org/ftp/python/3.11.9/python-3.11.9-amd64.exe -OutFile \"python-3.11.9-amd64.exe\""
+if exist "python-3.11.9-amd64.exe" (
+    echo %COLOR_CYAN%Running Python installer...%COLOR_RESET%
+    start /wait "python-3.11.9-amd64.exe" /quiet InstallAllUsers=1 PrependPath=1
+    del "python-3.11.9-amd64.exe"
+) else (
+    echo %COLOR_RED%Failed to download Python installer. Check your internet connection.%COLOR_RESET%
+    pause
+    exit /b
+)
+
+:: Verify the new installation
+python --version | findstr /r "3\.[1-9][0-9]*" >nul 2>&1
+if %errorlevel% neq 0 (
+    echo %COLOR_RED%Python installation failed. Please install it manually by downloading on https://www.python.org/ftp/python/3.11.9/python-3.11.9-amd64.exe.%COLOR_RESET%
+    pause
+    exit /b
+)
+echo %COLOR_GREEN%Python 3.11.9 installed successfully! %COLOR_RESET%
+
+:continue
+:: Virtual environment creation
+if not exist ".venv" (
+    echo %COLOR_CYAN%Creating Python 3.11.9 virtual environment...%COLOR_RESET%
+    python -m venv .venv
+    if %errorlevel% neq 0 (
+        echo %COLOR_RED%Failed to create the virtual environment. Ensure Python 3.11.9 is installed.%COLOR_RESET%
+        pause
+        exit /b
+    )
+)
+echo %COLOR_GREEN%Virtual environment created successfully! %COLOR_RESET%
+
+:: Activation venv
+echo %COLOR_CYAN%Activating virtual environment...%COLOR_RESET%
+call .venv\Scripts\activate
+if %errorlevel% neq 0 (
+    echo %COLOR_RED%Failed to activate the virtual environment.%COLOR_RESET%
+    pause
+    exit /b
+)
+echo %COLOR_GREEN%Virtual environment activated successfully! %COLOR_RESET%
+
+:: Updating pip and installing dependencies
+echo %COLOR_CYAN%Installing/updating Python packages...%COLOR_RESET%
+pip install -r requirements.txt --verbose
+if %errorlevel% neq 0 (
+    echo %COLOR_RED%Failed to install required packages. Check the requirements.txt file.%COLOR_RESET%
+    pause
+    exit /b
+)
+echo %COLOR_GREEN%Python packages installed successfully! %COLOR_RESET%
+
+:: Run Streamlit/TFinder
+echo %COLOR_CYAN%Launching the TFinder Streamlit app... (CTRL + C to shutdown) %COLOR_RESET%
+streamlit run TFinder-v1.py
+if %errorlevel% neq 0 (
+    echo %COLOR_RED%Failed to launch the Streamlit app. Check your script for errors.%COLOR_RESET%
+    pause
+    exit /b
+)
+
+:: Disabling venv on shutdown
+deactivate
+pause