Bio::DB::SeqVersion::gUser Contributed Perl DocumentBio::DB::SeqVersion::gi(3)NAMEBio::DB::SeqVersion::gi - interface to NCBI Sequence Revision History
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SYNOPSIS
Do not use this module directly, use Bio::DB::SeqVersion.
use Bio::DB::SeqVersion;
my $query = Bio::DB::SeqVersion->new(-type => 'gi');
# all GIs, which will include the GI used to query
my @all_gis = $query->get_all(2);
# the most recent GI, which may or may not be the GI used to query
my $live_gi = $query->get_recent(2);
# get all the visible data on the Sequence Revision page
my $array_ref = $query->get_history(11111111);
These methods can also take accession numbers as arguments, just like
the Sequence Revision page itself.
DESCRIPTION
All sequence entries at GenBank are identified by a pair of
identifiers, an accession and a numeric identifier, and this number is
frequently called a GI number (GenInfo Identifier). The accession is
stable, but each new version of the sequence entry for the accession
receives a new GI number (see
<http://www.ncbi.nlm.nih.gov/Sitemap/sequenceIDs.html> for more
information on GenBank identifiers). One accession can have one or more
GI numbers and the highest of these is the most recent, or "live", GI.
Information on an accession and its associated GI numbers is available
at the Sequence Revision History page at NCBI,
<http://www.ncbi.nlm.nih.gov/entrez/sutils/girevhist.cgi>, this
information is not available in file format. This module queries the
Web page and retrieves GI numbers and related data given an accession
(e.g. NP_111111, A11111, P12345) or a GI number (e.g. 2, 11111111) as
query.
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 - Brian Osborne
Email < osborne at optonline dot net >
CONTRIBUTORS
Torsten Seemann - torsten.seemann AT infotech.monash.edu.au
APPENDIX
The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _
new
Title : new
Usage : $gb = Bio::DB::SeqVersion::gi->new
Function: Creates a new query object
Returns : New query object
get_all
Title : get_all
Usage : my @gis = $q->get_all(2)
Function: Get all GI numbers given a GI number
Returns : An array of GI numbers, earliest GI number is the 0 element
Args : A single GI number (string)
get_recent
Title : get_recent
Usage : my $newest_gi = $q->get_recent(2)
Function: Get most recent GI given a single GI
Returns : String
Args : A single GI number (string)
get_history
Title : get_history
Usage : my $ref = $query_obj->get_history()
Function: Queries the NCBI Revision page, gets the data from the HTML table
Returns : Reference to an array of arrays where element 0 refers to the most
recent version and the last element refers to the oldest version.
In the second dimension the elements are:
0 GI number
1 Version
2 Update Date
3 Status
For example, to get the GI number of the first version:
$ref->[$#{@$ref}]->[0]
To get the Update Date of the latest version:
$ref->[0]->[2]
Args : One identifier (string)
_get_request
Title : _get_request
Usage : my $url = $self->_get_request
Function: GET using NCBI Revision page URL, uses Root::HTTPget
Returns : HTML
Args : One identifier (string)
_process_data
Title : _process_data
Usage : $self->_process_data($html)
Function: extract data from HTML
Args : HTML from Revision History page
Returns : reference to an array of arrays
perl v5.14.1 2011-07-22 Bio::DB::SeqVersion::gi(3)
