Changing patch loading scripts location.

misc-scripts/assembly_patches/remove_patch_karyotype.sql

+delete karyotype from attrib_type, seq_region_attrib, karyotype where attrib_type.code in ('patch_novel','patch_fix') and attrib_type.attrib_type_id = seq_region_attrib.attrib_type_id and seq_region_attrib.seq_region_id = karyotype.seq_region_id;

misc-scripts/assembly_patches/remove_patch_raw_compute.sql

+delete repeat_feature from attrib_type, seq_region_attrib, repeat_feature where attrib_type.code in ('patch_novel','patch_fix') and attrib_type.attrib_type_id = seq_region_attrib.attrib_type_id and seq_region_attrib.seq_region_id = repeat_feature.seq_region_id;
+
+delete prediction_exon from attrib_type, seq_region_attrib, prediction_exon where attrib_type.code in ('patch_novel','patch_fix') and attrib_type.attrib_type_id = seq_region_attrib.attrib_type_id and seq_region_attrib.seq_region_id = prediction_exon.seq_region_id;
+
+delete prediction_transcript from attrib_type, seq_region_attrib, prediction_transcript where attrib_type.code in ('patch_novel','patch_fix') and attrib_type.attrib_type_id = seq_region_attrib.attrib_type_id and seq_region_attrib.seq_region_id = prediction_transcript.seq_region_id;
+
+delete simple_feature from attrib_type, seq_region_attrib, simple_feature where attrib_type.code in ('patch_novel','patch_fix') and attrib_type.attrib_type_id = seq_region_attrib.attrib_type_id and seq_region_attrib.seq_region_id = simple_feature.seq_region_id;
+
+delete dna_align_feature from attrib_type, seq_region_attrib, dna_align_feature where attrib_type.code in ('patch_novel','patch_fix') and attrib_type.attrib_type_id = seq_region_attrib.attrib_type_id and seq_region_attrib.seq_region_id = dna_align_feature.seq_region_id and dna_align_feature_id not in (select feature_id from transcript_supporting_feature where feature_type = 'dna_align_feature') and dna_align_feature_id not in (select feature_id from supporting_feature where feature_type = 'dna_align_feature');
+
+delete protein_align_feature from attrib_type, seq_region_attrib, protein_align_feature where attrib_type.code in ('patch_novel','patch_fix') and attrib_type.attrib_type_id = seq_region_attrib.attrib_type_id and seq_region_attrib.seq_region_id = protein_align_feature.seq_region_id and protein_align_feature_id not in (select feature_id from transcript_supporting_feature where feature_type = 'protein_align_feature') and protein_align_feature_id not in (select feature_id from supporting_feature where feature_type = 'protein_align_feature');
+

misc-scripts/assembly_patches/remove_updated_and_deprecated_patches.pl

+#!/usr/local/ensembl/bin/perl -w
+
+use Bio::EnsEMBL::Registry;
+use Bio::EnsEMBL::Utils::Exception qw(throw);
+use Getopt::Long;
+
+use strict;
+
+my $pass;
+my $patchtype_file = "./data/patch_type";
+my $dbname;
+my $host;
+my $user;
+my $port = 3306;
+my $central_coord_system = 'supercontig';
+my $toplevel_coord_system = 'chromosome';
+
+&GetOptions(
+            'pass=s'         => \$pass,
+            'patchtype_file=s' => \$patchtype_file,
+            'host=s'         => \$host,
+            'dbname=s'       => \$dbname,
+            'user=s'         => \$user,
+            'port=n'         => \$port,
+           );
+
+open(TYPE,"<".$patchtype_file)         || die "Could not open file $patchtype_file";
+open(SQL,">delete_patch.sql") || die "Could not open delete_patch.sql for writing\n";
+#connect to the database
+
+my $dba = new Bio::EnsEMBL::DBSQL::DBAdaptor(
+    '-host'    => $host,
+    '-user'    => $user,
+    '-pass'    => $pass,
+    '-dbname'  => $dbname,
+    '-species' => "load"
+    );
+
+my $get_all_synonyms_sth = $dba->dbc->prepare("select synonym from seq_region, seq_region_synonym, coord_system where seq_region.name in (select seq_region.name from seq_region, seq_region_attrib, attrib_type where
+attrib_type.code in ('patch_fix','patch_novel') and attrib_type.attrib_type_id = seq_region_attrib.attrib_type_id and seq_region_attrib.seq_region_id = seq_region.seq_region_id) and seq_region.coord_system_id=coord_system.coord_system_id and coord_system.name = '".$central_coord_system."' and seq_region.seq_region_id=seq_region_synonym.seq_region_id")
+|| die "Could not prepare to get synonyms";
+
+if ($get_all_synonyms_sth == 0) {
+  throw("Could not prepare to get synonyms");
+}
+my $get_name_sth = $dba->dbc->prepare("select name from seq_region,seq_region_synonym where synonym = ? and seq_region_synonym.seq_region_id = seq_region.seq_region_id")
+|| die "Could not prepare to get name";
+
+if ($get_name_sth == 0) {
+  throw("Could not prepare to get name");
+}
+my $get_synonym_sth = $dba->dbc->prepare("select synonym from seq_region_synonym, seq_region, coord_system where seq_region. name = ? and seq_region.coord_system_id=coord_system.coord_system_id and coord_system.name = ? and seq_region.seq_region_id=seq_region_synonym.seq_region_id")
+  || die "Could not prepare to get synonym";
+
+if ($get_synonym_sth == 0) {
+  throw("Could not prepare to get synonym");
+}
+my $get_seq_region_id_sth = $dba->dbc->prepare("select seq_region_id from seq_region, coord_system where seq_region. name = ? and seq_region.coord_system_id=coord_system.coord_system_id and
+coord_system.name = ?")
+  || die "Could not prepare to get seq_region_id";
+
+if ($get_seq_region_id_sth == 0) {
+  throw("Could not prepare to get seq_region_id");
+}
+#get the full list of existing synonyms/accessions
+my $existing_synonym;
+my %existing_synonyms;
+
+$get_all_synonyms_sth->execute() || die "problem executing seq_region_id";
+$get_all_synonyms_sth->bind_columns(\$existing_synonym) || die "problem binding";
+while($get_all_synonyms_sth->fetch()){
+  print "Synonym ".$existing_synonym."\n";
+  $existing_synonyms{$existing_synonym} = 1;
+}
+
+
+#for the new files
+while (<TYPE>) {
+  chomp;
+  next if (/^#/);
+  my ($alt_scaf_name,$alt_scaf_acc,$type) = split(/\t/,$_);
+  if (!$alt_scaf_name || !$alt_scaf_acc || !$type) {
+    throw("Unable to find name, accession or type");
+  }
+
+  #check to see if this is an updated patch
+  my $synonym;
+  $get_synonym_sth->execute($alt_scaf_name, $central_coord_system) || die "problem executing get synonym";
+  $get_synonym_sth->bind_columns(\$synonym) || die "problem binding";
+  $get_synonym_sth->fetch();
+
+  if(defined($synonym)){
+    #if patch still exists (even if modified) record by setting to 0
+    #modified patches are dealt with here already
+    $existing_synonyms{$synonym} = 0;
+    #unchanged
+    if($synonym eq $alt_scaf_acc){
+      print $alt_scaf_name." exists and is unchanged\n";
+    }
+    #modified
+    else{
+      print $alt_scaf_name." has been modified acc ".$synonym." to ".$alt_scaf_acc."\n";
+      remove_patch($alt_scaf_name);
+    }
+  }
+  #new
+  else{
+    print $alt_scaf_name." is a new patch\n";
+  }
+
+}
+#removed
+my @exist_accs = keys  %existing_synonyms;
+foreach my $acc (@exist_accs){
+  if($existing_synonyms{$acc}){
+    my $name;
+    $get_name_sth->execute($acc) || die "problem executing get name";
+    $get_name_sth->bind_columns(\$name) || die "problem binding";
+    $get_name_sth->fetch();
+    print $name." with acc ".$acc." has been removed from the new set\n";
+    remove_patch($name);
+  }
+}
+
+
+sub remove_patch{
+
+  my $alt_scaf_name = shift;
+  #get the patch seq_region_ids (chrom and scaffold)
+  my($scaf_id, $chrom_id);
+  $get_seq_region_id_sth->execute($alt_scaf_name, $central_coord_system) || die "problem executing seq_region_id";
+  $get_seq_region_id_sth->bind_columns(\$scaf_id) || die "problem binding";
+  $get_seq_region_id_sth->fetch();
+
+  $get_seq_region_id_sth->execute($alt_scaf_name, $toplevel_coord_system) || die "problem executing seq_region_id";
+  $get_seq_region_id_sth->bind_columns(\$chrom_id) || die "problem binding";
+  $get_seq_region_id_sth->fetch();
+
+  #check for components only used in patch
+  my $scaf_comp;
+  my $get_region_components_sth = $dba->dbc->prepare("select distinct cmp_seq_region_id from assembly where asm_seq_region_id = ?") || die "Couldn't get components";
+  $get_region_components_sth->execute($scaf_id) || die "problem executing get components";
+  $get_region_components_sth->bind_columns(\$scaf_comp) || die "problem binding";
+  COMP: while($get_region_components_sth->fetch()){
+    #check each component
+    my $asm_id;
+    my $get_asm_ids_sth = $dba->dbc->prepare("select distinct asm_seq_region_id from assembly where cmp_seq_region_id = ?") || die "Couldn't get asm ids";
+    $get_asm_ids_sth->execute($scaf_comp) || die "problem executing get components";
+    $get_asm_ids_sth->bind_columns(\$asm_id) || die "problem binding";
+    while($get_asm_ids_sth->fetch()){
+      if($asm_id != $chrom_id and $asm_id != $scaf_id){
+        #print "Used outside of the patch\n";
+        next COMP;
+      }
+    }
+    #component only used in patch
+    #print $scaf_comp." only used in patch\n";
+    print SQL "delete from dna where seq_region_id = ".$scaf_comp.";\n";
+    print SQL "delete from seq_region_attrib where seq_region_id = ".$scaf_comp.";\n";
+    print SQL "delete from seq_region where seq_region_id = ".$scaf_comp.";\n";
+  }
+
+  print SQL "delete from seq_region_synonym where seq_region_id = ".$scaf_id.";\n";
+
+  print SQL "delete from seq_region_attrib where seq_region_id = ".$chrom_id.";\n";
+
+  print SQL "delete from assembly_exception where seq_region_id = ".$chrom_id.";\n";
+
+  print SQL "delete from assembly where asm_seq_region_id = ".$chrom_id.";\n";
+  print SQL "delete from assembly where asm_seq_region_id = ".$scaf_id.";\n";
+
+  print SQL "delete from seq_region where seq_region_id = ".$chrom_id.";\n";
+  print SQL "delete from seq_region where seq_region_id = ".$scaf_id.";\n";
+
+  print SQL "delete from splicing_event where seq_region_id = ".$chrom_id.";\n";
+
+  print SQL "delete from marker_feature where seq_region_id = ".$chrom_id.";\n";
+}
+