Summary

Bio::DB::EUtilities::efetch - retrieval of records from a list of IDs or the
user's environment.

Package variables

Inherit

Bio::DB::EUtilities

Synopsis

  my $efetch = Bio::DB::EUtilities->new(
                                       -verbose => 1,
                                       -cookie   => $esearch->next_cookie,
                                       -retmax   => $retmax,
                                       -rettype  => 'fasta'
                                        );

  print $efetch->get_response->content;

Description

EFetch retrieves data records from a list of
ID's. This can be accomplished directly (using id) or indirectly
(by using a Cookie. The following are a general list of parameters that can be used to take
advantage of Efetch. Up-to-date help for Efetch is available at this URL
(the information below is a summary of the options found there):

  http://eutils.ncbi.nlm.nih.gov/entrez/query/static/efetch_help.html

   One or more database available through EUtilities. EFetch currently only
supports database retrieval from the following databases:
pubmed, pmc (PubMed Central), journals, omim, nucleotide,
protein, genome, gene, snp (dbSBP), popset, and taxonomy.
   Also supported are sequences (nucleotide, protein, popset and genome), and
the three subsets of nucleotide: nuccore, nucest, nucgss
   a list of primary ID's
   Below are a list of IDs which can be used with EFetch:
   For sequence databases:
NCBI sequence number (GI), accession, accession.version, fasta,
GeneID, genome ID, seqid
   All other databases:
PMID (pubmed), MIM number (omim), GI number (nucleotide, protein),
Genome ID (genome), Popset ID (popset), SNP cluster ID (snp),
UniSTS ID (unists), UniGene cluster ID (unigene), MMDB-ID (structure),
PSSM-ID (cdd), 3D SDI (domains), TAXID (taxonomy), GEO ID (geo)
   limits results by dates (yyyy/mm/dd format, or by year)
   Output type based on the database. Not all return types are compatible with
all return modes (-retmode). For more information, see the specific
literature or sequence database links at URL above.
   Literature databases have the below return types:
uilist (all databases),
abstract, citation, medline (not omim),
full (journals and omim)
   Literature databases have the below return types:
native (full record, all databases),
fasta, seqid, acc (nucleotide or protein),
gb, gbc, gbwithparts (nucleotide only),
est (dbEST only),
gss (dbGSS only),
gp, gpc (protein only),
chr, flt, rsr, brief, docset (dbSNP only)
   EFetch is set, by default, to return a specific format for each Entrez database;
this is set in the %DATABASE hash in Bio::DB::EUtilities. To override this
format, you can set -retmode. The normal return modes are text, HTML, XML,
and ASN1. Error checking for the set return mode is currently not
implemented.
   Used for the output format for Taxonomy; set to uilist, brief, docsum,
xml
   The strand of DNA to show: 1=plus, 2=minus
   the start and end coordinates of the sequence to display
   The GI is often part of a biological blob containing other GIs

    * 0 - get the whole blob
    * 1 - get the bioseq for gi of interest (default in Entrez)
    * 2 - get the minimal bioseq-set containing the gi of interest
    * 3 - get the minimal nuc-prot containing the gi of interest
    * 4 - get the minimal pub-set containing the gi of interest

These are Bioperl-related settings and are not used as CGI parameters when
   The relevant EUtility to be used (efetch).
   Uses a Cookie-based search (see below)

Methods

Methods description

 Title   : parse_response
 Usage   : $db->_parse_response($content)
 Function: parse out response for cookie
 Returns : empty
 Args    : none
 Throws  : 'unparseable output exception'

Methods code

sub _initialize {

    my ($self, @args ) = @_;
    $self->SUPER::_initialize(@args);
    my ($retmode, $reldate, $mindate, $maxdate, $datetype, $rettype, $retstart, 
        $retmax, $report, $seq_start, $seq_stop, $strand, $complexity) = 
      $self->_rearrange([qw(RETMODE RELDATE MINDATE MAXDATE DATETYPE RETTYPE
        RETSTART RETMAX REPORT SEQ_START SEQ_STOP STRAND COMPLEXITY)], @args);    
    # set by default
    $self->_eutil($EUTIL);
    $datetype ||= 'mdat';
    $self->datetype($datetype) if $datetype;
    defined($retstart)       && $self->retstart($retstart);
    $retmode        && $self->retmode($retmode);
    $retmax         && $self->retmax($retmax);
    $rettype        && $self->rettype($rettype);
    $seq_start      && $self->seq_start($seq_start);
    $seq_stop       && $self->seq_stop($seq_stop);
    $strand         && $self->strand($strand);
    defined($complexity) && $self->complexity($complexity);
    $report         && $self->report($report);

}

sub parse_response {}

General documentation

User feedback is an integral part of the
evolution of this and other Bioperl modules. Send
your comments and suggestions preferably to one
of the Bioperl mailing lists. Your participation
is much appreciated.

  bioperl-l@lists.open-bio.org               - General discussion
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Report bugs to the Bioperl bug tracking system to
help us keep track the bugs and their resolution.
Bug reports can be submitted via the web.

  http://bugzilla.open-bio.org/

Email cjfields at uiuc dot edu

The rest of the documentation details each of the
object methods. Internal methods are usually
preceded with a _