[Nelsonlab-cmts] libnelson/Pg/celsius/bin gecIDsync,1.1,1.2

[<all...@su...>]

Update of /cvsroot/libnelson/Pg/celsius/bin
In directory sumo.genetics.ucla.edu:/tmp/cvs-serv8931/bin

Modified Files:
	gecIDsync 
Log Message:
now loads annotations to annot.allenday_gec


Index: gecIDsync
===================================================================
RCS file: /cvsroot/libnelson/Pg/celsius/bin/gecIDsync,v
retrieving revision 1.1
retrieving revision 1.2
diff -C2 -d -r1.1 -r1.2
*** gecIDsync	31 Jan 2006 01:14:42 -0000	1.1
--- gecIDsync	17 Feb 2006 02:15:47 -0000	1.2
***************
*** 9,13 ****
  
  my $dbh = DBI->connect('dbi:Pg:dbname=chado-celsius;host=soleus.ctrl.ucla.edu','','');
! $dbh->do('SET search_path TO cel, public');
  
  my $select1_sth = $dbh->prepare('SELECT cel_id FROM cel_dbxref, dbxref WHERE cel_dbxref.dbxref_id = dbxref.dbxref_id AND dbxref.accession LIKE ?');
--- 9,13 ----
  
  my $dbh = DBI->connect('dbi:Pg:dbname=chado-celsius;host=soleus.ctrl.ucla.edu','','');
! $dbh->do('SET search_path TO cel, annot, public');
  
  my $select1_sth = $dbh->prepare('SELECT cel_id FROM cel_dbxref, dbxref WHERE cel_dbxref.dbxref_id = dbxref.dbxref_id AND dbxref.accession LIKE ?');
***************
*** 16,19 ****
--- 16,20 ----
  my $insert1_sth = $dbh->prepare('INSERT INTO dbxref (db_id, accession) VALUES ((SELECT db_id FROM db WHERE name = ?),?)');
  my $insert2_sth = $dbh->prepare('INSERT INTO cel_dbxref (cel_id, dbxref_id) VALUES (?,?)');
+ my $insert3_sth = $dbh->prepare('INSERT INTO annot.allenday_gec (biomaterial_id, type_id) VALUES (?,(SELECT c.cvterm_id FROM cvterm AS c, dbxref AS x, db AS d WHERE c.dbxref_id = x.dbxref_id AND x.db_id = d.db_id AND x.accession = ? AND d.name = ?))');
  
  my @files = $dom->getElementsByTagName('file');
***************
*** 41,44 ****
--- 42,52 ----
    ( $x ) = $select2_sth->fetchrow_array();
    $insert2_sth->execute( $c, $x );
+ 
+   my @annots = $file->getElementsByTagName('annotation');
+   foreach my $annot ( @annots ) {
+     my $accession = $annot->getAttribute( 'accession' );
+     my ( $db, $acc ) = $accession =~ m/^(.+?):(.+?)$/;
+     $insert3_sth->execute( $c, $acc, $db );
+   }
  }