| Bio::DB::NCBIHelper(3pm) | User Contributed Perl Documentation | Bio::DB::NCBIHelper(3pm) |
Bio::DB::NCBIHelper - A collection of routines useful for queries to NCBI databases.
# 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
}
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
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
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.
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
Email jason@bioperl.org
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
Title : new Usage : Function: the new way to make modules a little more lightweight Returns : Args :
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
Title : default_format Usage : my $format = $self->default_format Function: returns default sequence format for this module Returns : string Args : none
Title : get_request Usage : my $url = $self->get_request Function: HTTP::Request Returns : Args : %qualifiers = a hash of qualifiers (ids, format, etc)
Title : get_seq_stream
Usage : my $seqio = $self->get_seq_stream(%qualifiers)
Function: builds a url and queries a web db
Returns : a Bio::SeqIO stream capable of producing sequence
Args : %qualifiers = a hash qualifiers that the implementing class
will process to make a url suitable for web querying
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.
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.
Title : postprocess_data
Usage : $self->postprocess_data ( 'type' => 'string',
'location' => \$datastr );
Function: Process downloaded data before loading into a Bio::SeqIO. This
works for Genbank and Genpept, other classes should override
it with their own method.
Returns : void
Args : hash with two keys:
'type' can be 'string' or 'file'
'location' either file location or string reference containing data
Title : request_format
Usage : my ($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
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
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
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.
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
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
Title : email
Usage : $db->email('foo@bar.edu')
Function: get/set email value
Returns : email (string) or undef
Args : string with a valid email address; note we do not vallidate this
currently!
Throws : if arg is not an integer or falls outside of noted range above
Note : This is required if you wish to speed up mulltiple requests faster
than 4s per request.
Overriding WebDBSeqI method to help newbies to retrieve sequences
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()
Title : delay_policy
Usage : $secs = $self->delay_policy
Function: NCBI requests a delay of 4 seconds between requests unless email is
provided. This method implements a 4 second delay; use 'delay()' to
override, though understand if no email is provided we are not
responsible for users being IP-blocked by NCBI
Returns : number of seconds to delay
Args : none
Title : cookie
Usage : ($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
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'
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'
| 2022-02-24 | perl v5.34.0 |