Bio::DB::NCBIHelper(3)User Contributed Perl DocumentatioBio::DB::NCBIHelper(3)NAMEBio::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
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.
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
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 retrievign 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:
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 = $self->delay_policy
Function: return number of seconds to delay between calls to remote db
Returns : number of seconds to delay
Args : none
NOTE: NCBI requests a delay of 3 seconds between requests. This method
implements that policy.
cookie
Title : cookie
Usage : ($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'
no_redirect
Title : no_redirect
Usage : $db->no_redirect($content)
Function: 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'
perl v5.14.1 2011-07-22 Bio::DB::NCBIHelper(3)
