Removed old probe mapping scripts

misc-scripts/probe_mapping/compare_mappings.pl

-use strict;
-
-use Getopt::Long;
-
-use Bio::EnsEMBL::DBEntry;
-use Bio::EnsEMBL::DBSQL::DBAdaptor;
-use Bio::EnsEMBL::Mapper::RangeRegistry;
-
-my ($s_host, $s_port, $s_user, $s_pass, $s_dbname, $t_host, $t_port, $t_user, $t_pass, $t_dbname, $array);
-
-GetOptions('source_host=s'      => \$s_host,
-           'source_user=s'      => \$s_user,
-           'source_port=i'      => \$s_port,
-           'source_pass=s'      => \$s_pass,
-           'source_dbname=s'    => \$s_dbname,
-	   'target_host=s'      => \$t_host,
-           'target_user=s'      => \$t_user,
-           'target_port=i'      => \$t_port,
-           'target_pass=s'      => \$t_pass,
-           'target_dbname=s'    => \$t_dbname,
-	   'array=s'            => \$array,
-           'help'               => sub { usage(); exit(0); });
-
-$s_port ||= 3306; $t_port ||= 3306;
-
-usage() if(!$s_user || !$s_dbname || !$s_host || !$t_dbname);
-
-$t_host = $s_host if (!$t_host);
-$t_port = $s_port if (!$t_port);
-$t_user = $s_user if (!$t_user);
-
-my $s_db = new Bio::EnsEMBL::DBSQL::DBAdaptor('-host'   => $s_host,
-					      '-port'   => $s_port,
-					      '-user'   => $s_user,
-					      '-pass'   => $s_pass,
-					      '-dbname' => $s_dbname,
-					      '-species'=> $s_dbname);
-
-my $t_db = new Bio::EnsEMBL::DBSQL::DBAdaptor('-host'   => $t_host,
-					      '-port'   => $t_port,
-					      '-user'   => $t_user,
-					      '-pass'   => $t_pass,
-					      '-dbname' => $t_dbname,
-					      '-species'=> $t_dbname);
-
-# TODO fix this when external db is sorted out
-my $restrict_sql = "x.external_db_id > 3000 AND x.external_db_id < 3210";
-$restrict_sql = " e.db_name='$array'" if ($array);
-
-run();
-
-sub run {
-
-  print "Using only array $array\n" if ($array);
-
-  # compare total counts first
-  my $count_sql = "SELECT COUNT(*) FROM xref x, object_xref ox, external_db e WHERE e.external_db_id=x.external_db_id AND x.xref_id=ox.xref_id AND ox.ensembl_object_type='Transcript' AND $restrict_sql";
-
-  my $s_sth = $s_db->dbc()->prepare($count_sql);
-  $s_sth->execute();
-  my $count = ($s_sth->fetchrow_array())[0];
-  print "Total oligo xrefs in $s_dbname: $count\n";
-
-  my $t_sth = $t_db->dbc()->prepare($count_sql);
-  $t_sth->execute();
-  $count = ($t_sth->fetchrow_array())[0];
-  print "Total oligo xrefs in $t_dbname: $count\n";
-
-  # cache all mappings from each database
-  # key format: transcript_stable_id:array:probe
-  my %source_mappings = cache_mappings($s_db);
-  my %target_mappings = cache_mappings($t_db);
-
-  # compare mappings
-  my $source_only = 0;
-  my $target_only = 0;
-  my $both = 0;
-
-  open(SOURCE_ONLY, ">source_only.txt");
-  open(TARGET_ONLY, ">target_only.txt");
-  open(BOTH,        ">both.txt");
-
-  foreach my $key (keys %source_mappings) {
-
-    if ($target_mappings{$key}) {
-      $both++;
-      print BOTH "$key\n";
-    } else {
-      $source_only++;
-      print SOURCE_ONLY "$key\n";
-    }
-
-  }
-
-  print "$both unique mappings in both databases\n";
-  print "$source_only mappings in source only\n";
-
-  foreach my $key (keys %target_mappings) {
-
-    if (!$source_mappings{$key}) {
-      $target_only++;
-      print TARGET_ONLY "$key\n";
-    }
-
-  }
-
-  print "$target_only mappings in target only\n";
-
-}
-
-# ----------------------------------------------------------------------
-
-sub cache_mappings {
-
-  my ($db, $print) = @_;
-
-  my %mappings;
-
-  # TODO - fix SQL when external_db changes
-  my $sth = $db->dbc()->prepare("SELECT tsi.stable_id, e.db_name, x.dbprimary_acc, t.biotype FROM xref x, external_db e, object_xref ox, transcript_stable_id tsi, transcript t WHERE x.xref_id=ox.xref_id AND x.external_db_id=e.external_db_id AND ox.ensembl_object_type='Transcript' AND ox.ensembl_id=t.transcript_id AND t.transcript_id=tsi.transcript_id AND $restrict_sql");
-  $sth->execute();
-  while (my @row = $sth->fetchrow_array()) {
-
-    my $key = $row[0] . "\t" . $row[3] . "\t". $row[1]. "\t" . $row[2];
-    $mappings{$key} = $key;
-
-    print "$key\n" if ($print);
-
-  }
-
-  $sth->finish();
-
-  return %mappings;
-
-}
-
-# ----------------------------------------------------------------------
-
-sub usage {
-
-  print << "EOF";
-
-  Compare oligo xrefs between 2 databases.
-
-  perl $0 {options}
-
-  Options ([..] indicates optional):
-
-  ORIGINAL XREFS:
-
-   --source_host          The database server to read the first set of xrefs from.
-		
-   [--source_port]        The port to use. Defaults to 3306.
-		
-   --source_user          Database username.
-		
-   --source_pass          Password for source_user, if required.
-		
-   --source_dbname        Database name.
-
-  NEW XREFS:
-
-   --target_host          The database server to read the second set of xrefs from.
-                          Defaults to source_host.
-		
-   [--target_port]        The port to use. Defaults to 3306.
-		
-   --target_user          Database username. Defaults to source_user.
-		
-   --target_pass          Password for target_user, if required.
-		
-   --target_dbname        Database name.
-
-  MISCELLANEOUS:
-
-  [--array]           Just compare results from this array.
-
-  [--help]            This text.
-
-
-EOF
-
-  exit(0);
-
-}