(c) Hasiba Asma

CheckSameLocus for Simulation

This is a Python script that processes the output files generated by the bedtools closest command. It analyzes the files in a specified directory to extract relevant information and generate a new output file for each input file.

Prerequisites

Python 3.x

Usage

python checkSameLocus_ForSimulation.py <directory>

directory: The directory that contains all the output files from the bedtools closest command. Make sure there are no other files in this directory.

Functionality

The script loops over all the files in the specified directory and performs the following operations for each file:

• Initializes dictionaries and lists for storing data.
• Reads the input file line by line and extracts relevant information.
• Calculates the size of the locus based on the extracted information.
• Creates a list of unique loci and updates the dictionaries accordingly.
• Saves the locus hits, size, and intron information in the output file.

The output file is named HitsAndSizePerLocus_<input_file_name>.

Output Format

The output file contains the following columns:

• Flanked Genes: Names of the left and right flanking genes separated by a hyphen.
• Hit Count: Number of hits in the locus.
• Locus Size: Size of the locus.
• Intron Status: Indicates whether the locus is intronic or not.
• Input File: Name of the input file from which the data was extracted.