removed obsolete scripts

misc-scripts/density_feature/vega_densities_multi_db.pl

-#
-# These script runs all density creation scripts on all
-# databases that match input pattern. It calls all configured
-# scripts of this directory with host, user,pass,port and dbname 
-# parameter.
-#
-use strict;
-use Getopt::Long;
-use DBI;
-
-#
-# configure this hash and command line parameter section for 
-#  adding new scripts
-#
-
-my %density_scripts = 
-  ( "gene"   => "vega_gene_density_calc.pl",
-    "gc"     => "percent_gc_calc.pl", 
-    "repeat" => "repeat_coverage_calc.pl",
-    "stats"  => "vega_seq_region_stats.pl",
-    "snp"    => "snp_lite_density.pl" );
-
-my @density_scripts = ();
-
-my ( $host, $user, $pass, $port, $dbpattern );
-
-GetOptions( "host=s", \$host,
-	    "user=s", \$user,
-	    "pass=s", \$pass,
-	    "port=i", \$port,
-	    "gene", sub { push( @density_scripts, $density_scripts{'gene'} ); },
-	    "gc", sub { push( @density_scripts, $density_scripts{'gc'} ); },
-	    "repeat", sub { push( @density_scripts, $density_scripts{'repeat'} ); },
-	    "stats", sub { push( @density_scripts, $density_scripts{'stats'} ); },
-	    "snp", sub { push( @density_scripts, $density_scripts{'snp'} ); },
-	    "dbpattern=s", \$dbpattern
-	  );
-
-if( !$host || !$user ) {
-  usage();
-}
-
-my $dsn = "DBI:mysql:host=$host";
-my $args = "-host $host ";
-if( $user ) {
-  $args .= "-user $user ";
-}
-
-if( $port ) {
-  $args .= "-port $port ";
-  $dsn .= ";port=$port";
-}
-
-if( $pass ) {
-  $args .= "-pass $pass ";
-}
-
-if( $host ) {
-  $args .= "-host $host ";
-}
-
-
-my $db = DBI->connect( $dsn, $user, $pass );
-
-my @dbnames = map {$_->[0] } @{ $db->selectall_arrayref( "show databases" ) };
-
-for my $dbname ( @dbnames ) {
-  if( $dbpattern ) {
-    if( $dbname !~ /$dbpattern/ ) {
-      next;
-    }
-  } else {
-    print STDERR "$dbname\n";
-    next;
-  }
-
-  if( ! @density_scripts ) {
-    print "Matches $dbname.\n";
-  } else {
-    for my $scriptname ( @density_scripts ) {
-      print( "/usr/local/ensembl/bin/perl $scriptname $args -dbname $dbname\n" );
-      system( "/usr/local/ensembl/bin/perl $scriptname $args -dbname $dbname" );
-    }
-  }
-}
-
-
-sub usage {
-  print STDERR "densities_multi_db.pl runs \n  ";
-  print STDERR <<EOF;
-
- with parameters -host [hostname] -user [username with write permit] 
-                 -pass [password] -port [portnumber]
- on all databases that match -dbpattern [some_db_regexp]
- on -gene, -repeat, -stats, -gc.
-
- Without -dbpattern it lists all available databases and does nothing.
-
-EOF
-  exit();
-}

misc-scripts/density_feature/vega_seq_region_stats.pl

-#!/usr/local/bin/perl
-
-=head1 NAME
-
-vega_seq_region_stats.pl -
-script to calculate gene and snp numbers for mapview stats
-
-=head1 SYNOPSIS
-
-
-=head1 DESCRIPTION
-
-
-=head1 LICENCE
-
-This code is distributed under an Apache style licence:
-Please see http://www.ensembl.org/code_licence.html for details
-
-=head1 AUTHOR
-
-Patrick Meidl <pm2@sanger.ac.uk>
-
-=head1 CONTACT
-
-Post questions to the EnsEMBL development list ensembl-dev@ebi.ac.uk
-
-=cut
-
-use strict;
-BEGIN {
-    $ENV{'ENSEMBL_SERVERROOT'} = "../../..";
-    unshift(@INC,"$ENV{'ENSEMBL_SERVERROOT'}/conf");
-    unshift(@INC,"$ENV{'ENSEMBL_SERVERROOT'}/ensembl-compara/modules");
-    unshift(@INC,"$ENV{'ENSEMBL_SERVERROOT'}/ensembl-draw/modules");
-    unshift(@INC,"$ENV{'ENSEMBL_SERVERROOT'}/ensembl-external/modules");
-    unshift(@INC,"$ENV{'ENSEMBL_SERVERROOT'}/ensembl-otter/modules");
-    unshift(@INC,"$ENV{'ENSEMBL_SERVERROOT'}/modules");
-    unshift(@INC,"$ENV{'ENSEMBL_SERVERROOT'}/ensembl/modules");
-    unshift(@INC,"$ENV{'ENSEMBL_SERVERROOT'}/bioperl-live");
-}
-
-use SiteDefs;
-use EnsWeb;
-use EnsEMBL::DB::Core;
-use Getopt::Long;
-
-my ($species, $run, $help);
-&GetOptions(
-    "species=s" => \$species,
-    "run=s"	=> \$run,
-    "help"      => \$help,
-    "h"         => \$help,
-);
-
-if($help || !($species && $run)){
-    print qq(Usage:
-    ./vega_seq_region_stats.pl
-        --species=Homo_sapiens
-        --run=gene,snp
-        [--help]\n\n);
-    exit;
-}
-
-$ENV{'ENSEMBL_SPECIES'} = $species;
-
-## set db user/pass to allow write access
-my $db_ref = $EnsWeb::species_defs->databases;
-$db_ref->{'ENSEMBL_DB'}{'USER'} = $EnsWeb::species_defs->ENSEMBL_WRITE_USER;
-$db_ref->{'ENSEMBL_DB'}{'PASS'} = $EnsWeb::species_defs->ENSEMBL_WRITE_PASS;
-
-## connect to databases
-my %run;
-@run{split(/,/, $run)} = 1;
-my @dbs = qw(core);
-push @dbs, 'glovar' if ($run{'snp'});
-my $databases = &EnsEMBL::DB::Core::get_databases(@dbs);
-
-die "Problem connecting to databases: $databases->{'error'}\n"
-    if  $databases->{'error'} ;
-warn "Database error: $databases->{'non_fatal_error'}\n"
-    if $databases->{'non_fatal_error'};
-
-## get slice and attribute adaptors, loop over all toplevel slices
-my $slice_adaptor = $databases->{'core'}->get_SliceAdaptor();
-my $attrib_adaptor = $databases->{'core'}->get_AttributeAdaptor();
-my $top_slices = $slice_adaptor->fetch_all("toplevel");
-
-foreach my $slice (@$top_slices) {
-    my %num;
-    my @attribs;
-    
-    print STDERR "Processing seq_region ", $slice->seq_region_name(), ":\n";
-
-    ## genes
-    if ($run{'gene'}) {
-        print STDERR "\tGenes...\n";
-        my @genes = @{$slice->get_all_Genes()};
-        foreach my $gene (@genes) {
-            my $type = $gene->type;
-            $num{$type}++;
-            if ($type =~ /seudogene$/) {
-                $num{'Total_Pseudogenes'}++;
-            }
-        }
-
-        print STDERR "Slice", $slice->seq_region_name(),
-            " has the following features:\n\n";
-        foreach my $type (keys %num) {
-            print STDERR "$type = $num{$type}\n";
-        }
-
-        push @attribs, Bio::EnsEMBL::Attribute->new
-        (-NAME => 'Known genes',
-         -CODE => 'KnownGeneCount',
-         -VALUE => $num{'Known'},
-         -DESCRIPTION => 'Total Number of Known genes');
-
-        push @attribs, Bio::EnsEMBL::Attribute->new
-        (-NAME => 'Novel CDS',
-         -CODE => 'NovelCDSCount',
-         -VALUE => $num{'Novel_CDS'},
-         -DESCRIPTION => 'Total Number of Novel CDSs');
-
-        push @attribs, Bio::EnsEMBL::Attribute->new
-        (-NAME => 'Novel transcripts',
-         -CODE => 'NovelTransCount',
-         -VALUE => $num{'Novel_Transcript'},
-         -DESCRIPTION => 'Total Number of Novel transcripts');
-
-        push @attribs, Bio::EnsEMBL::Attribute->new
-        (-NAME => 'Putative transcripts',
-         -CODE => 'PutTransCount',
-         -VALUE => $num{'Putative'},
-         -DESCRIPTION => 'Total Number of Putative transcripts');
-
-        push @attribs, Bio::EnsEMBL::Attribute->new
-        (-NAME => 'Predicted transcripts',
-         -CODE => 'PredTransCount',
-         -VALUE => $num{'Predicted_Gene'},
-         -DESCRIPTION => 'Total Number of Predicted transcripts');
-
-        push @attribs, Bio::EnsEMBL::Attribute->new
-        (-NAME => 'Total Pseudogenes',
-         -CODE => 'TotPsCount',
-         -VALUE => $num{'Total_Pseudogenes'},
-         -DESCRIPTION => 'Total Number of Pseudogenes');
-
-        push @attribs, Bio::EnsEMBL::Attribute->new
-        (-NAME => 'Unclassified pseudogenes',
-         -CODE => 'UnclassPsCount',
-         -VALUE => $num{'Pseudogene'},
-         -DESCRIPTION => 'Number of Unclassified pseudogenes');
-
-        push @attribs, Bio::EnsEMBL::Attribute->new
-        (-NAME => 'Processed pseudogenes',
-         -CODE => 'ProcPsCount',
-         -VALUE => $num{'Processed_pseudogene'},
-         -DESCRIPTION => 'Number of Processed pseudogenes');
-
-        push @attribs, Bio::EnsEMBL::Attribute->new
-        (-NAME => 'Unprocessed pseudogenes',
-         -CODE => 'UnprocPsCount',
-         -VALUE => $num{'Unprocessed_pseudogene'},
-         -DESCRIPTION => 'Number of Unprocessed pseudogenes');
-
-        push @attribs, Bio::EnsEMBL::Attribute->new
-        (-NAME => 'Ig Segments',
-         -CODE => 'IgSegCount',
-         -VALUE => $num{'Ig_Segment'},
-         -DESCRIPTION => 'Total Number of Ig Segments');
-
-        push @attribs, Bio::EnsEMBL::Attribute->new
-        (-NAME => 'Ig Pseudogene Segments',
-         -CODE => 'IgPsSegCount',
-         -VALUE => $num{'Ig_Pseudogene_Segment'},
-         -DESCRIPTION => 'Total Number of Ig Pseudogene Segments');
-    }
-
-    ## snps
-    if ($run{'snp'}) {
-        print STDERR "\tSNPs...\n";
-	my $snps = $slice->get_all_ExternalFeatures('GlovarSNP');
-	push @attribs, Bio::EnsEMBL::Attribute->new
-	(-NAME => 'SNPs',
-	 -CODE => 'SNPCount',
-	 -VALUE => scalar( @$snps ),
-	 -DESCRIPTION => 'Total Number of SNPs');
-    }
-    
-    $attrib_adaptor->store_on_Slice($slice, \@attribs);
-    #  print_chromo_stats([$slice]);
-}
-
-
-
-sub print_chromo_stats {
-    my $chromosomes = shift;
-    
-    foreach my $chr (@$chromosomes) {
-	print "\nchromosome: ",$chr->seq_region_name(),"\n";
-	foreach my $attrib (@{$chr->get_all_Attributes()}) {
-	    print "  ", $attrib->name(), ": ", $attrib->value(), "\n";
-	}
-    }
-}
-
-1;
-
-