Bio::DB::NCBIHelper(3pm)

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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('[email protected]')
 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

cookie

 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'