Intersection & Union of BED4 Intervals

A clean, dependency-free Python CLI for computing the union or intersection of two BED4 files. Designed for clarity, explicit edge-case handling, and easy reuse in bioinformatics pipelines.

• Input: two whitespace-separated BED4 files with columns: chrom start end name
• Output: a BED4 file you specify
• Operations: union (merge by feature name within a chromosome), isec (pairwise interval overlap per chromosome)
• Python: 3.8+

Please note: BED is typically 0-based, half-open; chromosome labels must match exactly (e.g., chr1 vs 1 are different).

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Motivation

Goal: Read two BED4 files and, based on user choice, compute either the union or the intersection.

Intersection (isec)
Report all non-empty overlaps between each interval in file 1 and each interval in file 2 on the same chromosome.

• Overlap rule (half-open intervals): [a,b) and [c,d) overlap iff a < d and c < b.
• Example: [30,50) & [50,70) → no overlap
• Example: [30,52) & [50,70) → overlap [50,52)
• The feature name in the output is taken from file 1.

Union (union)
Output all features that occur in at least one file.

• If a feature name occurs in only one file → include as-is.
• If a feature name occurs in both files on different chromosomes → exclude both.
• If a feature name occurs in both files on the same chromosome → output a single interval using the smallest covering span of both:
  • [30,40) + [70,90) → [30,90)
  • [30,50) + [40,45) → [30,50)

CLI contract (argparse)

• operation (union or isec)
• input1 path
• input2 path
• output path

The order of output lines is not important for the script.

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Quick Start

# Union (merge by feature name if on the same chromosome)
python mycode.py union main.bed.txt unionsecondfile.bed.txt union_results.bed.txt
cat union_results.bed.txt

# Intersection (interval overlap by chromosome; name is taken from file1)
python mycode.py isec  main.bed.txt intersectionsecondfile.bed.txt isec_results.bed.txt
cat isec_results.bed.txt

# CLI help
python mycode.py -h

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Features included

Robust parsing

• Skips blank lines and # comments
• Accepts whitespace-separated columns (tabs or spaces)
• Auto-swaps inverted intervals (start > end)
• Defaults name to . if the 4th column is missing

Union

• Groups intervals by name across both files
• Merges only when intervals with the same name are on the same chromosome
• Flags & drops “same name but different chromosome”

Intersection

• Checks pairwise overlaps by chromosome (no requirement to match names)
• Output name is inherited from the file1 interval

Clear output & errors

• Summary stats printed to stdout
• Warnings/parse errors printed to stderr (with line numbers)

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Usage

python mycode.py {union|isec} <input1.bed> <input2.bed> <output.bed>

-union: merge intervals by feature name if on the same chromosome. start = min(start_a, start_b); end = max(end_a, end_b) Pairs with identical names on different chromosomes are excluded.

-isec: report overlapping regions by chromosome for all pairs between file1 and file2. Overlap calculation:

overlap_start = max(start_a, start_b)
overlap_end   = min(end_a, end_b)
emit if overlap_start < overlap_end

Output name is taken from file1’s interval.

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How it works read_bed_file(path)

Validates file existence, parses into (chrom, start, end, name), skips malformed rows and non-integers, prints warnings with line numbers.

find_unions(intervals1, intervals2)

Concatenates both lists; groups by name. Ensures all intervals for a given name share the same chromosome; otherwise marks the group as invalid. Emits one merged interval per valid name.

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Examples (files included)

python mycode.py union main.bed.txt unionsecondfile.bed.txt union_results.bed.txt python mycode.py isec main.bed.txt intersectionsecondfile.bed.txt isec_results.bed.txt

The repository includes the following example inputs/outputs at the repo root:

• main.bed.txt

• unionsecondfile.bed.txt

• intersectionsecondfile.bed.txt

• union_results.bed.txt (generated by the command below)

• isec_results.bed.txt (generated by the command below)

Run the following please:

Union example

cat union_results.bed.txt

Intersection example

cat isec_results.bed.txt

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Project Structure

.
├── mycode.py
├── main.bed.txt
├── unionsecondfile.bed.txt
├── intersectionsecondfile.bed.txt
├── union_results.bed.txt         # generated
└── isec_results.bed.txt          # generated

Appendix: BED4 Files

A BED4 file has four columns (whitespace separated):

1. chrom – chromosome/contig label (e.g., chr1)

2. start – 0-based start (inclusive)

3. end – 0-based end (exclusive)

4. name – feature label (optional; defaults to . in this tool)

Lines beginning with # are treated as comments and ignored.

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Contact

Developed by Martina Debnath | MSc Genetics and Multiomics in Medicine | UCL

Thank you for using my intersection-and-union CLI <3

Feel free to reach out for collaboration.

GitHub: https://github.com/marti-dotcom

Email: martinadebnath@gmail.com