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).