find-in-gene

name	find-in-gene
description	Use when filtering EDirect `GENE` XML records by strand and coordinate overlap to emit matching gene names.
disable-model-invocation	true
user-invocable	true

find-in-gene

CLI tool from the bioconda package entrez-direct for filtering GENE XML on strand and interval overlap.

Quick Start

• Command: cat genes.xml | PATH=/home/vimalinx/miniforge3/envs/bio/bin:$PATH /home/vimalinx/miniforge3/envs/bio/bin/find-in-gene plus 1200 1800
• Local executable: /home/vimalinx/miniforge3/envs/bio/bin/find-in-gene
• Reference: See references/help.md for full usage details

When To Use This Tool

• Select gene names whose Min / Max span overlaps a query interval in GENE XML.
• Restrict matches to a specific strand value such as plus or minus.
• Use as a tiny xtract wrapper in larger EDirect XML pipelines.

Common Patterns

# 1) Find plus-strand genes overlapping a region
cat genes.xml | \
  PATH=/home/vimalinx/miniforge3/envs/bio/bin:$PATH \
  /home/vimalinx/miniforge3/envs/bio/bin/find-in-gene plus 1200 1800

# 2) Query minus-strand overlaps from an EDirect pipeline
upstream_gene_xml_command | \
  PATH=/home/vimalinx/miniforge3/envs/bio/bin:$PATH \
  /home/vimalinx/miniforge3/envs/bio/bin/find-in-gene minus 50000 52000

Recommended Workflow

1. Start from XML records that actually use the GENE pattern with Name, Strand, Min, and Max elements.
2. Pass strand first, then the lower and upper coordinate bounds.
3. Capture stdout as a simple list of matching gene names.
4. If the interval bounds are reversed, let the script swap them, but still verify the query window before automating it.

Guardrails

• Despite the error text mentioning only start and stop positions, the script practically needs three arguments: strand min max. Supplying only two causes xtract to fail with empty numeric constraints.
• A fourth argument is accepted by the shell wrapper but is not used anywhere in the filter.
• This wrapper is stdin-driven and emits only Name; it does not fetch gene records on its own.
• Like other EDirect helpers, it requires companion binaries such as xtract to be on PATH; absolute-path invocation alone is not sufficient in a bare shell.