/
displayStats.pl
executable file
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/
displayStats.pl
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#!/usr/bin/perl -w
use strict;
use FindBin;
use lib $FindBin::Bin;
use SeqComplex;
use Getopt::Long;
use Data::Dumper;
my %methodMetaData = (
"at" => { "title" => "Percent AT",
"x_units" => "AT%" },
"gc" => { "title" => "Percent GC",
"x_units" => "GC%" },
"ats" => { "title" => "AT Skew",
"x_units" => "(A-T)/(A+T)" },
"gcs" => { "title" => "GC Skew",
"x_units" => "(G-C)/(G+C)" },
"ce" => { "title" => "Shannon Entropy",
"x_units" => "bits" },
"cm" => { "title" => "Markov Model Complexity",
"x_units" => "entropy" },
"cl" => { "title" => "Linguisitic Complexity",
"x_units" => "word fraction" },
"ct" => { "title" => "Trifonov Complexity",
"x_units" => "word fraction" },
"cz" => { "title" => "Compression Factor ( gzip )",
"x_units" => "compression factor" },
"cwf" => { "title" => "Wootton and Federhen Complexity",
"x_units" => "complexity" },
"cpg" => { "title" => "Percent CpGs",
"x_units" => "CpG%" } );
=head1 NAME
displayStats.pl [-graph] -in <STATSFILE> > outputfile
=head1 DESCRIPTION
This script read in the output of gatherStats.pl and either
output a data table or a set of Google Charts HTML.
=cut
my $help = undef;
my $graph = undef;
my $graphBins = 100;
my $seq = "";
my $datafile = "";
usage()
if (
!GetOptions(
'help|h' => \$help,
'in=s' => \$datafile,
'graph|g' => \$graph
)
);
usage() if ( defined $help );
usage() if ( $datafile eq "" );
# MAIN
my %hdrData = runAllMethodsInline( "ACGTACGT" );
my @methods = sort keys( %hdrData );
my $data = serializeIN( $datafile );
my %rawData = %{$data};
if ( defined $graph )
{
# Autobin each data column
my %methodRanges = ();
foreach my $method ( keys( %rawData ) )
{
$methodRanges{$method}->{'min'} = -1;
$methodRanges{$method}->{'max'} = -1;
foreach my $file ( keys( %{ $rawData{$method} } ) )
{
foreach my $value ( @{ $rawData{$method}->{$file} } )
{
if ( $methodRanges{$method}->{'min'} == -1
|| $value < $methodRanges{$method}->{'min'} )
{
$methodRanges{$method}->{'min'} = $value;
}
if ( $methodRanges{$method}->{'max'} == -1
|| $value > $methodRanges{$method}->{'max'} )
{
$methodRanges{$method}->{'max'} = $value;
}
}
}
}
my %graphBinData = ();
my %binSizes = ();
foreach my $method ( keys( %rawData ) )
{
my $rangeLen =
$methodRanges{$method}->{'max'} - $methodRanges{$method}->{'min'};
my $binSize = $rangeLen / $graphBins;
if ( $binSize == 0 )
{
$binSize = $methodRanges{$method}->{'min'} / $graphBins;
$methodRanges{$method}->{'min'} =
$methodRanges{$method}->{'min'} - ( $graphBins * $binSize );
}
$binSizes{$method} = $binSize;
foreach my $file ( keys( %{ $rawData{$method} } ) )
{
foreach my $value ( @{ $rawData{$method}->{$file} } )
{
$value -= $methodRanges{$method}->{'min'};
my $bin = 0;
if ( $binSize != 0 )
{
$bin = sprintf( "%0.0f", $value / $binSize );
}
$graphBinData{$method}->{$file}->[ $bin ]++;
}
}
}
print "<HTML>\n";
print "<HEAD>\n";
print "<SCRIPT type=\"text/javascript\" src=\"https://www.gstatic.com/charts/loader.js\"></SCRIPT>\n";
print " <SCRIPT type=\"text/javascript\">\n";
print " google.charts.load('current', {packages: ['corechart', 'line']});\n";
print " google.charts.setOnLoadCallback(drawChart);\n";
print " function drawChart() {\n";
foreach my $method ( keys( %graphBinData ) )
{
my $binSize = $binSizes{$method};
my $methodPrefix = $method;
my $wordSize = 0;
if ( $methodPrefix =~ /^([a-zA-Z]+)(\d*)$/ )
{
$methodPrefix = $1;
$wordSize = $2 if ( $2 ne "" );
}
print " var data_$method = new google.visualization.DataTable();\n";
print " data_$method.addColumn('number','" . $methodMetaData{$methodPrefix}->{'x_units'} . "');\n";
foreach my $file ( sort keys( %{ $graphBinData{$method} } ) )
{
print " data_$method.addColumn('number',\'$file\');\n";
}
print " data_$method.addRows([\n";
my $bin = $methodRanges{$method}->{'min'};
if ( $binSize == 0 )
{
my $str = "[$bin, ";
if ( $methodPrefix =~ /at|gc|cpg/ )
{
$str = "[" . ( $bin * 100 ) . ", ";
}
foreach my $file ( sort keys( %{ $graphBinData{$method} } ) )
{
$str .= $graphBinData{$method}->{$file}->[ 0 ] . ",";
}
$str =~ s/,$//;
$str .= " ] ] );\n";
print "$str";
} else
{
my $str = "";
for ( my $i = 0 ; $i <= $graphBins ; $i++ )
{
if ( $methodPrefix =~ /at|gc|cpg/ )
{
$str .= "[" . ( $bin * 100 ) . ", ";
}else
{
$str .= "[$bin, ";
}
foreach my $file ( sort keys( %{ $graphBinData{$method} } ) )
{
my $value = $graphBinData{$method}->{$file}->[ $i ];
$value = 0 if ( !defined $value );
$str .= "$value,";
}
$str =~ s/,$//;
$str .= "],";
$bin += $binSize;
}
$str =~ s/,$//;
print "$str ] );\n";
}
print "var options_$method = {\n";
print " chart: {\n";
print " title: '" . $methodMetaData{$methodPrefix}->{'title'};
if ( $wordSize > 0 )
{
print " ( word size = $wordSize )";
}
print "'\n";
print " },\n";
print " width: 900,\n";
print " height: 500,\n";
print " series: { 0: {axis: 'bins'} },\n";
print " axes: { y: { bins: {label: '1k bins, 500bp overlap'} } }\n";
print "};\n";
print "var chart_$method = new google.charts.Line(document.getElementById('chart_$method'));\n";
print "chart_$method.draw(data_$method, options_$method);\n";
}
print "}\n";
print "</SCRIPT>\n";
print "</HEAD>\n";
print "<BODY>\n";
foreach my $method ( sort keys( %graphBinData ) )
{
print " <DIV ID=\"chart_$method\"></div>\n";
}
print "</BODY>\n";
print "</HTML>\n";
}
=head1 SUBROUTINES
=cut
sub usage
{
exec "pod2text $0";
exit 1;
}
##-------------------------------------------------------------------------##
## Use: my $val = serializeIN( $filename );
##
## $filename : A filename containing a serialized object
##
## Returns
##
## Uses the Data::Dumper module to read in data
## from a serialized PERL object or data structure.
##
##-------------------------------------------------------------------------##
sub serializeIN
{
my $fileName = shift;
my $fileContents = "";
my $oldSep = $/;
undef $/;
my $in;
open $in, "$fileName";
$fileContents = <$in>;
$/ = $oldSep;
close $in;
return eval( $fileContents );
}
##-------------------------------------------------------------------------##
## Use: serializeOUT( $data, $filename );
##
## $filename : A filename to be created
##
## Returns
##
## Uses the Data::Dumper module to save out the data
## structure as a text file. This text file can be
## read back into an object of this type.
##
##-------------------------------------------------------------------------##
sub serializeOUT
{
my $object = shift;
my $fileName = shift;
my $data_dumper = new Data::Dumper( [ $object ] );
$data_dumper->Purity( 1 )->Terse( 1 )->Deepcopy( 1 );
open OUT, ">$fileName";
print OUT $data_dumper->Dump();
close OUT;
}
=head1 AUTHOR
Robert Hubley
Juan Caballero
Institute for Systems Biology @ 2010-2015
=head1 CONTACT
rhubley@systemsbiology.org
=head1 LICENSE
This is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation, either version 3 of the License, or
(at your option) any later version.
This is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
GNU General Public License for more details.
You should have received a copy of the GNU General Public License
along with code. If not, see <http://www.gnu.org/licenses/>.
=cut