fix_cmp_overlaps.pl 6.33 KB
Newer Older
1
#!/usr/bin/env perl
2
# Copyright [1999-2016] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
3 4 5 6 7 8 9 10 11 12 13 14 15
# 
# 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.

16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235

=head1 NAME

fix_cmp_overlaps.pl - remove overlapping mappings between assemblies from the component coordinates

=head1 SYNOPSIS

fix_overlaps.pl [arguments]

Required arguments:

  --dbname, db_name=NAME              database name NAME
  --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
  --assembly=ASSEMBLY                 assembly version ASSEMBLY

  --altassembly=ASSEMBLY              alternative assembly version ASSEMBLY

  --chromosomes, --chr=LIST           only process LIST seq_regions

Optional arguments:

  

  --conffile, --conf=FILE             read parameters from FILE
                                      (default: conf/Conversion.ini)

  --logfile, --log=FILE               log to FILE (default: *STDOUT)
  --logpath=PATH                      write logfile to PATH (default: .)
  --logappend, --log_append           append to logfile (default: truncate)

  -v, --verbose=0|1                   verbose logging (default: false)
  -i, --interactive=0|1               run script interactively (default: true)
  -n, --dry_run, --dry=0|1            don't write results to database
  -h, --help, -?                      print help (this message)

=head1 DESCRIPTION


This script removes overlapping mappings from the component coordinates. 
Mappings are trimmed so they don't break the AssemblyMapper when
projecting between the non-reference to the reference assembly.


=cut

use strict;
use warnings;
no warnings 'uninitialized';

use FindBin qw($Bin);
use Getopt::Long;
use Pod::Usage;
use Bio::EnsEMBL::Utils::ConversionSupport;

$| = 1;

my $support = new Bio::EnsEMBL::Utils::ConversionSupport("$Bin/../../..");

# parse options
$support->parse_common_options(@_);
$support->parse_extra_options(
    'assembly=s',
    'altassembly=s',
    'chromosomes|chr=s@',
);
$support->allowed_params(
    $support->get_common_params,
    'assembly',
    'altassembly',
    'chromosomes',
);

if ($support->param('help') or $support->error) {
    warn $support->error if $support->error;
    pod2usage(1);
}

$support->comma_to_list('chromosomes');

# 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(
    'assembly',
    'altassembly',
    'chromosomes'
);

# database connection
my $dba = $support->get_database('ensembl');
my $dbh = $dba->dbc->db_handle;

my $assembly = $support->param('assembly');
my $altassembly = $support->param('altassembly');

my $sql = qq(
  SELECT a.*
  FROM assembly a, seq_region sr1, seq_region sr2,
       coord_system cs1, coord_system cs2
  WHERE a.asm_seq_region_id = sr1.seq_region_id
  AND a.cmp_seq_region_id = sr2.seq_region_id
  AND sr1.coord_system_id = cs1.coord_system_id
  AND sr2.coord_system_id = cs2.coord_system_id
  AND cs1.version = '$assembly'
  AND cs2.version = '$altassembly'
  AND sr2.name = ?
  ORDER BY a.cmp_start
);

my $sth = $dbh->prepare($sql);

my $fmt1 = "%10s %10s %10s %10s %3s\n";


foreach my $chr ($support->param('chromosomes')) {
  $support->log_stamped("\nToplevel seq_region $chr...\n");

  $sth->execute($chr);

  my @rows = ();

  # do an initial fetch
  my $last = $sth->fetchrow_hashref;

  # skip seq_regions for which we don't have data
  unless ($last) {
    $support->log("No mappings found. Skipping.\n", 1);
    next;
  }
  
  push @rows, $last;
  
  my $i = 0;
  my $j = 0;
  my $k = 0;
  
  while ($last and (my $r = $sth->fetchrow_hashref)) {
    
    # look for overlaps with last segment
    if ($last->{'cmp_end'} >= $r->{'cmp_start'}) {

      $i++;
      
      # debug warnings
      $support->log_verbose('last:   '.sprintf($fmt1, map { $last->{$_} }
        qw(asm_start asm_end cmp_start cmp_end ori)), 1);
      $support->log_verbose('before: '.sprintf($fmt1, map { $r->{$_} }
        qw(asm_start asm_end cmp_start cmp_end ori)), 1);

      # skip if this segment ends before the last one
      if ($r->{'cmp_end'} <= $last->{'cmp_end'}) {
        $support->log_verbose("skipped\n\n", 1);
        next;
      }
    
      my $overlap = $last->{'cmp_end'} - $r->{'cmp_start'} + 1;

      $r->{'cmp_start'} += $overlap;

      if ($r->{'ori'} == -1) {
        $r->{'asm_end'} -= $overlap;
      } else {
        $r->{'asm_start'} += $overlap;
      }
      
      $support->log_verbose('after:  '.sprintf($fmt1, map { $r->{$_} }
        qw(asm_start asm_end cmp_start cmp_end ori))."\n", 1);
    }

    push @rows, $r;
    $last = $r;
  }

  $support->log("Fixed $i mappings.\n", 1);


  if (!$support->param('dry_run') && $i > 0  ) {

      # delete all current mappings from the db and insert the corrected ones
      my $c = $dbh->do(qq(
    DELETE a
    FROM assembly a, seq_region sr1, seq_region sr2,
         coord_system cs1, coord_system cs2
    WHERE a.asm_seq_region_id = sr1.seq_region_id
    AND a.cmp_seq_region_id = sr2.seq_region_id
    AND sr1.coord_system_id = cs1.coord_system_id
    AND sr2.coord_system_id = cs2.coord_system_id
    AND cs1.version = '$assembly'
    AND cs2.version = '$altassembly'
    AND sr2.name = '$chr'
  ));

      $support->log("\nDeleted $c entries from the assembly table.\n");

      # now insert the fixed entries
      $sql = qq(INSERT INTO assembly VALUES (?, ?, ?, ?, ?, ?, ?));
      my $sth1 = $dbh->prepare($sql);
  
      foreach my $r (@rows) {
	  $sth1->execute(map { $r->{$_} } qw(asm_seq_region_id cmp_seq_region_id asm_start asm_end cmp_start cmp_end ori));
      }

      $support->log("Added ".scalar(@rows)." fixed entries to the assembly table.\n");

  }


}

$sth->finish;

# finish logfile
$support->finish_log;