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
- Point
EDIRECT_LOCAL_ARCHIVE at a valid local archive/postings root.
- 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.
- Use wrapped output for downstream
x* tools, or add -raw when the next stage expects plain UID lines.
- 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.
1---2name: xsearch3description: Use when searching a local NCBI EDirect archive/postings index with Boolean, title, word, or pair queries inside the `x*` local-cache workflow.4---56# xsearch78Local 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.910## Quick Start1112- **Command:** `xsearch -query "<search terms>"`13- **Local executable:** `/home/vimalinx/miniforge3/envs/bio/bin/xsearch`14- **Critical environment:** `EDIRECT_LOCAL_ARCHIVE`1516## When To Use This Tool1718- Searching a prepared local PubMed-style archive instead of the live NCBI service19- Building an `ENTREZ_DIRECT` UID set for downstream `xlink`, `xfilter`, or `xfetch` steps20- Running Boolean or fielded local queries such as `AND`, `NOT`, `[TREE]`, or `[YEAR]`21- Doing title-oriented lookup modes like `-title`, `-match`, `-exact`, `-words`, or `-pairs`2223## Common Patterns2425```bash26# Boolean query against the local archive27export EDIRECT_LOCAL_ARCHIVE=/path/to/local/archive28xsearch -db pubmed -query 'C14.907.617.812* [TREE] AND 2015:2018 [YEAR]'29```3031```bash32# Title lookup33export EDIRECT_LOCAL_ARCHIVE=/path/to/local/archive34xsearch -title 'Genetic Control of Biochemical Reactions in Neurospora.'35```3637```bash38# Emit raw UIDs instead of ENTREZ_DIRECT XML39export EDIRECT_LOCAL_ARCHIVE=/path/to/local/archive40xsearch -raw -query 'CRISPR AND 2024 [YEAR]'41```4243## Recommended Workflow44451. Point `EDIRECT_LOCAL_ARCHIVE` at a valid local archive/postings root.462. 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.473. Use wrapped output for downstream `x*` tools, or add `-raw` when the next stage expects plain UID lines.484. If a query fails immediately, verify the local postings directory before debugging the search syntax.4950## Guardrails5152- This is a local archive/postings tool, not a remote `esearch` replacement.53- `-h`/`-help` are safe and show usage examples; `-version` prints the EDirect version string.54- 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`.55- Source inspection shows `-query` wraps UID hits in `ENTREZ_DIRECT` XML unless `-raw` is set; `-match`, `-exact`, and `-title` call `rchive` directly instead.56- `-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`.57- If you omit `-db`, the script defaults to `pubmed`.
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