• NAME - BioSQL-base.pm
• SYNOPSIS
• DESCRIPTION
• AUTHOR Hilmar Lapp
  • store_seq
  • delete_seq
  • delete_biodatabase
  • db
  • dbharness

NAME - BioSQL-base.pm

SYNOPSIS

    # synopsis goes here

DESCRIPTION

This modules provides methods to insert and remove the parent entities needed by many (probably all) of the different tests for child entities.

AUTHOR Hilmar Lapp

Email hlapp at gnf.org

store_seq

 Title   : store_seq
 Usage   : $seq = $biosql->store_seq($stream, "rodent");
 Function: Reads the next sequence from the given Bio::SeqIO stream and
           stores it under the namespace given by 2nd argument.
 Returns : The sequence object that was stored, with the PK in
           $seq->primary_id(), and undef if there was no sequence in the stream
 Args    : SeqIO stream (object) and namespace (a string)

delete_seq

 Title   : delete_seq
 Usage   : $ok = $biosql->delete_seq($seq);
 Function: Deletes the given sequence from the database.
 Returns : True for success and false otherwise.
 Args    : A Bio::PrimarySeqI compliant object

delete_biodatabase

 Title   : delete_biodatabase
 Usage   : $ok = $biosql->delete_biodatabase($biodatabase);
 Function: Deletes the given biodatabase (namespace) from the database.
 Returns : True for success and false otherwise.
 Args    : namespace (a string)

db

 Title   : db
 Usage   : $dbadaptor = $biosql->db();
 Function: 
 Returns : The DBAdaptor object in use to wrap the BioSQL database.
 Args    : On set (optional), the DBAdaptor object to be used.

dbharness

 Title   : dbharness
 Usage   : $dbharness = $biosql->dbharness();
 Function: 
 Returns : The DBTestHarness object in use.
 Args    : On set (optional), the DBTestHarness object to be used.