no longer relevant

scripts/denormalize

-#!/usr/local/bin/perl
-
-use strict;
-
-use Bio::EnsEMBL::DBSQL::DBAdaptor;
-use Bio::EnsEMBL::Clone;
-use Bio::EnsEMBL::RawContig;
-
-use Getopt::Long;
-
-my $host     = 'ecs1a';
-my $dbname   = 'mouse_sc011015_alistair';
-my $newhost  = 'ecs1f';
-my $newdbname = 'mouse_denormalize_test2';
-my $newpath   = 'CHR';
-my $dbuser   = 'ensadmin';
-my $pass     = 'ensembl';
-my $path     = 'sanger_20011015_2';
-my $genes    = 0;
-my $feature  = 0;
-my $genewise = 0;
-my $repeat   = 0;
-my $chunk    = 5000000;
-my $threshold = 0;
-my $chr_name;
-
-$| = 1;
-
-&GetOptions( 'host:s'    => \$host,
-             'dbuser:s'  => \$dbuser,
-             'dbname:s'  => \$dbname,
-	     'genes'     => \$genes,
-	     'feature'   => \$feature,
-	     'repeat'    => \$repeat,
-             'path=s'    => \$path,
-             'pass:s'    => \$pass,
-	     'chunk:n'   => \$chunk,
-	     'threshold:n' => \$threshold,
-	     'chrname:s'   => \$chr_name,
-             );
-
-print STDERR "Time in dumpgff " . time . "\n";
-
-my $db = new Bio::EnsEMBL::DBSQL::DBAdaptor(-host             => $host,
-					    -user             => $dbuser,
-					    -dbname           => $dbname,
-                                            -pass             => $pass);
-
-my $newdb = new Bio::EnsEMBL::DBSQL::DBAdaptor(-host             => $newhost,
-					       -user             => $dbuser,
-					       -dbname           => $newdbname,
-					       -pass             => $pass);
-
-print STDERR "Time after db  " . time . "\n";
-
-print STDERR "Connected to database\n";
-
-$db->assembly_type($path);
-
-my $slice_adp = $db->get_SliceAdaptor();
-my $chr_adp   = $db->get_ChromosomeAdaptor();
-my @chrs   = @{$chr_adp->fetch_all};
-
-my %analysis;
-
-CHR: foreach my $chr (@chrs) {
-  next CHR unless $chr->name eq $chr_name;
-
-  my $length = $chr->length;
-  print STDERR "Chromosome $chr length $length\n";
-
-  my $current = 1;
-  
-  while ($current <= $length) {
-    print STDERR "Time before chunk " . time . "\n";
-    my $end = $current + $chunk -1;
-
-    if ($end > $length) {
-      $end = $length;
-    }
-    
-    my $slice = $slice_adp->fetch_by_chr_start_end($chr,
-						   $current,
-						   $end);
-
-    my $repeats  = $slice->get_all_RepeatFeatures      if ($repeat);
-    my $feat     = $slice->get_all_SimilarityFeatures  if ($feature);
-
-    my $seq      = $slice->seq;
-
-    my $cloneid  = $chr . ".$current-$end";
-
-    my $clone  = new Bio::EnsEMBL::Clone;
-
-    $clone->htg_phase(3);
-    $clone->id($cloneid);
-    
-    my $contigid = $cloneid;
-
-    my $contig   = new Bio::EnsEMBL::RawContig;
-    
-    $contig->name($contigid);
-    $contig->seq($seq);
-
-    print STDERR "Contig id " . $contigid . "\n";
-
-    print STDERR "Repeats are " . scalar(@$repeats) . "\n";
-
-    foreach my $f (@$repeats) {
-      $f->contig($contig);
-    }
-
-    foreach my $f (@$feat) {
-			if ($f->analysis->db ne "") {
-			  if ($f->score > $threshold) {
-					$f->contig($contig);
-					$f->analysis->program_version(1);
-				}
-      } else {
-	      $f->analysis->program_version(1);
-	      $f->contig($contig);
-      }
-    }
-    
-    $clone->add_Contig($contig);
-    
-    eval {
-      $newdb->get_CloneAdaptor->store($clone);
-      print STDERR "Written ".$clone->id." scaffold into db\n";
-    };
-    
-    if( $@ ) {
-      print STDERR "Could not write clone into database, error was $@\n";
-    } else {
-      my $contig = 
-				$newdb->get_RawContigContigAdaptor->fetch_by_name($contigid);
-      
-      # put into the golden path
-      
-      my $len = ($end - $current + 1);
-
-      my $query = "insert into assembly values('$chr','$chr'," . $contig->dbID . ",$current,$end,1,$len,1,$len,1,'$newpath')";
-      
-      my $sth = $newdb->prepare($query);
-      
-      my $res = $sth->execute;
-    
-    }
-    $current += $chunk;
-  }
-}
-
-
-sub print_analysis {
-  my ($analysis) = @_;
-
-  print STDERR "Analysis\n";
-  print STDERR "Id " . $analysis->id . "\n";
-  print STDERR "Db" . $analysis->db . "\n";
-  print STDERR "Db_file " . $analysis->db_file . "\n";
-  print STDERR "Db_version " . $analysis->db_version . "\n";
-  print STDERR "Program " . $analysis->program . "\n";
-  print STDERR "Program_version " . $analysis->program_version . "\n";
-  print STDERR "Program_file " . $analysis->program_file . "\n";
-  print STDERR "Gff_source " . $analysis->gff_source . "\n";
-  print STDERR "Gff_feature " . $analysis->gff_feature . "\n";
-  print STDERR "Module " . $analysis->module . "\n";
-  print STDERR "Module_version " . $analysis->module_version . "\n";
-  print STDERR "Parameters " . $analysis->parameters . "\n";
-  print STDERR "Created " . $analysis->created . "\n";
-  print STDERR "Logic_name " . $analysis->logic_name . "\n";
-}
-