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Manual Reference Pages  -  BIO::DB::NCBIHELPER (3)

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NAME

Bio::DB::NCBIHelper - A collection of routines useful for queries to NCBI databases.

CONTENTS

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: 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.



  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_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 BioPerls 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: NCBI requests a delay of 3 seconds between requests. This method
            implements that policy.
  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



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