The London Perl and Raku Workshop takes place on 26th Oct 2024. If your company depends on Perl, please consider sponsoring and/or attending.
 / 
BioPerl-1.007002
River stage two • 60 direct dependents • 65 total dependents
/ 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(['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: https://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

Support

Please direct usage questions or support issues to the mailing list:

bioperl-l@bioperl.org

rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible.

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.

https://github.com/bioperl/bioperl-live/issues

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 _

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 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 = $self->delay_policy
Function: NCBI requests a delay of 3 seconds between requests. This method
          implements that policy.
Returns : number of seconds to delay
Args    : none
Title   : cookie
Usage   : ($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'