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