[Gmod-schema-cmts] schema/chado/load/bin bulk_load_gff3.PLS,1.18,1.19

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

Update of /cvsroot/gmod/schema/chado/load/bin
In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv19694

Modified Files:
	bulk_load_gff3.PLS 
Log Message:
Fixed (I think) non-reserved tag loading


Index: bulk_load_gff3.PLS
===================================================================
RCS file: /cvsroot/gmod/schema/chado/load/bin/bulk_load_gff3.PLS,v
retrieving revision 1.18
retrieving revision 1.19
diff -C2 -d -r1.18 -r1.19
*** bulk_load_gff3.PLS	28 Apr 2005 20:16:41 -0000	1.18
--- bulk_load_gff3.PLS	28 Apr 2005 21:09:52 -0000	1.19
***************
*** 101,131 ****
  =over
  
- =item Reference sequences
- 
- This loader requires that the reference sequence features be already
- loaded into the database (for instance, by using gmod_load_gff3.pl).
- Future versions of this bulk loader will not have this restriction.
- 
  =item Parents/children order
  
  Parents must come before children in the GFF file.
  
! =item Several GFF tags (both reserved and custom) not supported
! 
! These include:
  
! =over
  
! =item Gap
  
! =item Any custom (ie, lowercase-first) tag is supported, provided they already have an entry in the cvterm table
  
- =back
  
! =item No sequences
  
! This loader does not load DNA sequences, though chromosome sequences
! can be loaded with gmod_load_gff3 when the reference sequence features
! are loaded.
  
  =item Analysis
--- 101,130 ----
  =over
  
  =item Parents/children order
  
  Parents must come before children in the GFF file.
  
! =item The Gap GFF reserved tag not supported
  
! Just flat out not supported--if you would like to see support, contact 
! the authors
  
! =item Any custom (ie, lowercase-first) tag is supported
  
! Custom tags are supported, provided they already have an entry in the cvterm table.
! For example, if you have a custom tab, 'orf_classification', you need
! an entry in the dbxref and cvterm tables something like this:
  
  
!   INSERT INTO dbxref (db_id,accession)
!     VALIES ( (SELECT db_id FROM db WHERE name='null'),
!              'autocreated:orf_classification');
!   INSERT INTO cvterm (name,dbxref_id,cv_id) 
!     VALUES ('orf_classification',
!              (SELECT cv_id FROM cv WHERE name='local'),
!              (SELECT dbxref_id FROM dbxref WHERE accession='autocreated:orf_classification'));
  
! You may also need to create an appropriate controlled vocabulary
! in the cv table and an entry in the db table.
  
  =item Analysis
***************
*** 583,591 ****
    if ( @unreserved_tags > 0 ) {
      foreach my $tag (@unreserved_tags) {
-       next unless (ref($feature->annotation) eq 'Bio::Annotation::SimpleValue');
        next if $tag eq 'source';
        next if $tag eq 'phase';
        next if $tag eq 'seq_id';
!       my @values = map {$_->value} $feature->annotation->get_Annotations($tag);
  
        unless ($auto_cv_id){
--- 582,591 ----
    if ( @unreserved_tags > 0 ) {
      foreach my $tag (@unreserved_tags) {
        next if $tag eq 'source';
        next if $tag eq 'phase';
        next if $tag eq 'seq_id';
!       next if $tag eq 'type';
!       next if $tag eq 'score';
!       next if $tag eq 'dbxref';
  
        unless ($auto_cv_id){
***************
*** 611,615 ****
    INSERT INTO cvterm (cv_id,name,dbxref_id)
      VALUES ((select cv_id from cv where name='autocreated'), '$tag',
!             (select dbxref_id from dbxref where accession='autocreated:$tag');
  
  and then rerun this loader.  You other main option is to 
--- 611,615 ----
    INSERT INTO cvterm (cv_id,name,dbxref_id)
      VALUES ((select cv_id from cv where name='autocreated'), '$tag',
!             (select dbxref_id from dbxref where accession='autocreated:$tag'));
  
  and then rerun this loader.  You other main option is to