xsearch

Local search front-end built on xcommon.sh plus rchive. It defaults to pubmed, supports -query, -match, -exact, -title, -words, and -pairs, and usually emits an ENTREZ_DIRECT wrapper unless you switch to -raw or use one of the direct rchive lookup modes.

Quick Start

• Command: xsearch -query "<search terms>"
• Local executable: /home/vimalinx/miniforge3/envs/bio/bin/xsearch
• Critical environment: EDIRECT_LOCAL_ARCHIVE

When To Use This Tool

• Searching a prepared local PubMed-style archive instead of the live NCBI service
• Building an ENTREZ_DIRECT UID set for downstream xlink, xfilter, or xfetch steps
• Running Boolean or fielded local queries such as AND, NOT, [TREE], or [YEAR]
• Doing title-oriented lookup modes like -title, -match, -exact, -words, or -pairs

Common Patterns

# Boolean query against the local archive
export EDIRECT_LOCAL_ARCHIVE=/path/to/local/archive
xsearch -db pubmed -query 'C14.907.617.812* [TREE] AND 2015:2018 [YEAR]'

# Title lookup
export EDIRECT_LOCAL_ARCHIVE=/path/to/local/archive
xsearch -title 'Genetic Control of Biochemical Reactions in Neurospora.'

# Emit raw UIDs instead of ENTREZ_DIRECT XML
export EDIRECT_LOCAL_ARCHIVE=/path/to/local/archive
xsearch -raw -query 'CRISPR AND 2024 [YEAR]'

Recommended Workflow

1. Point EDIRECT_LOCAL_ARCHIVE at a valid local archive/postings root.
2. Pick the search mode that matches the lookup you need: -query for general Boolean search, -title/-match/-exact for title-style matching, or -words/-pairs for tokenized title scoring.
3. Use wrapped output for downstream x* tools, or add -raw when the next stage expects plain UID lines.
4. If a query fails immediately, verify the local postings directory before debugging the search syntax.

Guardrails

• This is a local archive/postings tool, not a remote esearch replacement.
• -h/-help are safe and show usage examples; -version prints the EDirect version string.
• Live testing without EDIRECT_LOCAL_ARCHIVE failed with Must supply path to local data by setting EDIRECT_LOCAL_ARCHIVE environment variable followed by Unable to get folder Postings for database pubmed.
• Source inspection shows -query wraps UID hits in ENTREZ_DIRECT XML unless -raw is set; -match, -exact, and -title call rchive directly instead.
• -words and -pairs tokenize the query through word-at-a-time and filter-stop-words, then rank title hits with sort-uniq-count-rank -n.
• If you omit -db, the script defaults to pubmed.