From ea6c2f376258254c82325ac4bfb209eaf56c88d3 Mon Sep 17 00:00:00 2001
From: Arne Stabenau <stabenau@sanger.ac.uk>
Date: Wed, 8 Dec 2004 10:30:56 +0000
Subject: [PATCH] snp_lite_density replaced by variation_density.pl
---
.../density_feature/snp_lite_density.pl | 200 ------------------
1 file changed, 200 deletions(-)
delete mode 100644 misc-scripts/density_feature/snp_lite_density.pl
diff --git a/misc-scripts/density_feature/snp_lite_density.pl b/misc-scripts/density_feature/snp_lite_density.pl
deleted file mode 100644
index 11ce92be9c..0000000000
--- a/misc-scripts/density_feature/snp_lite_density.pl
+++ /dev/null
@@ -1,200 +0,0 @@
-#
-# script to calculate the snp density with help of
-# attached lite database. Only works if argument database
-# is a core database and lite can be found by substituting
-# s/_core_/_lite_/
-#
-# blocksize condition is 4_000 per genome?
-
-
-use strict;
-
-use Bio::EnsEMBL::DBSQL::DBAdaptor;
-use Bio::EnsEMBL::DensityType;
-use Bio::EnsEMBL::DensityFeature;
-use Bio::EnsEMBL::Lite::DBAdaptor;
-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);
-
-if( ! lite_attach( $db )) {
- die( "Couldnt attache lite to $dbname" );
-}
-
-#
-# 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();
-
-my $top_slices = $slice_adaptor->fetch_all( "toplevel" );
-
-
-my ( $block_size, $genome_size );
-for my $slice ( @$top_slices ) {
- $genome_size += $slice->length();
-}
-
-$block_size = int( $genome_size / 4000 );
-
-my $analysis = new Bio::EnsEMBL::Analysis (-program => "snp_lite_density.pl",
- -database => "ensembl",
- -gff_source => "snp_lite_density.pl",
- -gff_feature => "density",
- -logic_name => "snpDensity");
-
-$aa->store( $analysis );
-
-
-#
-# Create new density type.
-#
-my $dt = Bio::EnsEMBL::DensityType->new(-analysis => $analysis,
- -block_size => $block_size,
- -value_type => 'sum');
-$dta->store($dt);
-
-
-#
-# Now the actual feature calculation loop
-#
-
-my ( $current_start, $current_end );
-
-
-
-foreach my $slice (@$top_slices){
-
- $current_start = 1;
-
- print "SNP densities for ".$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;
-
- #
- # How many snps fall into this subslice
- #
- foreach my $snp (@{$sub_slice->get_all_SNPs()}){
- if( $snp->start >= 1 ) {
- $count++
- }
- }
-
- my $df = Bio::EnsEMBL::DensityFeature->new
- (-seq_region => $slice,
- -start => $current_start,
- -end => $current_end,
- -density_type => $dt,
- -density_value => $count);
-
- $current_start = $current_end + 1;
-
- $dfa->store($df);
- }
-}
-
-
-#
-# tries to attach lite.
-#
-
-sub lite_attach {
- my $db = shift;
-
- my $core_db_name;
- $core_db_name = $db->dbname();
- if( $core_db_name !~ /_core_/ ) {
- return 0;
- }
- #
- # get a lost of all databases on that server
- #
- my $sth = $db->dbc->prepare( "show databases" );
- $sth->execute();
- my $all_db_names = $sth->fetchall_arrayref();
- my %all_db_names = map {( $_->[0] , 1)} @$all_db_names;
- my $snp_db_name = $core_db_name;
- $snp_db_name =~ s/_core_/_lite_/;
- if( ! exists $all_db_names{ $snp_db_name } ) {
- return 0;
- }
-
- my $snp_db = Bio::EnsEMBL::Lite::DBAdaptor->new
- ( -host => $db->host(),
- -user => $db->username(),
- -pass => $db->password(),
- -port => $db->port(),
- -dbname => $snp_db_name );
- $db->add_db_adaptor( "lite", $snp_db );
- return 1;
-}
-
-
-
-#
-# 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";
- }
-}
-
-
-
-
-
-
-
--
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