diff --git a/misc-scripts/density_feature/vega_gene_density_calc.pl b/misc-scripts/density_feature/vega_gene_density_calc.pl
deleted file mode 100644
index b35465731a3814e35b2c60a77bdb38cf79222e58..0000000000000000000000000000000000000000
--- a/misc-scripts/density_feature/vega_gene_density_calc.pl
+++ /dev/null
@@ -1,305 +0,0 @@
-#
-# script to calculate the gene density features on a database
-# should work on any species database
-#
-
-#
-# It will only run on databases with genes ...
-# boundary condition: on average there should be 2 genes per block
-#
-
-# this is a modified version of gene_density.calc.pl written for vega by st3 - is a bit slow since when looking for each type of gene it actually retrieves all genes but then only records those of the correct type.
-
-
-use strict;
-
-use lib '../../modules/','../../../bioperl-live';
-use Data::Dumper;
-
-use Bio::EnsEMBL::DBSQL::DBAdaptor;
-use Bio::EnsEMBL::DensityType;
-use Bio::EnsEMBL::DensityFeature;
-use Getopt::Long;
-
-my ( $host, $user, $pass, $port, $dbname );
-
-my ( $block_count, $genome_size, $block_size );
-
-GetOptions( "host=s", \$host,
- "user=s", \$user,
- "pass=s", \$pass,
- "port=i", \$port,
- "dbname=s", \$dbname
- );
-
-my $db = new Bio::EnsEMBL::DBSQL::DBAdaptor(-host => $host,
- -user => $user,
- -port => $port,
- -pass => $pass,
- -dbname => $dbname);
-
-my $sth = $db->prepare( "select count(*) from gene" );
-$sth->execute();
-
-my ( $gene_count ) = $sth->fetchrow_array();
-
-if( ! $gene_count ) {
- print STDERR "No gene density for $dbname.\n";
- exit();
-} else {
- $block_count = $gene_count >> 1;
-}
-
-#
-# Could be database without seq_regions
-# Then have to try and attach core db
-#
-$sth = $db->prepare( "select count(*) from seq_region" );
-$sth->execute();
-my ( $seq_region_count ) = $sth->fetchrow_array();
-if( ! $seq_region_count ) {
- #
- # for the time being only do core dbs
- # no dbs with no seq regions
- #
- print STDERR "No gene density for $dbname, no seq_regions.\n";
- exit();
-
- if( ($dbname =~ /_estgene_/ ) || ( $dbname =~ /_vega_/ )) {
- my $dna_db_name = $dbname;
- $dna_db_name =~ s/(_estgene_|_vega_)/_core_/;
- my $dna_db = new Bio::EnsEMBL::DBSQL::DBAdaptor
- (-host => $host,
- -user => $user,
- -port => $port,
- -pass => $pass,
- -dbname => $dna_db_name );
- print STDERR "Attaching $dna_db_name to $dbname.\n";
- $db->dnadb( $dna_db );
- } else {
- print STDERR "No gene density for $dbname, no seq_regions.\n";
- exit();
- }
-}
-
-#
-# Get the adaptors needed;
-#
-
-my $dfa = $db->get_DensityFeatureAdaptor();
-my $dta = $db->get_DensityTypeAdaptor();
-my $aa = $db->get_AnalysisAdaptor();
-my $slice_adaptor = $db->get_SliceAdaptor();
-
-#
-# block size estimation
-#
-
-my $top_slices = $slice_adaptor->fetch_all('toplevel');
-for my $slice ( @$top_slices ) {
- $genome_size += $slice->length();
-}
-
-$block_size = int( $genome_size / $block_count );
-
-#which types of geens are we interested in?
-my $analysis_names = {
- 'pseudoGeneDensity'=>[
- 'Processed_pseudogene',
- 'Pseudogene',
- 'Unprocessed_pseudogene'],
- 'knownGeneDensity'=>'Known',
- 'novelCDSDensity'=>'Novel_CDS',
- 'novelTransDensity'=>'Novel_Transcript',
- 'putativeTransDensity'=>'Putative',
- 'predictedTransDensity'=>'Predicted_Gene',
- 'predictedIgPseudoDensity'=>'Ig_Pseudogene_Segment',
- 'IgSegDensity'=>'Ig_Segment'
- };
-my $total_successes;
-my $known_successess;
-my $novel_cds_successes;
-my $novel_trans_successes;
-my $putative_successes;
-my $pseudo_successes;
-my $predicted_trans_successes;
-my $predictedIGPseudo_successes;
-my $IgSegment_successes;
-my $failures;
-
-# Now the actual feature calculation loop, looking for each gene type in turn
-
-foreach my $anal_name (keys %$analysis_names) {
-
- my %gene_names;
-
-#create analysis object for each gene type
- my $analysis = new Bio::EnsEMBL::Analysis (-program => "vega_gene_density_calc.pl",
- -database => "ensembl",
- -gff_source => "vega_gene_density_calc.pl",
- -gff_feature => "density",
- -logic_name => $anal_name);
- $aa->store( $analysis );
-
- print "FETCHING DATA ON GENES OF TYPE $analysis_names->{$anal_name}:\n"; # I know this doesn't display correctly for pseudogenes, tough!
-
- $analysis = $aa->fetch_by_logic_name($anal_name);
-
- #
- # Create new density type for each gene type
- my $dt = Bio::EnsEMBL::DensityType->new(-analysis => $analysis,
- -block_size => $block_size,
- -value_type => 'sum');
- $dta->store($dt);
-
- my ( $current_start, $current_end );
-
- foreach my $slice (@$top_slices){
- $current_start = 1;
- my @density_features=();
- print "Gene densities for ".$slice->seq_region_name().
- " with block size $block_size\n";
-
- while($current_start <= $slice->end()) {
- $current_end = $current_start+$block_size-1;
- if( $current_end > $slice->end() ) {
- $current_end = $slice->end();
- }
-
- my $sub_slice = $slice->sub_Slice( $current_start, $current_end );
- my $count =0;
-
- #
- # retrieve info for all genes on the subslice, but count only those of a particular type
- #
-
- foreach my $gene (@{$sub_slice->get_all_Genes()}){
-#only count each gene once for each gene type loop
- if (exists $gene_names{$gene->stable_id}) {
- next;
- }
- else {
- $gene_names{$gene->stable_id} = 1;
- }
-#pseudogenes first...
- my $classification = $gene->type;
- if ($anal_name eq 'pseudoGeneDensity'){
- my $check = 0;
- foreach my $pseudo_type (@{$analysis_names->{$anal_name}}) {
- if (($classification eq $pseudo_type) & ($check<1)) {
- $count++;
- $check = 1;
- $total_successes++;
- $pseudo_successes++;
- }
- else {
- $failures++;
- }
- }
- }
-#then the other types
- elsif ($classification eq $analysis_names->{$anal_name}) {
- if ($anal_name eq 'knownGeneDensity') {
- $count++;
- $total_successes++;
- $known_successess++;
- } elsif ($anal_name eq 'novelCDSDensity') {
- $count++;
- $total_successes++;
- $novel_cds_successes++;
- } elsif ($anal_name eq 'novelTransDensity') {
- $count++;
- $total_successes++;
- $novel_trans_successes++;
- } elsif ($anal_name eq 'putativeTransDensity') {
- $count++;
- $total_successes++;
- $putative_successes++;
- } elsif ($anal_name eq 'predictedTransDensity') {
- $count++;
- $total_successes++;
- $predicted_trans_successes++;
- } elsif ($anal_name eq 'predictedIgPseudoDensity') {
- $count++;
- $total_successes++;
- $predictedIGPseudo_successes++;
- } elsif ($anal_name eq 'IgSegDensity') {
- $count++;
- $total_successes++;
- $IgSegment_successes++;
- }
- else {
- $failures++;
- }
- }
- }
-
- push @density_features, Bio::EnsEMBL::DensityFeature->new
- (-seq_region => $slice,
- -start => $current_start,
- -end => $current_end,
- -density_type => $dt,
- -density_value => $count);
-
- $current_start = $current_end + 1;
- # print STDERR ".";
- }
- $dfa->store(@density_features);
- print "Created ", scalar @density_features, " gene density features.\n";
- # print_features(\@density_features);
- }
-}
-print "number of genes in db = $gene_count\n";
-print "total number of succesfull identifications = $total_successes\n";
-print "number of known genes = $known_successess\n";
-print "number of novel cds = $novel_cds_successes\n";
-print "number of novel trans = $novel_trans_successes\n";
-print "number of putative trans = $putative_successes\n";
-print "number of pseudogenes = $pseudo_successes\n";
-print "number of predicted transgenes = $predicted_trans_successes\n";
-print "number of IG Pseudogene Segments = $predictedIGPseudo_successes\n";
-print "number of IG Segments = $IgSegment_successes\n";
-# this gives totally the wrong number of failures and is not to be relied upon at all!
-#if ($failures > 0) {
-# print "warning, you have some unmatched genes: a lot less than $failures\n";
-#}
-
-#
-# 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();
- }
- }
- if( !$max ) { $max = 1 };
-
- 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";
- }
-}
-
-
-
-
-
-
-