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

       edirect(1), esearch(1), nquire(1), exclude-uid-lists(1).

NCBI                                               2021-01-20                                         EFILTER(1)