filter-stop-words

name	filter-stop-words
description	Use when processing text or queries in Entrez workflows to remove common stop words from input streams
disable-model-invocation	true
user-invocable	true

filter-stop-words

Quick Start

• Command: tokenize | filter-stop-words
• Local executable: /home/vimalinx/miniforge3/envs/bio/bin/filter-stop-words
• Full reference: See references/help.md

When To Use This Tool

• Remove common stop words from a one-token-per-line text stream.
• Clean tokenized search/query text before downstream term processing.
• Replace removed stop words with + markers when you need placeholder positions in the stream.

Common Patterns

# 1) Remove stop words from a token stream
printf 'the\ngene\nand\nmarker\n' | filter-stop-words

# 2) Replace removed stop words with plus signs
printf 'the\ngene\nand\nmarker\n' | filter-stop-words -plus

Recommended Workflow

1. Tokenize the text so each candidate word is on its own line.
2. Pipe that stream into filter-stop-words.
3. Decide whether you want removed words dropped entirely or replaced with + via -plus.
4. Feed the cleaned token stream into the next text-processing stage.

Guardrails

• Filtering is line-oriented. If you feed full phrases instead of one token per line, the stop-word list will not behave as expected.
• The wrapper has no real --help / --version interface.
• The first command-line token is always consumed by the script; normal use should stick to no argument or -plus.
• In default mode removed stop words disappear completely, which can change query semantics if positional placeholders matter.