/ 
bioperl-1.5.2_005-RCb
/ Bio::DB::NCBIHelper

NAME

Bio::DB::NCBIHelper - A collection of routines useful for queries to NCBI databases.

SYNOPSIS

# Do not use this module directly.

# get a Bio::DB::NCBIHelper object somehow
my $seqio = $db->get_Stream_by_acc(['MUSIGHBA1']);
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

Mailing Lists

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@bioperl.org                  - General discussion
http://bioperl.org/wiki/Mailing_lists  - About the mailing lists

Reporting Bugs

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/

AUTHOR - Jason Stajich

Email jason@bioperl.org

APPENDIX

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

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/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
          than get_Stream_by_[id/acc]().
Example :
Returns : a Bio::SeqIO stream object
Args    : $query :   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
 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

Bio::DB::WebDBSeqI methods

Overriding WebDBSeqI method to help newbies to retrieve sequences

get_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: return number of seconds to delay between calls to remote db
Returns : number of seconds to delay
Args    : none

NOTE: NCBI requests a delay of 3 seconds between requests.  This method
      implements that policy.
Title   : cookie
Usage   : ($cookie,$querynum) = $db->cookie
Function: return the NCBI query cookie
Returns : list of (cookie,querynum)
Args    : none

NOTE: this information is used by Bio::DB::GenBank in conjunction with efetch.

_parse_response

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