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EFILTER(1) | NCBI Entrez Direct User's Manual | EFILTER(1) |
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).
SEE ALSO¶
2021-01-20 | NCBI |