nhance-sh

name	nhance-sh
description	Use when trying the `nhance.sh` shortcut wrapper around `nquire` for pathway, gene-to-pathway, LitVar, or citation-match lookups against NCBI-related endpoints.
disable-model-invocation	true
user-invocable	true

nhance-sh

Quick Start

• Command: nhance.sh <shortcut> <query>
• Local executable: /home/vimalinx/miniforge3/envs/bio/bin/nhance.sh
• Supported shortcuts from the local source: -pathway, -gene-to-pathway, -litvar, -citmatch

When To Use This Tool

• Try the packaged shortcut wrapper for a few common nquire-based lookups.
• Resolve a Reactome pathway, gene-to-pathway mapping, LitVar entity, or heuristic citation match without building the raw nquire call yourself.
• Prototype an EDirect-side lookup quickly before deciding whether a lower-level nquire command is more reliable.
• Not for general-purpose EDirect requests; this wrapper only special-cases four shortcut modes.

Common Patterns

# 1) Pathway lookup shortcut
nhance.sh -pathway Reactome:R-HSA-70171

# 2) Gene-to-pathway lookup shortcut
nhance.sh -gene-to-pathway 1956

# 3) Citation matching shortcut
nhance.sh -citmatch "nucleotide sequences required for tn3 transposition immunity"

Recommended Workflow

1. Decide whether your request really matches one of the four hard-coded shortcut modes.
2. Pass exactly one query argument after the shortcut flag.
3. Inspect the returned XML or PMID-style result and fall back to raw nquire if you need tighter control.
4. Treat this wrapper as a convenience layer, not as the authoritative interface for complex EDirect querying.

Guardrails

• The wrapper has no real built-in help or version path; nhance.sh --help exits silently with no useful output.
• Only -pathway, -gene-to-pathway, -litvar, and -citmatch are recognized as active shortcut modes.
• Missing shortcut payloads fail explicitly, for example ERROR: Missing -pathway argument.
• In the current local environment, active shortcut calls fail early with Escape: command not found, so the wrapper is not presently reliable without that missing shell helper.
• Plain nhance.sh or unrecognized leading arguments can exit successfully with no output at all, which makes silent failure easy to miss.
• Successful use also depends on nquire, transmute, and xtract being on PATH, plus live network access to the underlying NCBI / PubChem endpoints.