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Bio::DB::NCBIHelper.3pm
Langue: en
Version: 2008-01-11 (mandriva - 01/05/08)
Section: 3 (Bibliothèques de fonctions)
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
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.orgAPPENDIX
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
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'
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