script that will calculate if the assembly table has overlapping regions in same coord_system

misc-scripts/overlapping_regions.pl

+#!/software/bin/perl -w
+
+=head1 NAME
+
+overlapping_regions.pl - calculates overlapping regions in the assembly table
+
+=head1 SYNOPSIS
+
+overlapping_regions.pl [arguments]
+
+Required arguments:
+
+  --host, --dbhost, --db_host=HOST    database host HOST
+  --port, --dbport, --db_port=PORT    database port PORT
+  --user, --dbuser, --db_user=USER    database username USER
+  --pass, --dbpass, --db_pass=PASS    database passwort PASS
+  
+  --pattern, --dbpattern=PATTERN      patch databases where name matches PATTERN
+                                      Note that this is a database pattern of
+                                      the form %core_41% rather than a regexp
+ 
+Optional arguments:
+
+  -n, --dry, --dry_run=0|1            don't write results to database
+  -h, --help, -?                      print help (this message)
+
+Please note that where an argument expects a value, this is true for all
+alternative argument styles.
+
+=head1 DESCRIPTION
+
+This is a script that will calculate if an assembly has overlapping regions
+in same coordinate system (e.g. 2 chr_1 stored in the assembly table, one as
+the current, the other as an old version). It will store a new entry in the meta
+table. If there are overlapping regions, can cause problems when moving features
+between coordinate systems. The pattern is a string that can be used in an
+'IN' clause in SQL (e.g. "%_core_%"; if you want to patch only a single
+database, use a pattern without % expansion, e.g. "homo_sapiens_core_38_36").
+
+=head1 EXAMPLES
+
+   perl overlapping_regions.pl -host ens-staging -user ensadmin -pass xxxx
+        -pattern "%core_55_%" -port 3306 -dry_run 0
+
+=head1 LICENCE
+
+This code is distributed under an Apache style licence:
+Please see http://www.ensembl.org/code_licence.html for details
+
+=head1 AUTHOR
+
+Daniel Rios <dani@ebi.ac.uk>, Ensembl core API team
+
+=head1 CONTACT
+
+Please post comments/questions to the Ensembl development list
+<ensembl-dev@ebi.ac.uk>
+
+=cut
+
+
+use strict;
+use warnings;
+no warnings 'uninitialized';
+use FindBin qw($Bin);
+use vars qw($SERVERROOT);
+
+BEGIN {
+    $SERVERROOT = "$Bin/../..";
+    unshift(@INC, "$SERVERROOT/ensembl/modules");
+}
+
+use Getopt::Long;
+use Pod::Usage;
+use Bio::EnsEMBL::Utils::ConversionSupport;
+use DBI;
+
+$| = 1;
+
+my $support = new Bio::EnsEMBL::Utils::ConversionSupport($SERVERROOT);
+
+# parse options
+$support->parse_common_options(@_);
+$support->parse_extra_options(
+  'pattern|dbpattern=s'
+			      );
+my @params = map { $_ unless ($_ =~ /dbname/) } $support->get_common_params;
+$support->allowed_params(
+  @params,
+  'pattern'
+			 );
+
+if ($support->param('help') or $support->error) {
+    warn $support->error if $support->error;
+    pod2usage(1);
+}
+
+# ask user to confirm parameters to proceed
+$support->confirm_params;
+
+# get log filehandle and print heading and parameters to logfile
+$support->init_log;
+
+$support->check_required_params(
+  'pattern'
+);
+
+# connect to database
+my $dbh = $support->get_dbconnection;
+
+# get all database names that match pattern
+my ($sth, $sql);
+$sql = "SHOW DATABASES LIKE '".$support->param('pattern')."'";
+$sth = $dbh->prepare($sql);
+$sth->execute;
+
+# loop over databases
+while (my ($dbname) = $sth->fetchrow_array) {
+   $support->log_stamped("$dbname\n");
+  
+  if ($support->user_proceed("\nCalculate overlapping regions for $dbname?")) {
+      #this query will detect if there are overlapping regions in same coord_system
+      #starting in position 1. 
+      $dbh->do("use $dbname;");
+      $sql = qq(SELECT count(*) FROM assembly as1, seq_region s1, assembly as2, seq_region s2 
+		WHERE as1.asm_seq_region_id = s1.seq_region_id AND as2.asm_seq_region_id = s2.seq_region_id 
+		AND s1.coord_system_id = s2.coord_system_id AND as1.asm_start = as2.asm_start 
+		AND as1.asm_end = as2.asm_end AND as1.cmp_seq_region_id = as2.cmp_seq_region_id 
+		AND as1.asm_seq_region_id <> as2.asm_seq_region_id AND as1.asm_start = 1);
+      my $sth1 = $dbh->prepare($sql);
+      $sth1->execute;
+      my $val = $sth1->fetch();
+      my $overlaps;
+      #let's see if we write it in the database
+      if ($val->[0] > 0){
+	  $support->log("\tDatabase has overlapping regions. This might make give wrong results when mapping features\n");
+	  $overlaps = 'true';
+      }
+      else{
+	  $support->log("\tDatabase looks correct\n");
+	  $overlaps = 'false';
+      }
+      if (defined $support->param('dry_run') and !$support->param('dry_run')){
+	  #let's write results to the database. First remove previous entry
+	  $sql = qq(DELETE FROM meta where meta_key = 'assembly.overlapping_regions');
+	  $dbh->do($sql);
+	  #and now will insert it
+	  $sql = qq(INSERT INTO meta (species_id,meta_key,meta_value) VALUES (1,'assembly.overlapping_regions',$overlaps));
+	  $dbh->do($sql);
+      }
+     $support->log("Done\n"); 
+  }
+
+}
+$support->finish_log;