Compare assigned display xrefs between two databases, optionally by source.

misc-scripts/xref_mapping/compare_xrefs_by_source.pl

+# Compare xrefs between 2 databases by source
+
+use strict;
+
+use DBI;
+use Bio::EnsEMBL::DBSQL::DBAdaptor;
+use Bio::EnsEMBL::DBSQL::SliceAdaptor;
+use Bio::EnsEMBL::Slice;
+use Bio::EnsEMBL::Analysis;
+use Getopt::Long;
+
+my ($old_host, $old_user, $old_pass, $old_port, $old_dbname, $new_host, $new_user, $new_pass, $new_port, $new_dbname, $source);
+
+GetOptions( "old_host=s",   \$old_host,
+	    "old_user=s",   \$old_user,
+	    "old_pass=s",   \$old_pass,
+	    "old_port=i",   \$old_port,
+	    "old_dbname=s", \$old_dbname,
+	    "new_host=s",   \$new_host,
+	    "new_user=s",   \$new_user,
+	    "new_pass=s",   \$new_pass,
+	    "new_port=i",   \$new_port,
+	    "new_dbname=s", \$new_dbname,
+	    "source=s",     \$source,
+	    "help",         \&usage
+	  );
+
+my $old_dbi = DBI->connect("dbi:mysql:host=$old_host;port=$old_port;database=$old_dbname",
+			   $old_user, $old_pass,
+			   {'RaiseError' => 1}) || die "Can't connect to database $old_dbname";
+
+my $new_dbi = DBI->connect("dbi:mysql:host=$new_host;port=$new_port;database=$new_dbname",
+			   $new_user, $new_pass,
+			   {'RaiseError' => 1}) || die "Can't connect to database $new_dbname";
+
+
+# if one source specified, use that, otherwise loop over them all
+
+if ($source) {
+
+  compare($source);
+
+} else {
+
+  my $old_extdb_sth = $old_dbi->prepare("SELECT db_name FROM external_db WHERE db_name NOT LIKE 'AFFY%' AND status LIKE 'KNOWN%'");
+  my $ext_db;
+  $old_extdb_sth->execute();
+  $old_extdb_sth->bind_columns(\$ext_db);
+  while ($old_extdb_sth->fetch()) {
+
+    compare($ext_db);
+
+  }
+
+}
+
+
+
+sub compare {
+
+  my $source = shift;
+
+  # Read & cache all old stable_id-display_xref mappings
+
+  #print "Caching old gene stable ID - $source display_xref mappings from $old_dbname\n";
+
+  my $sql = "SELECT gsi.stable_id, x.dbprimary_acc FROM xref x, gene_stable_id gsi, gene g, external_db e WHERE gsi.gene_id=g.gene_id AND g.display_xref_id=x.xref_id AND e.external_db_id=x.external_db_id AND e.db_name='" . $source . "'";
+
+  #print "\n\n$sql\n\n";
+  my $old_sth = $old_dbi->prepare($sql);
+
+  my ($stable_id, $accession);
+  my %old_stable_id_2_accession;
+  $old_sth->execute();
+  $old_sth->bind_columns(\$stable_id, \$accession);
+  while ($old_sth->fetch()) {
+
+    $old_stable_id_2_accession{$stable_id} = $accession;
+
+  }
+
+  my ($match, $mismatch, $added) = (0,0,0);
+
+  # Compare these with new ones
+  my $new_sth = $new_dbi->prepare($sql);
+
+  $new_sth->execute();
+  $new_sth->bind_columns(\$stable_id, \$accession);
+  while ($new_sth->fetch()) {
+
+    if (exists($old_stable_id_2_accession{$stable_id})) {
+      if ($old_stable_id_2_accession{$stable_id} eq $accession) {
+	$match++;
+      } else {
+	$mismatch++;
+      }
+    } else {
+      $added++;
+    }
+  }
+
+
+  printf "%30s\tmatch: %d\tmismatch: %d\tadded: %d\n", $source, $match, $mismatch, $added  if ($match || $mismatch || $added);
+
+}
+
+
+
+sub usage {
+
+  print <<EOF;
+Usage: perl compare_xrefs_by_source.pl
+
+Compare assigned display xrefs between two databases, optionally by source.
+
+Options:
+
+       -old_host -old_user -old_pass -old_port -old_dbname  : old database connection details
+       -new_host -new_user -new_pass -new_port -new_dbname  : new database connection details
+
+       -source : source to compare (e.g. RefSeq_dna). If no source is specified, all sources
+                 from old database are checked.
+
+Note only non-Affy sources of status "KNOWN" or "KNOWNXREF" are compared, and if no differences
+are detected, nothing is reported.
+
+EOF
+
+  exit(0);
+
+}