/SAMOSA_ZMW_Selector_Script

Enhanced zmw_selector.py + New run_zmw_selector.sh

Primary LanguagePython

SAMOSA ZMW Selector Script

  1. Enhanced zmw_selector.py: Refined the original script to improve efficiency and functionality.
  2. New run_zmw_selector.sh: Added a shell script for streamlined execution of the Python script, including environment setup and error detection.

Overview

This repository contains the refined zmw_selector.py script and the newly added run_zmw_selector.sh script for enhanced functionality and efficiency in extracting Pacific Bioscience's Zero-Mode Waveguides (ZMWs) near predicted transcription factor binding sites. The original script is credited to the Ramani Lab's SAMOSA project.

Features

Enhancements in zmw_selector.py

  • Automatic BAM Indexing: The script now checks for the existence of a BAM index file. If none exists or if the existing index is outdated, the script generates a new index file based on the BAM file's creation date.
  • Improved Error Handling: Added comprehensive error handling to manage various edge cases and ensure robust script execution.
  • Refactored Code: Simplified and cleaned the code for better readability and maintainability.

New run_zmw_selector.sh Script

  • Environment Setup: The shell script activates a Conda environment linked to a Jupyter kernel, ensuring all required packages are available.
  • Error Detection: Implemented echo statements within the shell script to identify and report potential errors, aiding in quick troubleshooting.
  • Batch Processing: Allows the user to pass a directory of BAM files, processing each file sequentially and outputting individual ZMW TSV files.

Prerequisites for Shell Script Usage

  • Conda installed and configured.
  • Jupyter Notebook installed.
  • Required Python packages listed in zmw_selector_updated.py import section (provided in the repository).