efilter1

Filter and/or sort ncbi entrez search results

Usage

efilter [-help] [-query str] [-days N] [-datetype field] [-mindate date] [-maxdate date] [-pub type] [-journal name] [-released when] [-country name] [-feature type] [-location type] [-molecule type] [-organism type] [-source type] [-division code] [-keyword purpose] [-purpose why] [-status alive] [-type type] [-class class]

Overview

efilter filters and/or sorts results from a previous Entrez Direct search.

Options

Query Specification

-query str: Limit results to those matching the given query string.

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.

Publication Filters

-pub type: abstract, clinical, english, free, historical, journal, medline, preprint, published, retracted, retraction, review, or structured.

-journal name: pnas, "j bacteriol", ...

-released when: last_week, last_month, last_year, or prev_years.

Sequence Filters

-country name: usa:minnesota, united_kingdom, "pacific ocean", ...

-feature type: gene, mrna, cds, mat_peptide, ...

-location type: mitochondrion, chloroplast, plasmid, or plastid.

-molecule type: genomic, mrna, trna, rrna, or ncrna.

-organism type: animals, archaea, bacteria, eukaryotes, fungi, human, insects, mammals, plants, prokaryotes, protists, rodents, viruses, ...

-source type: genbank, insd, pdb, pir, refseq, select, swissprot, or tpa.

-division code: 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.

-keyword purpose

-purpose why: baseline or targeted.

Gene Filters

-status alive

-type type: coding or pseudo.

SNP Filters

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

Assembly Filters

-status status: latest or replaced.

Miscellaneous Arguments

-help: Print usage information.

Releases

5 releases since Debian 9 (Stretch); the text changed 4 times.

-class since Debian 10 (Buster); -country since Debian 10 (Buster); -division since Debian 12 (Bookworm); -journal since Debian 10 (Buster); -keyword since Debian 12 (Bookworm); -purpose since Debian 12 (Bookworm); -query since Debian 11 (Bullseye); -released since Debian 10 (Buster).

-field until Debian 10 (Buster); -kind until Debian 11 (Bullseye); -label until Debian 10 (Buster); -pairs until Debian 10 (Buster); -pathway until Debian 11 (Bullseye); -sort until Debian 10 (Buster); -spell until Debian 10 (Buster).