intersect-uid-lists

name	intersect-uid-lists
description	Use when keeping only the Entrez or NCBI UIDs present in both of two UID files.
disable-model-invocation	true
user-invocable	true

intersect-uid-lists

Quick Start

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

When To Use This Tool

• Keep only IDs shared by two independent Entrez result sets.
• Build overlap cohorts, for example records matching both a disease query and a species query.
• Confirm which previously processed IDs are still present in a refreshed search.
• Use this instead of exclude-uid-lists or difference-uid-lists when you want the shared core set.

Common Patterns

# 1) Keep only UIDs that appear in both searches
intersect-uid-lists disease.ids species.ids > overlap.ids

# 2) Count the shared UID set between two snapshots
intersect-uid-lists old.ids new.ids | wc -l

# 3) Preview the first overlapping IDs before refetching
intersect-uid-lists query_a.ids query_b.ids | sed -n '1,20p'

Recommended Workflow

1. Save the two UID sets you want to compare as one-UID-per-line files.
2. Run intersect-uid-lists to compute the shared set.
3. Inspect or count the overlap before feeding it into expensive downstream steps.
4. Use the resulting list with efetch, xtract, or other local archive utilities.

Guardrails

• The real implementation is comm -12 <(sort "$1") <(sort "$2") | sort -n, so it returns only the shared IDs.
• The wrapper sorts inputs internally, so output order reflects numeric sorting rather than input order.
• This command expects exactly two files and has no real built-in help/version interface.
• Passing --help or --version can still produce sort / comm noise instead of clean documentation output.