table of contents
| Bio::DB::SeqVersion::gi(3pm) | User Contributed Perl Documentation | Bio::DB::SeqVersion::gi(3pm) |
NAME¶
Bio::DB::SeqVersion::gi - interface to NCBI Sequence Revision History page
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 <https://www.ncbi.nlm.nih.gov/genbank/sequenceids/#historical_note> 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, <https://www.ncbi.nlm.nih.gov/genbank/sequencerevisionhistory/>, 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:
https://github.com/bioperl/bioperl-live/issues
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_status¶
Title : get_status Usage : my $newest_gi = $q->get_status(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
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)
Note : Status of the GI was returned here previously as the last element in
the row of elemnts above; however the status is currently only
returned for the GI requested (e.g. a single value). One can get
the status for this using the get_status() method above
_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
| 2018-10-27 | perl v5.26.2 |