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proximity-operations

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Performs proximity operations on genomic intervals with bedtools (closest, window, flank, slop) and pybedtools - nearest-feature queries with signed/strand-aware distance, fixed-radius window searches, strand-aware promoter construction, and interval extension. Covers the closest -d/-D a/b/ref/-t/-k/-io/-iu/-id flags, the -D ref strand sign-flip, silent chromosome-end clipping in slop/flank, -t all tie double-counting, and the critical distinction between a geometry answer (nearest TSS) and a biology answer (which gene an element regulates). Use when assigning peaks or variants to genes, defining promoters from a gene model, building distance-to-TSS distributions, finding features within a window, or extending intervals - and when deciding whether nearest-gene is a fair prior (GWAS locus) or a trap (distal enhancer).

When to use

• assigning peaks or variants to genes
• defining promoters from a gene model
• building distance-to-TSS distributions
• finding features within a window
• extending intervals
• nearest-feature queries with signed distance
• strand-aware promoter construction
• fixed-radius window searches

When not to use

• presenting nearest gene as a regulatory call for a distal element
• real enhancer-to-gene linking without validation
• causal gene assignment for GWAS loci without colocalization

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