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_seq_stream

 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

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

email

 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.

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()

delay_policy

  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

_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'