Provided by: libbio-perl-perl_1.7.2-2_all bug


       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:


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AUTHOR - Jason Stajich



       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_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;
        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

   Bio::DB::WebDBSeqI methods
       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   : _check_id
         Usage   :
         Returns : a Bio::DB::RefSeq reference or throws
         Args    : $id(s), $string

         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
        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'