diff --git a/misc-scripts/density_feature/density_feature_fetch.pl b/misc-scripts/density_feature/density_feature_fetch.pl
new file mode 100644
index 0000000000000000000000000000000000000000..ca2e8d8a69f14bd5a452e25e55519ec4966a6998
--- /dev/null
+++ b/misc-scripts/density_feature/density_feature_fetch.pl
@@ -0,0 +1,97 @@
+#!/usr/bin/perl -w
+
+#
+# Ignore file anme this should calculate the gene count for a chromosome (X)
+#
+
+
+use strict;
+use lib '/tmp_mnt/nfs6/vol_vol1_homes/ianl/CVS/ensembl/modules';
+use lib '/tmp_mnt/nfs6/vol_vol1_homes/ianl/read_only/bioperl-live';
+
+
+use Data::Dumper;
+
+#use dbi;
+use Bio::EnsEMBL::DBSQL::DBAdaptor;
+use Bio::EnsEMBL::DBSQL::SliceAdaptor;
+use Bio::EnsEMBL::DBSQL::DensityFeatureAdaptor;
+use Bio::EnsEMBL::DBSQL::DensityTypeAdaptor;
+use Bio::EnsEMBL::Slice;
+use Bio::EnsEMBL::Analysis;
+use Bio::EnsEMBL::DensityType;
+use Bio::EnsEMBL::DensityFeature;
+print "hello\n";
+
+my $host = '127.0.0.1';
+my $user = 'ensro';
+#my $pass = 'ensembl';
+my $dbname = 'homo_sapiens_core_20_34';
+my $port = '5050';
+
+my $db = new Bio::EnsEMBL::DBSQL::DBAdaptor(-host => $host,
+ -user => $user,
+ -port => $port,
+# -pass => $pass,
+ -dbname => $dbname);
+
+
+my $slice_adaptor = $db->get_SliceAdaptor();
+my $dfa = $db->get_DensityFeatureAdaptor();
+
+
+my $num_of_blocks = 20;
+my $interpolate = 1;
+
+
+#comment out as appropriate.
+#my $type="GeneDensity";
+#my $type="PercentGC";
+my $type ="PercentageRepeat";
+
+foreach my $chrom (qw(X Y)){
+ if($interpolate){
+ print "getting density feature for chromosome $chrom with $num_of_blocks blocks\n";
+ }
+ else{
+ print "getting ALL density feature for chromosome $chrom\n";
+ }
+ my $slice = $slice_adaptor->fetch_by_region('chromosome',$chrom);
+
+
+ my @features = @{$dfa->fetch_all_by_Slice($slice,$type, $num_of_blocks, $interpolate)};
+
+ print_features(\@features);
+}
+
+
+#
+# helper to draw an ascii representation of the density features
+#
+sub print_features {
+ my $features = shift;
+
+ return if(!@$features);
+
+ my $sum = 0;
+ my $length = 0;
+# my $type = $features->[0]->{'density_type'}->value_type();
+
+ print("\n");
+ my $max=0;
+ foreach my $f (@$features) {
+ if($f->density_value() > $max){
+ $max=$f->density_value();
+ }
+ }
+ foreach my $f (@$features) {
+ my $i=1;
+ for(; $i< ($f->density_value()/$max)*40; $i++){
+ print "*";
+ }
+ for(my $j=$i;$j<40;$j++){
+ print " ";
+ }
+ print " ".int($f->density_value())."\t".$f->start()."\t".$f->end()."\n";
+ }
+}
diff --git a/misc-scripts/density_feature/gene_density_calc.pl b/misc-scripts/density_feature/gene_density_calc.pl
new file mode 100644
index 0000000000000000000000000000000000000000..c4fb0c3c406572254037c7e575c6f8d20cc81508
--- /dev/null
+++ b/misc-scripts/density_feature/gene_density_calc.pl
@@ -0,0 +1,158 @@
+#!/usr/bin/perl -w
+
+#
+# Ignore file anme this should calculate the gene count for a chromosome (X)
+#
+
+
+use strict;
+
+#use dbi;
+use Bio::EnsEMBL::DBSQL::DBAdaptor;
+use Bio::EnsEMBL::DBSQL::SliceAdaptor;
+use Bio::EnsEMBL::DBSQL::DensityFeatureAdaptor;
+use Bio::EnsEMBL::DBSQL::DensityTypeAdaptor;
+use Bio::EnsEMBL::Slice;
+use Bio::EnsEMBL::Analysis;
+use Bio::EnsEMBL::DensityType;
+use Bio::EnsEMBL::DensityFeature;
+
+my $host = '127.0.0.1';
+my $user = 'ensadmin';
+my $pass = 'ensembl';
+my $dbname = 'homo_sapiens_core_20_34';
+my $port = '5050';
+
+my $db = new Bio::EnsEMBL::DBSQL::DBAdaptor(-host => $host,
+ -user => $user,
+ -port => $port,
+ -pass => $pass,
+ -dbname => $dbname);
+
+
+
+my $block_size = 1e6;
+
+#
+# Get the adaptors needed;
+#
+
+my $slice_adaptor = $db->get_SliceAdaptor();
+my $dfa = $db->get_DensityFeatureAdaptor();
+my $dta = $db->get_DensityTypeAdaptor();
+my $aa = $db->get_AnalysisAdaptor();
+
+
+
+#
+# Create new analysis object for density calculation.
+#
+
+my $analysis = new Bio::EnsEMBL::Analysis (-program => "gene_density_calc.pl",
+ -database => "ensembl",
+ -gff_source => "gene_density_calc.pl",
+ -gff_feature => "density",
+ -logic_name => "GeneDensity");
+
+$aa->store($analysis);
+
+print "New analysis : ".$analysis->dbID." at ".$analysis->created."\n";
+
+#
+# Create new density type.
+#
+
+my $dt = Bio::EnsEMBL::DensityType->new(-analysis => $analysis,
+ -block_size => $block_size,
+ -value_type => 'sum');
+
+$dta->store($dt);
+
+print "New density type : ".$dt->dbID."\n";
+
+foreach my $chrom (qw(X Y)){
+ print "creating density feature for chromosome $chrom with block size of $block_size\n";
+
+ my $slice = $slice_adaptor->fetch_by_region('chromosome',$chrom);
+
+ my $start = $slice->start();
+ my $end = ($start + $block_size)-1;
+ my $term = $slice->start+$slice->length;
+
+ my @density_features=();
+ while($start < $term){
+
+ my $sub_slice = $slice_adaptor->fetch_by_region('chromosome',$chrom,$start,$end);
+
+ my $count =0;
+
+ #
+ # Store info for genes (ignore pseudo genes)
+ #
+
+ foreach my $gene (@{$sub_slice->get_all_Genes()}){
+ if($gene->analysis()->logic_name() ne "pseudogene" and $gene->start >=1 ){
+ $count++
+ }
+ }
+
+ push @density_features, Bio::EnsEMBL::DensityFeature->new(-seq_region => $slice,
+ -start => $start,
+ -end => $end,
+ -density_type => $dt,
+ -density_value => $count);
+
+ $start = $end+1;
+ $end = ($start + $block_size)-1;
+ }
+ $dfa->store(@density_features);
+ print scalar @density_features;
+ print_features(\@density_features);
+}
+
+
+
+
+
+
+
+#
+# helper to draw an ascii representation of the density features
+#
+sub print_features {
+ my $features = shift;
+
+ return if(!@$features);
+
+ my $sum = 0;
+ my $length = 0;
+# my $type = $features->[0]->{'density_type'}->value_type();
+
+ print("\n");
+ my $max=0;
+ foreach my $f (@$features) {
+ if($f->density_value() > $max){
+ $max=$f->density_value();
+ }
+ }
+ foreach my $f (@$features) {
+ my $i=1;
+ for(; $i< ($f->density_value()/$max)*40; $i++){
+ print "*";
+ }
+ for(my $j=$i;$j<40;$j++){
+ print " ";
+ }
+ print " ".$f->density_value()."\t".$f->start()."\n";
+ }
+# my $avg = undef;
+# $avg = $sum/$length if($length < 0);
+# print("Sum=$sum, Length=$length, Avg/Base=$sum");
+}
+
+
+
+
+
+
+
diff --git a/misc-scripts/density_feature/percent_gc_calc.pl b/misc-scripts/density_feature/percent_gc_calc.pl
new file mode 100644
index 0000000000000000000000000000000000000000..d58d29a63f533c4bfdbba2b26efce02b797e7a7d
--- /dev/null
+++ b/misc-scripts/density_feature/percent_gc_calc.pl
@@ -0,0 +1,147 @@
+#!/usr/bin/perl -w
+
+#
+# Ignore file anme this should calculate the gene count for a chromosome (X)
+#
+
+
+use strict;
+
+#use dbi;
+use Bio::EnsEMBL::DBSQL::DBAdaptor;
+use Bio::EnsEMBL::DBSQL::SliceAdaptor;
+use Bio::EnsEMBL::DBSQL::DensityFeatureAdaptor;
+use Bio::EnsEMBL::DBSQL::DensityTypeAdaptor;
+use Bio::EnsEMBL::Slice;
+use Bio::EnsEMBL::Analysis;
+use Bio::EnsEMBL::DensityType;
+use Bio::EnsEMBL::DensityFeature;
+
+my $host = '127.0.0.1';
+my $user = 'ensadmin';
+my $pass = 'ensembl';
+my $dbname = 'homo_sapiens_core_20_34';
+my $port = '5050';
+
+my $db = new Bio::EnsEMBL::DBSQL::DBAdaptor(-host => $host,
+ -user => $user,
+ -port => $port,
+ -pass => $pass,
+ -dbname => $dbname);
+
+
+
+my $block_size = 1e6;
+
+
+#
+# Get the adaptors needed;
+#
+
+my $slice_adaptor = $db->get_SliceAdaptor();
+my $dfa = $db->get_DensityFeatureAdaptor();
+my $dta = $db->get_DensityTypeAdaptor();
+my $aa = $db->get_AnalysisAdaptor();
+
+
+#
+# Create new analysis object for density calculation.
+#
+
+my $analysis = new Bio::EnsEMBL::Analysis (-program => "percent_gc_calc.pl",
+ -database => "ensembl",
+ -gff_source => "percent_gc_calc.pl",
+ -gff_feature => "density",
+ -logic_name => "PercentGC");
+
+$aa->store($analysis);
+
+print "New analysis : ".$analysis->dbID." at ".$analysis->created."\n";
+
+#
+# Create new density type.
+#
+
+my $dt = Bio::EnsEMBL::DensityType->new(-analysis => $analysis,
+ -block_size => $block_size,
+ -value_type => 'ratio');
+
+$dta->store($dt);
+
+print "New density type : ".$dt->dbID."\n";
+
+foreach my $chrom (qw(X Y)){
+ print "creating density feature for chromosome $chrom with block size of $block_size\n";
+
+ my $slice = $slice_adaptor->fetch_by_region('chromosome',$chrom);
+
+ my $start = $slice->start();
+ my $end = ($start + $block_size)-1;
+ my $term = $slice->start+$slice->length;
+
+ my @density_features=();
+ while($start < $term){
+ my $sub_slice = $slice_adaptor->fetch_by_region('chromosome',$chrom,$start,$end);
+
+ my $gc = $sub_slice->get_base_count()->{'%gc'};
+ print STDERR $start."\n";
+ push @density_features, Bio::EnsEMBL::DensityFeature->new(-seq_region => $slice,
+ -start => $start,
+ -end => $end,
+ -density_type => $dt,
+ -density_value => $gc);
+
+ $start = $end+1;
+ $end = ($start + $block_size)-1;
+ }
+ $dfa->store(@density_features);
+ print scalar @density_features;
+ print_features(\@density_features);
+}
+
+
+
+
+
+
+
+#
+# helper to draw an ascii representation of the density features
+#
+sub print_features {
+ my $features = shift;
+
+ return if(!@$features);
+
+ my $sum = 0;
+ my $length = 0;
+# my $type = $features->[0]->{'density_type'}->value_type();
+
+ print("\n");
+ my $max=0;
+ foreach my $f (@$features) {
+ if($f->density_value() > $max){
+ $max=$f->density_value();
+ }
+ }
+ foreach my $f (@$features) {
+ my $i=1;
+ for(; $i< ($f->density_value()/$max)*40; $i++){
+ print "*";
+ }
+ for(my $j=$i;$j<40;$j++){
+ print " ";
+ }
+ print " ".$f->density_value()."\t".$f->start()."\n";
+ }
+# my $avg = undef;
+# $avg = $sum/$length if($length < 0);
+# print("Sum=$sum, Length=$length, Avg/Base=$sum");
+}
+
+
+
+
+
+
+
diff --git a/misc-scripts/density_feature/repeat_coverage_calc.pl b/misc-scripts/density_feature/repeat_coverage_calc.pl
new file mode 100644
index 0000000000000000000000000000000000000000..2f5983a686fa9d9235a359a88bc8b01db169c74c
--- /dev/null
+++ b/misc-scripts/density_feature/repeat_coverage_calc.pl
@@ -0,0 +1,150 @@
+#!/usr/bin/perl -w
+
+#use dbi;
+use Bio::EnsEMBL::DBSQL::DBAdaptor;
+use Bio::EnsEMBL::DBSQL::SliceAdaptor;
+use Bio::EnsEMBL::DBSQL::DensityFeatureAdaptor;
+use Bio::EnsEMBL::DBSQL::DensityTypeAdaptor;
+use Bio::EnsEMBL::Slice;
+use Bio::EnsEMBL::Analysis;
+use Bio::EnsEMBL::DensityType;
+use Bio::EnsEMBL::DensityFeature;
+use Bio::EnsEMBL::Mapper::RangeRegistry;
+use strict;
+
+my $host = '127.0.0.1';
+my $user = 'ensadmin';
+my $pass = 'ensembl';
+my $dbname = 'homo_sapiens_core_20_34';
+my $port = '5050';
+
+my $db = new Bio::EnsEMBL::DBSQL::DBAdaptor(-host => $host,
+ -user => $user,
+ -port => $port,
+ -pass => $pass,
+ -dbname => $dbname);
+
+
+
+my $block_size = 1e6;
+
+
+#
+# Get the adaptors needed;
+#
+
+my $slice_adaptor = $db->get_SliceAdaptor();
+my $dfa = $db->get_DensityFeatureAdaptor();
+my $dta = $db->get_DensityTypeAdaptor();
+my $aa = $db->get_AnalysisAdaptor();
+
+
+
+#
+# Create new analysis object for density calculation.
+#
+
+my $analysis = new Bio::EnsEMBL::Analysis (-program => "repeat_coverage_calc.pl",
+ -database => "ensembl",
+ -gff_source => "repeat_coverage_calc.pl",
+ -gff_feature => "density",
+ -logic_name => "PercentageRepeat");
+
+$aa->store($analysis);
+
+print "New analysis : ".$analysis->dbID." at ".$analysis->created."\n";
+
+#
+# Create new density type.
+#
+
+my $dt = Bio::EnsEMBL::DensityType->new(-analysis => $analysis,
+ -block_size => $block_size,
+ -value_type => 'ratio');
+
+$dta->store($dt);
+
+print "New density type : ".$dt->dbID."\n";
+
+foreach my $chrom (qw(X Y)){
+ print "creating density feature for chromosome $chrom with block size of $block_size\n";
+
+ my $slice = $slice_adaptor->fetch_by_region('chromosome',$chrom);
+
+ my $start = $slice->start();
+ my $end = ($start + $block_size)-1;
+ my $term = $slice->start+$slice->length;
+
+ my @density_features=();
+ while($start < $term){
+ my $sub_slice = $slice_adaptor->fetch_by_region('chromosome',$chrom,$start,$end);
+
+ my $rr = Bio::EnsEMBL::Mapper::RangeRegistry->new();
+
+ foreach my $repeat (@{$sub_slice->get_all_RepeatFeatures()}){
+ $rr->check_and_register("1",$repeat->start,$repeat->end);
+ }
+
+ my $count = 0;
+ foreach my $non_repeat (@{$rr->check_and_register("1",1,$block_size)}){
+ $count += ($non_repeat->[1]-$non_repeat->[0])+1;
+ }
+
+ print "repeat-> ".$count." are none repeat regions out of $block_size\n";
+ my $percentage_repeat = (($block_size-$count)/$block_size)*100;
+ push @density_features, Bio::EnsEMBL::DensityFeature->new(-seq_region => $slice,
+ -start => $start,
+ -end => $end,
+ -density_type => $dt,
+ -density_value => $percentage_repeat);
+
+ $start = $end+1;
+ $end = ($start + $block_size)-1;
+ }
+ $dfa->store(@density_features);
+ print scalar @density_features;
+ print_features(\@density_features);
+}
+
+
+
+#
+# helper to draw an ascii representation of the density features
+#
+sub print_features {
+ my $features = shift;
+
+ return if(!@$features);
+
+ my $sum = 0;
+ my $length = 0;
+# my $type = $features->[0]->{'density_type'}->value_type();
+
+ print("\n");
+ my $max=0;
+ foreach my $f (@$features) {
+ if($f->density_value() > $max){
+ $max=$f->density_value();
+ }
+ }
+ foreach my $f (@$features) {
+ my $i=1;
+ for(; $i< ($f->density_value()/$max)*40; $i++){
+ print "*";
+ }
+ for(my $j=$i;$j<40;$j++){
+ print " ";
+ }
+ print " ".$f->density_value()."\t".$f->start()."\n";
+ }
+# my $avg = undef;
+# $avg = $sum/$length if($length < 0);
+# print("Sum=$sum, Length=$length, Avg/Base=$sum");
+}
+
+
+
+
+
+
+