Project 1: Quick Bed Sort

Goal: Merge multiple compressed BED files, filter them against a "chromosome rulebook," and sort them first by chromosome (custom order) and then by start position.

Files

• shuf.a.bed.gzand shuf.b.bed.gz
• Quick_bed_sort.py: The main Python script.
• standard_selection.tsv: A text file listing chromosomes to keep, in the specific desired order.

Setup & Usage

1. Generate the Rulebook (if not present): This command creates the standard human chromosome order (chr1-22, X, Y).

   (echo chr{1..22} | tr ' ' '\n'; echo chrX; echo chrY) > standard_selection.tsv

2. Run the Script:

   python Quick_bed_sort.py

Output: The script creates a file X.standard.sorted.bed containing the final sorted BED file.