whole new rewrite

misc-scripts/xref_mapping/XrefParser/MGI_curated_transcriptParser.pm

@@ -31,46 +31,29 @@ sub run_script {
 
   my ($type, $my_args) = split(/:/,$file);
   
-  my $cuser = "ensro";
-  my $chost = "";
-  my $cport = "3306";
-  my $cdbname = "";
-  my $cpass;
-
-  my $vuser = "ensro";
-  my $vhost = "";
-  my $vport = "3306";
-  my $vdbname = "";
-  my $vpass;
-
-  if($my_args =~ /chost[=][>](\S+?)[,]/){
-    $chost = $1;
+  my $user  ="ensro";
+  my $host;
+  my $port;
+  my $dbname;
+  my $pass;
+
+  if($my_args =~ /host[=][>](\S+?)[,]/){
+    $host = $1;
   }
-  if($my_args =~ /cport[=][>](\S+?)[,]/){
-    $cport =  $1;
+  if($my_args =~ /port[=][>](\S+?)[,]/){
+    $port =  $1;
   }
-  if($my_args =~ /cdbname[=][>](\S+?)[,]/){
-    $cdbname = $1;
+  if($my_args =~ /dbname[=][>](\S+?)[,]/){
+    $dbname = $1;
   }
-  if($my_args =~ /cpass[=][>](\S+?)[,]/){
-    $cpass = $1;
+  if($my_args =~ /pass[=][>](\S+?)[,]/){
+    $pass = $1;
   }
-
-  if($my_args =~ /vhost[=][>](\S+?)[,]/){
-    $vhost = $1;
-  }
-  if($my_args =~ /vport[=][>](\S+?)[,]/){
-    $vport =  $1;
-  }
-  if($my_args =~ /vdbname[=][>](\S+?)[,]/){
-    $vdbname = $1;
-  }
-  if($my_args =~ /vpass[=][>](\S+?)[,]/){
-    $vpass = $1;
+  if($my_args =~ /user[=][>](\S+?)[,]/){
+    $user = $1;
   }
 
-
-  my $xref_count = 0;
+  print "Using $host $dbname for Vega\n";
 
 
   my $clone_source_id =
@@ -78,104 +61,61 @@ sub run_script {
   my $curated_source_id =
     $self->get_source_id_for_source_name('MGI_curated_transcript');
  
-  my %name_to_mgi_number = %{ $self->get_label_to_acc( "MGI", $species_id ) };
-  my %name_to_mgi_desc = %{ $self->get_label_to_desc( "MGI", $species_id, "descriptions") };
+  my $sql = 'select tsi.stable_id, x.display_label from xref x, object_xref ox , transcript_stable_id tsi, external_db e where e.external_db_id = x.external_db_id and x.xref_id = ox.xref_id and tsi.transcript_id = ox.ensembl_id and e.db_name like ?';
 
-  my $core_sql = 'select tsi.stable_id, x.dbprimary_acc from transcript_stable_id tsi, transcript t, object_xref ox, xref x, external_db e where tsi.transcript_id = t.transcript_id and ox.ensembl_id = t.transcript_id and ox.ensembl_object_type = "Transcript" and ox.xref_id = x.xref_id and x.external_db_id = e.external_db_id and e.db_name like "%OTTT"';
 
-  my $vega_sql = 'select x.dbprimary_acc, x.display_label from xref x, external_db e where  x.external_db_id = e.external_db_id and e.db_name like "Vega_transcript" and display_label not like "OTT%"';
-  
   my %ott_to_vega_name;
   my %ott_to_enst;
   
-  my $dbi2 = $self->dbi2($chost, $cport, $cuser, $cdbname, $cpass);
+  my $dbi2 = $self->dbi2($host, $port, $user, $dbname, $pass);
   if(!defined($dbi2)){
     return 1;
   }
   
 
-  my $sth = $dbi2->prepare($core_sql); 
-  $sth->execute() or croak( $dbi2->errstr() );
+  my $sth = $dbi2->prepare($sql);   # funny number instead of stable id ?????
+  $sth->execute("Vega_transcript") or croak( $dbi2->errstr() );
   while ( my @row = $sth->fetchrow_array() ) {
-    $ott_to_enst{$row[1]} = $row[0];
+    $ott_to_vega_name{$row[0]} = $row[1];
   }
   $sth->finish;
-  
-  my $dbi3 = $self->dbi2($vhost, $vport, $vuser, $vdbname, $vpass);
-  if(!defined($dbi3)){
-    return 1;
+
+  $sth = $dbi2->prepare($sql);   # funny number instead of stable id ?????
+  $sth->execute("ENST_CDS") or croak( $dbi2->errstr() );
+  while ( my @row = $sth->fetchrow_array() ) {
+    $ott_to_enst{$row[0]} = $row[1];
   }
-  
-  
-  $sth = $dbi3->prepare($vega_sql); 
-  $sth->execute() or croak( $dbi3->errstr() );
+  $sth->finish;
+
+  $sth = $dbi2->prepare($sql);
+  $sth->execute("ENST_ident") or croak( $dbi2->errstr() );
   while ( my @row = $sth->fetchrow_array() ) {
-    # [0] OTTMUST...,   [1] Mrpl15-001 etc 
-    my $desc= "";
-    if(defined($ott_to_enst{$row[0]})){
+    $ott_to_enst{$row[0]} = $row[1];
+  }
+  $sth->finish;
+
+
+  my $xref_count = 0;
+
+  foreach my $ott (keys %ott_to_enst){
+    if(defined($ott_to_vega_name{$ott})){
       my $id = $curated_source_id;
-      my $name = $row[1];
-      $name =~ s/^WU://;
-      my $prim_acc = $name;
-      my $stable_id = $ott_to_enst{$row[0]};
+      my $name  = $ott_to_vega_name{$ott};
+      $name =~ s/WU://;
       if($name =~ /[.]/){
-        $id = $clone_source_id;
+	$id = $clone_source_id;
       }
-      else{
-	my $mgi_name = $name;
-	# find MGI name 
-	my($mgi_bit, $num) = split(/-\d\d\d/,$name);
-	if(defined($name_to_mgi_number{$mgi_bit})){
-	  $prim_acc = $name_to_mgi_number{$mgi_bit};
-	}
-	if(defined($name_to_mgi_desc{$mgi_bit})){
-	  $desc = $name_to_mgi_desc{$mgi_bit};
-	}
-	else{
-	  print "$mgi_bit has no description\n" if($verbose);
-	}
-      }
-      my $xref_id = $self->add_xref($prim_acc, "" , $name , $desc, $id, $species_id, "DIRECT");
+      my $xref_id = $self->add_xref($name, "" , $name , "", $id, $species_id, "DIRECT");
       $xref_count++;
       
-      $self->add_direct_xref($xref_id, $ott_to_enst{$row[0]}, "Transcript", "");
-
-      
+      $self->add_direct_xref($xref_id, $ott_to_enst{$ott}, "transcript", "");
     }
   }
 
   print "$xref_count direct xrefs succesfully parsed\n" if($verbose);
-
-  #Finally add the synonyms:-
-  my $synonym_sql = (<<SYNO);
-SELECT x2.xref_id, s.synonym
-  FROM synonym s
-    INNER JOIN xref x1 ON  x1.xref_id = s.xref_id
-    INNER JOIN xref x2 ON  x2.accession = x1.accession 
-    INNER JOIN source s1 ON s1.source_id = x1.source_id
-    INNER JOIN source s2 ON s2.source_id = x2.source_id    
-      WHERE x2.xref_id != x1.xref_id
-	AND s2.name = "MGI_curated_transcript" 
-        AND s1.name = "MGI" 
-        AND s1.priority_description = "descriptions"
-SYNO
- 
-
-  $sth = $self->dbi()->prepare($synonym_sql);
-  
-  $sth->execute() or croak( $self->dbi()->errstr() );
-  while ( my @row = $sth->fetchrow_array() ) {
-    $self->add_synonym($row[0], $row[1]);
-  }
-  $sth->finish;  
-
-
   return 0;
 }
 
 
-
-
-
 1;