Reference

Bio::DB::SeqVersion::gi(3pm)

interface to NCBI Sequence Revision History page

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.

  [email protected]                  - General discussion
  http://bioperl.org/wiki/Mailing_lists  - About the mailing lists

Support

Please direct usage questions or support issues to the mailing list:

[email protected]

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

History