difference-uid-lists

name	difference-uid-lists
description	Use when finding the symmetric difference between two Entrez or NCBI UID files.
disable-model-invocation	true
user-invocable	true

difference-uid-lists

Quick Start

• Command: difference-uid-lists FILE1 FILE2
• Local executable: /home/vimalinx/miniforge3/envs/bio/bin/difference-uid-lists
• Full reference: references/help.md

When To Use This Tool

• Keep only IDs that appear in exactly one of two UID files.
• Compare an older and newer search result to see which IDs were added or dropped.
• Audit drift between two snapshots of the same Entrez query.
• Use this instead of exclude-uid-lists when you need both sides' uniques, not just FILE1 minus FILE2.

Common Patterns

# 1) Find IDs that changed between two saved searches
difference-uid-lists old.ids new.ids > changed.ids

# 2) Count how many UIDs are unique to either cohort
difference-uid-lists case.ids control.ids | wc -l

# 3) Review the changed IDs before refetching records
difference-uid-lists baseline.ids rerun.ids | sed -n '1,20p'

Recommended Workflow

1. Prepare exactly two one-UID-per-line files.
2. Run difference-uid-lists to compute the symmetric difference.
3. Inspect or count the output before feeding it into downstream fetch or QC steps.
4. Switch to exclude-uid-lists or intersect-uid-lists if you actually need a directional subtraction or shared set.

Guardrails

• The real implementation is comm -3 <(sort "$1") <(sort "$2") | tr -d '\t' | sort -n, so it returns IDs unique to either file.
• The wrapper sorts inputs internally; original input order is discarded.
• This command expects exactly two files and has no real built-in help/version path.
• Passing --help or --version does not show clean custom docs; it leaks through to sort and can still emit comm / missing-file noise.