[Gmod-schema-cmts] schema/chado/load/bin new_bulk_load_gff3.PLS,1.5,1.6

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

Update of /cvsroot/gmod/schema/chado/load/bin
In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv14313/load/bin

Modified Files:
	new_bulk_load_gff3.PLS 
Log Message:
started work on handling CDS features, though I've yet to write the handle_CDS method


Index: new_bulk_load_gff3.PLS
===================================================================
RCS file: /cvsroot/gmod/schema/chado/load/bin/new_bulk_load_gff3.PLS,v
retrieving revision 1.5
retrieving revision 1.6
diff -C2 -d -r1.5 -r1.6
*** new_bulk_load_gff3.PLS	13 Apr 2006 20:39:17 -0000	1.5
--- new_bulk_load_gff3.PLS	21 Apr 2006 20:49:57 -0000	1.6
***************
*** 516,561 ****
  }
  
! 
! #######################################################
! # Load cache with existing synonym, dbxref, and
! # analysis records.  prevents failure of load if they
! # already existed.
! #
! #
! # I don't want to do this due to overhead issues
! #my %label = (
! #             #add more tables here.  key is tablename,
! #             #value is label to lookup by.
! #             analysis => 'name',
! #             synonym  => 'name',
! #             dbxref   => 'accession',
! #            );
! #
! #my $iterator;
! #
! #foreach my $table (keys %label){
! #  print STDERR "caching $table... ";
! #  my $class = 'Chado::'.ucfirst($table);
! #  $iterator = $class->retrieve_all();
! #  my $label = $label{$table};
! #  while(my $obj = $iterator->next()){
! #    $cache{$table}{$obj->$label} = $obj;
! #  }
! #  print STDERR "done!\n";
! #}
! #
! #
! # End load cache.
! #######################################################
! 
! 
! 
! ########################
! 
! #######################################################
! #prepare a bunch of sql queries to be used in the loop:
! #
! 
! $chado->organism_id($ORGANISM) or die "$ORGANISM organism not found in the database";
  
  $chado->file_handles();
--- 516,521 ----
  }
  
! $chado->organism_id($ORGANISM) 
!    or die "$ORGANISM organism not found in the database";
  
  $chado->file_handles();
***************
*** 579,589 ****
  warn "(This may take a while ...)\n";
  
! while(my $feature = $gffio->next_feature()){
  
    my $nextfeature    = $chado->nextfeature();
    my $nextfeatureloc = $chado->nextfeatureloc();
  
-   my $featuretype = $feature->type->name;
- 
    my $type           = $chado->get_type($featuretype);
    my ($src, $seqlen) = $chado->get_src_seqlen($feature);
--- 539,557 ----
  warn "(This may take a while ...)\n";
  
! my $feature_iterator;
! FEATURE:
! while(my $feature = $feature_iterator->next_feature || $gffio->next_feature){
! 
!   my $featuretype = $feature->type->name;
! 
!   if ($featuretype =~ /CDS/) {
!     #handle_CDS returns a feature iterator if it has a complete set
!     my $feature_iterator = $chado->handle_CDS($feature);
!     next FEATURE; 
!   }
  
    my $nextfeature    = $chado->nextfeature();
    my $nextfeatureloc = $chado->nextfeatureloc();
  
    my $type           = $chado->get_type($featuretype);
    my ($src, $seqlen) = $chado->get_src_seqlen($feature);
***************
*** 634,638 ****
    }
  
-   #FIXME potential $chado->nextfeature bug
    if ($ANALYSIS 
        && $featuretype =~ /match/  
--- 602,605 ----