NAME

efilter - filter and/or sort NCBI Entrez search results

SYNOPSIS

efilter (efetch -filter) [-help] [-q[uery] str] [-sort field] [-days N] [-datetype field] [-mindate date] [-maxdate date] [-field field] [-pairs field] [-spell] [-pub type] [-journal name] [-released when] [-country name] [-feature type] [-location type] [-molecule type] [-organism type] [-source type] [-division code] [-status alive] [-type type] [-class class] [-kind pathway] [-pathway type]

DESCRIPTION

efilter filters and/or sorts results from a previous edirect(1) search.

It has two implementations: a shell implementation on top of nquire(1) and a historical Perl implementation that amounts to running edirect -filter, enabled by setting the environment variable USE_NEW_EDIRECT to a false value as described in the ENVIRONMENT section. Some options are implementation-specific, as detailed below.

OPTIONS

Query Specification

-q str (Perl implementation only)
-query str: Limit results to those matching the given query string.

Document Order

-sort field (Perl implementation only): Sort results by the given field.

Date Constraint

-days N: Keep only results from the past N days.
-datetype field: Which date field (in abbreviated form) to consider.
-mindate date: Start of date range.
-maxdate date: End of date range.

Limit by Field

-field field (Perl implementation only): Query words individually in field.
-pairs field (Perl implementation only): Query overlapping word pairs.

Spell Check

-spell (Perl implementation only): Correct misspellings in query.

Publication Filters

-pub type: abstract, clinical, english, free, historical, journal, preprint, review, structured.
-journal name: pnas, "j bacteriol", ...
-released when: last_week, last_month, last_year, prev_years.

Sequence Filters

-country name: usa:minnesota, united_kingdom, "pacific ocean", ...
-feature type: gene, mrna, cds, mat_peptide, ...
-location type: mitochondrion, chloroplast, plasmid, plastid.
-molecule type: genomic, mrna, trna, rrna, ncrna.
-organism type: animals, archaea, bacteria, eukaryotes, fungi, human, insects, mammals, plants, prokaryotes, protists, rodents, viruses, ...
-source type: genbank, insd, pdb, pir, refseq, swissprot, tpa
-division code (shell implementation only): Three-letter GenBank division code: bct, con, env, est, gss, htc, htg, inv, mam, pat, phg, pln, pri, rod, sts, syn, una, vrl, or vrt.

Gene Filters

-status alive
-type type: coding, pseudo.

SNP Filters

-class class: acceptor, donor, coding, frameshift, indel, intron, missense, nonsense, synonymous.

Biosystems Filters

-kind pathway
-pathway type: reactome, wikipathways.

Miscellaneous Arguments

-help: Print usage information.

ENVIRONMENT

USE_NEW_EDIRECT: Whether to use the current shell implementation or revert to the historical Perl implementation. Canonical true values are 1, on (case-insensitive), true (case-insensitive), and yes (case-insensitive); canonical false values are 0, off (case-insensitive), false (case-insensitive), and no (case-insensitive).