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(['MUSIGHBA1']); 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 the postprocess_data manpage(). The NCBI query URLs used are http://www.ncbi.nlm.nih.gov as the base URL, /cgi-bin/Entrez/qserver.cgi as the query interface for batch mode, and /entrez/utils/qmap.cgi for single-query mode.

Mailing Lists
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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 email or the web: bioperl-bugs@bio.perl.org http://bio.perl.org/bioperl-bugs/ Email jason@chg.mc.duke.edu 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.

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 NCBI databases."