[Gmod-schema-cmts] schema/chado/load/bin load_gff3.PLS,1.55,1.56

[Scott C. <sco...@us...>]

Update of /cvsroot/gmod/schema/chado/load/bin
In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv27591/load/bin

Modified Files:
	load_gff3.PLS 
Log Message:
added the ability to specify an ontology on the command line


Index: load_gff3.PLS
===================================================================
RCS file: /cvsroot/gmod/schema/chado/load/bin/load_gff3.PLS,v
retrieving revision 1.55
retrieving revision 1.56
diff -C2 -d -r1.55 -r1.56
*** load_gff3.PLS	30 Dec 2004 03:56:20 -0000	1.55
--- load_gff3.PLS	10 Jan 2005 21:28:09 -0000	1.56
***************
*** 41,52 ****
  can be abbreviated to one letter.
  
!   --cache      (optional, defaults to 1000)         The number of features to cache before
                                                      committing to the database
!   --force      (optional, defaults to false)        Force the file to load, even if it has already
                                                      been loaded before
    --gfffile    (required)                           The name of the GFF3 file
    --organism   (optional, defaults to 'Human')      Common name of the organism
!   --srcdb      (optional, defaults to 'DB:refseq')  The name of the source database
!   --uniquename (optional                            The tag to use to provide feature.uniquename
  
  =head1 DESCRIPTION
--- 41,61 ----
  can be abbreviated to one letter.
  
!   --cache      (optional, defaults to 1000)         The number of features
!                                                     to cache before
                                                      committing to the database
!   --force      (optional, defaults to false)        Force the file to load,
!                                                     even if it has already
                                                      been loaded before
    --gfffile    (required)                           The name of the GFF3 file
    --organism   (optional, defaults to 'Human')      Common name of the organism
!   --srcdb      (optional, defaults to 'DB:refseq')  The name of the source
!                                                     database
!   --uniquename (optional)                           The tag to use to provide
!                                                     feature.uniquename
!   --ontology   (optional)                           Ontology to use instead
!                                                     of the default.  Note that
!                                                     this should be detected
!                                                     automatically, but isn't
!                                                     yet.
  
  =head1 DESCRIPTION
***************
*** 156,160 ****
  warn $TMPGFF if DEBUG;
  
! my ( $ORGANISM, $SRC_DB, $GFFFILE, $UNIQUENAME, $CACHE_SIZE, $FORCE_LOAD );
  my ( $progress, $next_update, $linecount ) =
    ( undef, undef, undef );    #progressbar;
--- 165,169 ----
  warn $TMPGFF if DEBUG;
  
! my ( $ORGANISM,$SRC_DB,$GFFFILE,$UNIQUENAME,$CACHE_SIZE,$FORCE_LOAD,$ONTOLOGY );
  my ( $progress, $next_update, $linecount ) =
    ( undef, undef, undef );    #progressbar;
***************
*** 725,728 ****
--- 734,738 ----
          'cache:s'    => \$CACHE_SIZE,
          'force'      => \$FORCE_LOAD,
+         'ontology:s' => \$ONTOLOGY,
        )
        or ( system( 'pod2text', $0 ), exit -1 );
***************
*** 731,734 ****
--- 741,745 ----
      $SRC_DB     ||= 'DB:refseq';
      $CACHE_SIZE ||= 1000;
+     $ONTOLOGY   ||= 'Sequence Ontology Feature Annotation';
  
      die "\nYou must specify a GFF file\n" unless $GFFFILE;
***************
*** 779,784 ****
          }
      );
!     ($so) = Chado::Cv->search( { name => 'Sequence Ontology Feature Annotation' } );
!     die "Unable to find SOFA in cv table; that is a pretty big problem" unless $so;
  
      # find needed cvterm and other pieces of information
--- 790,795 ----
          }
      );
!     ($so) = Chado::Cv->search( { name => $ONTOLOGY } );
!     die "Unable to find $ONTOLOGY in cv table; that is a pretty big problem" unless $so;
  
      # find needed cvterm and other pieces of information