bio-genome-intervals-proximity-operations

Version Compatibility

Reference examples tested with: bedtools 2.31+

Before using code patterns, verify installed versions match. If versions differ:

• Python: pip show <package> then help(module.function) to check signatures
• CLI: <tool> --version then <tool> --help to confirm flags

If code throws ImportError, AttributeError, or TypeError, introspect the installed package and adapt the example to match the actual API rather than retrying.

Proximity Operations

"Find nearest features or extend intervals" → Identify the closest genomic feature to each interval, or expand intervals by a fixed flank size.

• CLI: bedtools closest -a peaks.bed -b genes.bed, bedtools slop -b 1000
• Python: a.closest(b), a.slop(b=1000, g=genome) (pybedtools)

Operations for finding nearby features and extending intervals using bedtools and pybedtools.

Closest - Find Nearest Feature

CLI

# Find nearest gene to each peak
bedtools closest -a peaks.bed -b genes.bed > peaks_with_nearest.bed

# Report distance to nearest feature
bedtools closest -a peaks.bed -b genes.bed -d > with_distance.bed

# Ignore overlapping features (find next nearest)
bedtools closest -a peaks.bed -b genes.bed -io > nearest_non_overlap.bed

# Ignore features on different strands
bedtools closest -a peaks.bed -b genes.bed -s > same_strand.bed

# Ignore features on same strand (opposite strand only)
bedtools closest -a peaks.bed -b genes.bed -S > opposite_strand.bed

# Only upstream features (5' direction relative to A strand)
bedtools closest -a peaks.bed -b genes.bed -D a -iu > upstream_only.bed

# Only downstream features
bedtools closest -a peaks.bed -b genes.bed -D a -id > downstream_only.bed

# Report multiple ties
bedtools closest -a peaks.bed -b genes.bed -t all > all_ties.bed

# First tie only
bedtools closest -a peaks.bed -b genes.bed -t first > first_tie.bed

Python

import pybedtools

a = pybedtools.BedTool('peaks.bed')
b = pybedtools.BedTool('genes.bed')

# Basic closest
result = a.closest(b)

# With distance
result = a.closest(b, d=True)

# Ignore overlaps
result = a.closest(b, io=True)

# Same strand only
result = a.closest(b, s=True)

# Report all ties
result = a.closest(b, t='all')

result.saveas('closest.bed')