[Gmod-schema-cmts] schema/chado/load/bin bulk_load_gff3.PLS,1.48,1.49

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

Update of /cvsroot/gmod/schema/chado/load/bin
In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv6731/load/bin

Modified Files:
	bulk_load_gff3.PLS 
Log Message:
fixed for the case where the reference feature (ie, column 1) is given as '.'
(at least, I think it is fixed...)


Index: bulk_load_gff3.PLS
===================================================================
RCS file: /cvsroot/gmod/schema/chado/load/bin/bulk_load_gff3.PLS,v
retrieving revision 1.48
retrieving revision 1.49
diff -C2 -d -r1.48 -r1.49
*** bulk_load_gff3.PLS	16 Sep 2005 16:20:40 -0000	1.48
--- bulk_load_gff3.PLS	12 Oct 2005 15:10:50 -0000	1.49
***************
*** 805,809 ****
  
  #don't write a featureloc entry for srcfeatures
!   unless ($src == $nextfeature) {
  #need to convert from base to interbase coords
      my $start = $feature->start eq '.' ? '\N' : ($feature->start - 1);
--- 805,809 ----
  
  #don't write a featureloc entry for srcfeatures
!   unless ($src eq '\N' or $src == $nextfeature) {
  #need to convert from base to interbase coords
      my $start = $feature->start eq '.' ? '\N' : ($feature->start - 1);
***************
*** 1432,1474 ****
    my $dbh = shift;
  
!   $dbh->do("ALTER TABLE feature DROP CONSTRAINT feature_c1");
!   $dbh->do("DROP INDEX feature_name_ind1");
!   $dbh->do("DROP INDEX feature_idx1");
!   $dbh->do("DROP INDEX feature_idx2");
!   $dbh->do("DROP INDEX feature_idx3");
!   $dbh->do("DROP INDEX feature_idx4");
!   $dbh->do("DROP INDEX feature_idx5");
  
!   $dbh->do("ALTER TABLE featureloc DROP CONSTRAINT featureloc_c1");
!   $dbh->do("DROP INDEX featureloc_idx1");
!   $dbh->do("DROP INDEX featureloc_idx2");
!   $dbh->do("DROP INDEX featureloc_idx3");
  
!   $dbh->do("ALTER TABLE feature_dbxref DROP CONSTRAINT feature_dbxref_c1");
!   $dbh->do("DROP INDEX feature_dbxref_idx1");
!   $dbh->do("DROP INDEX feature_dbxref_idx2");
  
!   $dbh->do("ALTER TABLE feature_relationship DROP CONSTRAINT feature_relationship_c1");
!   $dbh->do("DROP INDEX feature_relationship_idx1");
!   $dbh->do("DROP INDEX feature_relationship_idx2");
!   $dbh->do("DROP INDEX feature_relationship_idx3");
  
!   $dbh->do("ALTER TABLE feature_cvterm DROP CONSTRAINT feature_cvterm_c1");
!   $dbh->do("DROP INDEX feature_cvterm_idx1");
!   $dbh->do("DROP INDEX feature_cvterm_idx2");
!   $dbh->do("DROP INDEX feature_cvterm_idx3");
  
!   $dbh->do("ALTER TABLE synonym DROP CONSTRAINT synonym_c1");
!   $dbh->do("DROP INDEX synonym_idx1");
!   $dbh->do("DROP INDEX synonym_idx2");
  
!   $dbh->do("ALTER TABLE feature_synonym DROP CONSTRAINT feature_synonym_c1");
!   $dbh->do("DROP INDEX feature_synonym_idx1");
!   $dbh->do("DROP INDEX feature_synonym_idx2");
!   $dbh->do("DROP INDEX feature_synonym_idx3");
  
!   $dbh->do("ALTER TABLE analysisfeature DROP CONSTRAINT analysisfeature_c1"); 
!   $dbh->do("DROP INDEX analysisfeature_idx1");
!   $dbh->do("DROP INDEX analysisfeature_idx2");
  }
  
--- 1432,1474 ----
    my $dbh = shift;
  
!   $dbh->do("ALTER TABLE feature DROP CONSTRAINT feature_c1") or die "$!";
!   $dbh->do("DROP INDEX feature_name_ind1") or die "$!";
!   $dbh->do("DROP INDEX feature_idx1") or die "$!";
!   $dbh->do("DROP INDEX feature_idx2") or die "$!";
!   $dbh->do("DROP INDEX feature_idx3") or die "$!";
!   $dbh->do("DROP INDEX feature_idx4") or die "$!";
!   $dbh->do("DROP INDEX feature_idx5") or die "$!";
  
!   $dbh->do("ALTER TABLE featureloc DROP CONSTRAINT featureloc_c1") or die "$!";
!   $dbh->do("DROP INDEX featureloc_idx1") or die "$!";
!   $dbh->do("DROP INDEX featureloc_idx2") or die "$!";
!   $dbh->do("DROP INDEX featureloc_idx3") or die "$!";
  
!   $dbh->do("ALTER TABLE feature_dbxref DROP CONSTRAINT feature_dbxref_c1") or die "$!";
!   $dbh->do("DROP INDEX feature_dbxref_idx1") or die "$!";
!   $dbh->do("DROP INDEX feature_dbxref_idx2") or die "$!";
  
!   $dbh->do("ALTER TABLE feature_relationship DROP CONSTRAINT feature_relationship_c1") or die "$!";
!   $dbh->do("DROP INDEX feature_relationship_idx1") or die "$!";
!   $dbh->do("DROP INDEX feature_relationship_idx2") or die "$!";
!   $dbh->do("DROP INDEX feature_relationship_idx3") or die "$!";
  
!   $dbh->do("ALTER TABLE feature_cvterm DROP CONSTRAINT feature_cvterm_c1") or die "$!";
!   $dbh->do("DROP INDEX feature_cvterm_idx1") or die "$!";
!   $dbh->do("DROP INDEX feature_cvterm_idx2") or die "$!";
!   $dbh->do("DROP INDEX feature_cvterm_idx3") or die "$!";
  
!   $dbh->do("ALTER TABLE synonym DROP CONSTRAINT synonym_c1") or die "$!";
!   $dbh->do("DROP INDEX synonym_idx1") or die "$!";
!   $dbh->do("DROP INDEX synonym_idx2") or die "$!";
  
!   $dbh->do("ALTER TABLE feature_synonym DROP CONSTRAINT feature_synonym_c1") or die "$!";
!   $dbh->do("DROP INDEX feature_synonym_idx1") or die "$!";
!   $dbh->do("DROP INDEX feature_synonym_idx2") or die "$!";
!   $dbh->do("DROP INDEX feature_synonym_idx3") or die "$!";
  
!   $dbh->do("ALTER TABLE analysisfeature DROP CONSTRAINT analysisfeature_c1") or die "$!";
!   $dbh->do("DROP INDEX analysisfeature_idx1") or die "$!";
!   $dbh->do("DROP INDEX analysisfeature_idx2") or die "$!";
  }