filter-based-on-FC-and-FDR

Filter DE genes based on log2Folchange, FDR value or both

Deseq2_Annotated_Data_Processing

This repository contains a Python script for processing and filtering annotated data generated by the DESeq2 differential expression analysis tool. The script takes a DESeq2 annotated file as input, applies filtering criteria based on log2 fold change and adjusted p-values, and generates a modified output file.

Prerequisites

• Python 3.x

Usage

1. Clone the repository to your local machine or download the script file directly.
2. Open a terminal or command prompt.
3. Navigate to the directory where the script is located.
4. Execute the script using the following command:

   python filter_FDR_FC.py [input_file]
   

   Replace [input_file] with the path to the DESeq2 annotated file you want to process.
5. The processed output file will be generated in the same directory as the input file with a modified name.

The provided Python script (filter_FDR_FC.py) processes a DESeq2 annotated file by filtering the data based on log2 fold change and adjusted p-values. Here's a breakdown of the code:

1. The script imports the sys module to retrieve command-line arguments.
2. The input file path is obtained from the command-line arguments and opened for reading (f1).
3. The output file path is generated by replacing the input file name with "1.5_FC_New" (output). A new file is opened for writing (out).
4. The header line from the input file is read and written to the output file.
5. For each line in the input file:
   • The line is stored in a variable l for writing to the output file later.
   • The line is stripped of leading/trailing whitespaces and split into a list based on tab separators.
   • The gene ID, log2 fold change, and adjusted p-value are extracted from the line.
   • If the adjusted p-value is less than 0.05 and the log2 fold change is greater than 1 or less than -1, the line is written to the output file.
6. Once all lines have been processed, the script finishes execution, and the output file is closed.

License

This project is licensed under the MIT License. Feel free to modify and use the code according to your needs.