ENSCORESW-1106: retire overlapping_regions script

misc-scripts/overlapping_regions.pl

-#!/usr/bin/env perl
-# Copyright [1999-2014] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-# 
-# Licensed under the Apache License, Version 2.0 (the "License");
-# you may not use this file except in compliance with the License.
-# You may obtain a copy of the License at
-# 
-#      http://www.apache.org/licenses/LICENSE-2.0
-# 
-# Unless required by applicable law or agreed to in writing, software
-# distributed under the License is distributed on an "AS IS" BASIS,
-# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
-# See the License for the specific language governing permissions and
-# limitations under the License.
-
-
-=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                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 AUTHOR
-
-Daniel Rios <dani@ebi.ac.uk>, Ensembl core API team
-
-=head1 CONTACT
-
-Please post comments/questions to the Ensembl development list
-<http://lists.ensembl.org/mailman/listinfo/dev>
-
-=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);
-$sth->execute;
-
-if ($support->param('dry_run')) {
-  $support->log_stamped("Dry run. Results will not be written to the database.\n\n");
-}
-# loop over databases
-while (my ($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");
-	  $overlaps = 'false';
-      }
-      if (!$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;