exclude-uid-lists

name	exclude-uid-lists
description	Use when subtracting one Entrez or NCBI UID file from another and keeping only IDs unique to the first file.
disable-model-invocation	true
user-invocable	true

exclude-uid-lists

Quick Start

• Command: exclude-uid-lists <keep-list> <exclude-list>
• Local executable: /home/vimalinx/miniforge3/envs/bio/bin/exclude-uid-lists
• Full reference: See references/help.md for detailed options and usage

When To Use This Tool

• Remove already seen or unwanted IDs from a primary UID file.
• Keep only FILE1 entries that do not appear in FILE2.
• Filter out processed, withdrawn, or blacklisted identifiers before a downstream fetch.
• Use this instead of difference-uid-lists when direction matters.

Common Patterns

# 1) Remove already processed UIDs from a fresh search result
exclude-uid-lists current.ids processed.ids > todo.ids

# 2) Drop a blacklist from a master UID list
exclude-uid-lists all_hits.ids blacklist.ids > filtered.ids

# 3) Count the remaining UIDs after subtraction
exclude-uid-lists source.ids remove.ids | wc -l

Recommended Workflow

1. Put the source IDs in the first file and the IDs to remove in the second file.
2. Run exclude-uid-lists and redirect the output to a new keep-list.
3. Inspect the count or first few IDs before downstream fetching.
4. Feed the filtered list into efetch, xtract, or another local-archive step.

Guardrails

• The real implementation is comm -23 <(sort "$1") <(sort "$2") | sort -n, so the result is directional: FILE1 minus FILE2.
• The wrapper sorts both inputs internally, so original ordering is lost.
• This command expects exactly two files and has no clean built-in help/version behavior.
• Passing --help or --version can still trigger sort / comm errors because the wrapper interprets them as file arguments.