SYNOPSIS
# Do not use this module directly.
# get a Bio::DB::NCBIHelper object somehow
my $seqio = $db->get_Stream_by_acc(['J00522']);
foreach my $seq ( $seqio->next_seq ) {
# process seq
}
DESCRIPTION
Provides a single place to setup some common methods for querying NCBI web databases. This module just centralizes the methods for constructing a URL for querying NCBI GenBank and NCBI GenPept and the common HTML stripping done in postprocess_data().The base NCBI query URL used is: http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi
FEEDBACK
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AUTHOR - Jason Stajich
Email [email protected]APPENDIX
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _new
Title : new Usage : Function: the new way to make modules a little more lightweight Returns : Args :
get_params
Title : get_params
Usage : my %params = $self->get_params($mode)
Function: returns key,value pairs to be passed to NCBI database
for either 'batch' or 'single' sequence retrieval method
Returns : a key,value pair hash
Args : 'single' or 'batch' mode for retrieval
default_format
Title : default_format Usage : my $format = $self->default_format Function: returns default sequence format for this module Returns : string Args : none
get_request
Title : get_request Usage : my $url = $self->get_request Function: HTTP::Request Returns : Args : %qualifiers = a hash of qualifiers (ids, format, etc)
get_Stream_by_batch
Title : get_Stream_by_batch
Usage : $seq = $db->get_Stream_by_batch($ref);
Function: Retrieves Seq objects from Entrez 'en masse', rather than one
at a time. For large numbers of sequences, this is far superior
than get_Stream_by_id or get_Stream_by_acc.
Example :
Returns : a Bio::SeqIO stream object
Args : $ref : either an array reference, a filename, or a filehandle
from which to get the list of unique ids/accession numbers.
NOTE: deprecated API. Use get_Stream_by_id() instead.
get_Stream_by_query
Title : get_Stream_by_query
Usage : $seq = $db->get_Stream_by_query($query);
Function: Retrieves Seq objects from Entrez 'en masse', rather than one
at a time. For large numbers of sequences, this is far superior
to get_Stream_by_id and get_Stream_by_acc.
Example :
Returns : a Bio::SeqIO stream object
Args : An Entrez query string or a Bio::DB::Query::GenBank object.
It is suggested that you create a Bio::DB::Query::GenBank object and get
the entry count before you fetch a potentially large stream.
postprocess_data
Title : postprocess_data
Usage : $self->postprocess_data ( 'type' => 'string',
'location' => \$datastr );
Function: Process downloaded data before loading into a Bio::SeqIO. This
works for Genbank and Genpept, other classes should override
it with their own method.
Returns : void
Args : hash with two keys:
'type' can be 'string' or 'file'
'location' either file location or string reference containing data
request_format
Title : request_format
Usage : my ($req_format, $ioformat) = $self->request_format;
$self->request_format("genbank");
$self->request_format("fasta");
Function: Get/Set sequence format retrieval. The get-form will normally not
be used outside of this and derived modules.
Returns : Array of two strings, the first representing the format for
retrieval, and the second specifying the corresponding SeqIO format.
Args : $format = sequence format
redirect_refseq
Title : redirect_refseq Usage : $db->redirect_refseq(1) Function: simple getter/setter which redirects RefSeqs to use Bio::DB::RefSeq Returns : Boolean value Args : Boolean value (optional) Throws : 'unparseable output exception' Note : This replaces 'no_redirect' as a more straightforward flag to redirect possible RefSeqs to use Bio::DB::RefSeq (EBI interface) instead of retrieving the NCBI records
complexity
Title : complexity Usage : $db->complexity(3) Function: get/set complexity value Returns : value from 0-4 indicating level of complexity Args : value from 0-4 (optional); if unset server assumes 1 Throws : if arg is not an integer or falls outside of noted range above Note : From efetch docs, the complexity regulates the display: 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
strand
Title : strand Usage : $db->strand(1) Function: get/set strand value Returns : strand value if set Args : value of 1 (plus) or 2 (minus); if unset server assumes 1 Throws : if arg is not an integer or is not 1 or 2 Note : This differs from BioPerl's use of strand: 1 = plus, -1 = minus 0 = not relevant. We should probably add in some functionality to convert over in the future.
seq_start
Title : seq_start Usage : $db->seq_start(123) Function: get/set sequence start location Returns : sequence start value if set Args : integer; if unset server assumes 1 Throws : if arg is not an integer
seq_stop
Title : seq_stop Usage : $db->seq_stop(456) Function: get/set sequence stop (end) location Returns : sequence stop (end) value if set Args : integer; if unset server assumes 1 Throws : if arg is not an integer
Bio::DB::WebDBSeqI methods
Overriding WebDBSeqI method to help newbies to retrieve sequencesget_Stream_by_acc
Title : get_Stream_by_acc
Usage : $seq = $db->get_Stream_by_acc([$acc1, $acc2]);
Function: gets a series of Seq objects by accession numbers
Returns : a Bio::SeqIO stream object
Args : $ref : a reference to an array of accession numbers for
the desired sequence entries
Note : For GenBank, this just calls the same code for get_Stream_by_id()
_check_id
Title : _check_id Usage : Function: Returns : a Bio::DB::RefSeq reference or throws Args : $id(s), $string
delay_policy
Title : delay_policy
Usage : $secs = $self->delay_policy
Function: NCBI requests a delay of 3 seconds between requests. This method
implements that policy.
Returns : number of seconds to delay
Args : none
cookie
Title : cookie
Usage : ($cookie,$querynum) = $db->cookie
Function: return the NCBI query cookie, this information is used by
Bio::DB::GenBank in conjunction with efetch, ripped from
Bio::DB::Query::GenBank
Returns : list of (cookie,querynum)
Args : none
_parse_response
Title : _parse_response
Usage : $db->_parse_response($content)
Function: parse out response for cookie, this is a trimmed-down version
of _parse_response from Bio::DB::Query::GenBank
Returns : empty
Args : none
Throws : 'unparseable output exception'
no_redirect
Title : no_redirect
Usage : $db->no_redirect($content)
Function: DEPRECATED - Used to indicate that Bio::DB::GenBank instance retrieves
possible RefSeqs from EBI instead; default behavior is now to
retrieve directly from NCBI
Returns : None
Args : None
Throws : Method is deprecated in favor of positive flag method 'redirect_refseq'