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Bio::DB::NCBIHelper.3pm

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(['MUSIGHBA1']);
  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.

   http://bugzilla.open-bio.org/
 
 

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 _

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/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
             than get_Stream_by_[id/acc]().
   Example :
   Returns : a Bio::SeqIO stream object
   Args    : $query :   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
  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 retrievign 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:
 
     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
 
 

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: return number of seconds to delay between calls to remote db
   Returns : number of seconds to delay
   Args    : none
 
   NOTE: NCBI requests a delay of 3 seconds between requests.  This method
         implements that policy.
 
 

cookie

  Title   : cookie
  Usage   : ($cookie,$querynum) = $db->cookie
  Function: return the NCBI query cookie
  Returns : list of (cookie,querynum)
  Args    : none
 
 

NOTE: this information is used by Bio::DB::GenBank in conjunction with efetch.

_parse_response

  Title   : _parse_response
  Usage   : $db->_parse_response($content)
  Function: parse out response for cookie
  Returns : empty
  Args    : none
  Throws  : 'unparseable output exception'
 
 

no_redirect

  Title   : no_redirect
  Usage   : $db->no_redirect($content)
  Function: 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'