percent_gc_calc.pl

#!/usr/local/ensembl/bin/perl -w

#
# Calculate the GC content for top level seq_regions
#   small regions 500bp to be able to display on contigview
#   big regions genomesize / 4000 for 4000 features on the genome


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;
use Getopt::Long;

my ( $host, $user, $pass, $port, $dbname  );

GetOptions( "host|h=s", \$host,
	    "user|u=s", \$user,
	    "pass|p=s", \$pass,
	    "port=i",   \$port,
	    "dbname|d=s", \$dbname,
	    "help" ,     \&usage
	  );

usage() if (!$host || !$user || !$pass || !$dbname);

my $db = new Bio::EnsEMBL::DBSQL::DBAdaptor(-host => $host,
					    -user => $user,
					    -port => $port,
					    -pass => $pass,
					    -dbname => $dbname);


my $bin_count  = 150;
my $max_slices = 100;

#
# Check wether the script should run on given database
#
my $sth = $db->dbc->prepare( "select count(*) from dna" );
$sth->execute();
my ( $dna_count )  = $sth->fetchrow_array();
if( ! $dna_count ) {
  print STDERR "No dna, no gc content for $dbname.\n";
  exit();
}



print STDOUT "Deleting old PercentGC features\n";
$sth = $db->dbc->prepare(
  qq(
DELETE df, dt, a, ad
FROM density_feature df, density_type dt, analysis a, analysis_description ad
WHERE a.analysis_id=dt.analysis_id
AND ad.analysis_id = a.analysis_id
AND dt.density_type_id=df.density_type_id
AND a.logic_name='percentgc') );
$sth->execute();

#
# 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();

# Sort slices by coordinate system rank, then by length.
my @sorted_slices =
  sort( {      $a->coord_system()->rank() <=> $b->coord_system()->rank()
            || $b->seq_region_length() <=> $a->seq_region_length()
  } @{ $slice_adaptor->fetch_all('toplevel') } );

#
# 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",
             -description => 'Percentage of G/C bases in the sequence.',
             -display_label => 'GC content',
             -displayable   => 1 );

$aa->store($analysis);
$aa->update($analysis);

#
# Create new density type.
#


my $density_type = Bio::EnsEMBL::DensityType->new
  (-analysis   => $analysis,
   -region_features => $bin_count,
   -value_type => 'ratio');

$dta->store($density_type);


my ( $current_start, $current_end, $current );
my $slice_count = 0;
my $block_size;

while ( my $slice = shift @sorted_slices ){

  $block_size = $slice->length() / $bin_count;

  my @density_features=();

  print STDOUT "GC percentage for ".$slice->seq_region_name().
    " with block size $block_size\n";

  $current_end = 0;
  $current = 0;

  while ($current_end < $slice->length) {

    $current += $block_size;
    $current_start = $current_end+1;
    $current_end = int( $current + 1 );

    if ( $current_end < $current_start ) { 
      $current_end = $current_start;
    }

    if ( $current_end > $slice->end() ) {
      $current_end = $slice->end();
    }


    my $sub_slice = $slice->sub_Slice( $current_start , $current_end );

    my $gc = $sub_slice->get_base_count()->{'%gc'};
    my $df =  Bio::EnsEMBL::DensityFeature->new
      (-seq_region    => $slice,
       -start         => $current_start,
       -end           => $current_end,
       -density_type  => $density_type,
       -density_value => $gc);
    #print join ("\t", $slice, $current_start, $current_end, $density_type, $gc, "\n");
    $dfa->store($df);

  }

  last if ( $slice_count++ > $max_slices );
}



#
# 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");
}


sub usage {
  my $indent = ' ' x length($0);
  print <<EOF; exit(0);


What does it do?

First, it needs the dna table to be populated. It then deletes
all PercentGC entries from the analysis, density_type and 
density_feature tables. All toplevel slices are fetched and sorted
from longest to shortest. Each slice is divided into 150 bins
(blocks). For each of the blocks or sub-slices, the %gc is
calculated.

Input data: dna sequence, top level seq regions 
Output tables: analysis (logic_name: percentgc), analysis description, 
               density_type, density_feature


When to run it in the release cycle?

It can be run after genebuilders have finished their Xrefs 
(script not affected by projected Xrefs).


Which databases to run it on?

Run on core databases for new species or if one of the following changed:
  - dna sequence
  - assembly


How long does it take?

It takes about 15 mins to run for a database in normal queue,


Usage:

  $0 -h host [-port port] -u user -p password \\
  $indent -d database \\
  $indent [-help]  \\

  -h|host              Database host to connect to

  -port                Database port to connect to (default 3306)

  -u|user              Database username

  -p|pass              Password for user

  -d|dbname            Database name

  -help                This message


EOF

}