/bio-genome-intervals-proximity-operations

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--- name: bio-genome-intervals-proximity-operations description: Find nearest features, search within windows, and extend intervals using closest, window, flank, and slop operations. Use when performing TSS proximity analysis, assigning enhancers to genes, defining promoter regions, or finding nearby genomic features. tool_type: mixed primary_tool: bedtools measurable_outcome: Execute skill workflow successfully with valid output within 15 minutes. allowed-tools:

• read_file
• run_shell_command

---

Proximity Operations

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')

Window - Find Features Within Distance

CLI

# Find genes within 10kb of peaks
bedtools window -a peaks.bed -b genes.bed -w 10000 > genes_within_10kb.bed

# Asymmetric window (5kb upstream, 2kb downstream of A)
bedtools window -a peaks.bed -b genes.bed -l 5000 -r 2000 > asymmetric.bed

# Same strand only
bedtools window -a peaks.bed -b genes.bed -w 10000 -sm > same_strand.bed

# Strand-aware window (upstream/downstream relative to strand)
bedtools window -a peaks.bed -b genes.bed -l 5000 -r 2000 -sw > strand_aware.bed

Python

import pybedtools

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

# Symmetric window
result = a.window(b, w=10000)

# Asymmetric window
result = a.window(b, l=5000, r=2000)

# Same strand
result = a.window(b, w=10000, sm=True)

result.saveas('window.bed')

Slop - Extend Interval Boundaries

CLI

# Extend both ends by 100bp (requires genome file)
bedtools slop -i peaks.bed -g genome.txt -b 100 > extended.bed

# Extend 5' end by 500bp, 3' end by 100bp
bedtools slop -i peaks.bed -g genome.txt -l 500 -r 100 > asymmetric.bed

# Strand-aware extension (upstream/downstream)
bedtools slop -i peaks.bed -g genome.txt -l 500 -r 100 -s > strand_aware.bed

# Extend by percentage
bedtools slop -i peaks.bed -g genome.txt -b 0.5 -pct > extend_50pct.bed

# Header passthrough
bedtools slop -i peaks.bed -g genome.txt -b 100 -header > with_header.bed

Python

import pybedtools

bed = pybedtools.BedTool('peaks.bed')

# Symmetric extension
result = bed.slop(g='genome.txt', b=100)

# Asymmetric extension
result = bed.slop(g='genome.txt', l=500, r=100)

# Strand-aware
result = bed.slop(g='genome.txt', l=500, r=100, s=True)

# Percentage
result = bed.slop(g='genome.txt', b=0.5, pct=True)

result.saveas('extended.bed')

Flank - Get Flanking Regions

CLI

# Get 100bp flanks on both sides (not original interval)
bedtools flank -i peaks.bed -g genome.txt -b 100 > flanks.bed

# Get upstream flank only
bedtools flank -i peaks.bed -g genome.txt -l 100 -r 0 > upstream.bed

# Get downstream flank only
bedtools flank -i peaks.bed -g genome.txt -l 0 -r 100 > downstream.bed

# Strand-aware flanking
bedtools flank -i peaks.bed -g genome.txt -l 500 -r 0 -s > upstream_strand.bed

# Percentage of interval size
bedtools flank -i peaks.bed -g genome.txt -b 0.5 -pct > flank_50pct.bed

Python

import pybedtools

bed = pybedtools.BedTool('peaks.bed')

# Both flanks
result = bed.flank(g='genome.txt', b=100)

# Upstream only (left)
result = bed.flank(g='genome.txt', l=100, r=0)

# Strand-aware upstream
result = bed.flank(g='genome.txt', l=500, r=0, s=True)

result.saveas('flanks.bed')

Shift - Move Intervals

CLI

# Shift all intervals downstream by 100bp
bedtools shift -i peaks.bed -g genome.txt -s 100 > shifted.bed

# Shift upstream (negative)
bedtools shift -i peaks.bed -g genome.txt -s -100 > shifted_up.bed

# Shift by percentage
bedtools shift -i peaks.bed -g genome.txt -s 0.5 -pct > shift_50pct.bed

# Shift with chromosome-specific values
bedtools shift -i peaks.bed -g genome.txt -s 100 -p 200 > shifted.bed  # plus strand +100, minus +200

Python

import pybedtools

bed = pybedtools.BedTool('peaks.bed')

# Shift downstream
result = bed.shift(g='genome.txt', s=100)

# Shift upstream
result = bed.shift(g='genome.txt', s=-100)

result.saveas('shifted.bed')

Common Patterns

Find Peaks Within 10kb of TSS

# Get TSS from genes (assumes BED6+ with strand)
awk -v OFS='\t' '{
    if ($6 ==