--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/lib/CPT/Analysis/PAUSE.pm	Mon Jun 05 02:50:07 2023 +0000
@@ -0,0 +1,197 @@
+package CPT::Analysis::PAUSE;
+
+# ABSTRACT: Library for use in PAUSE analysis
+use strict;
+use warnings;
+use Moose;
+use List::Util qw(sum);
+use Statistics::Descriptive;
+
+sub max ($$) { shift; $_[ $_[0] < $_[1] ] }
+sub min ($$) { shift; $_[ $_[0] > $_[1] ] }
+
+sub derivative {
+	my ( $self, $data_ref ) = @_;
+	my @data = @{$data_ref};
+	my @new_data;
+	foreach ( my $i = 0 ; $i < scalar(@data) - 1 ; $i++ ) {
+		$new_data[ $i + 1 ] = $data[ $i + 1 ] - $data[$i];
+	}
+	return \@new_data;
+}
+
+sub find_peaks {
+	my ( $self, %data ) = @_;
+	use IPC::Run3;
+	use File::Temp qw/tempfile/;
+
+	# Store to CSV File
+	my @starts = @{ $data{data} };
+	my ( $fh0, $filename0 ) = tempfile('galaxy.pause.XXXXXXX');
+	printf $fh0 ( "%s,%s\n", 'position', 'count' );
+	for ( my $i = 0 ; $i < scalar(@starts) ; $i++ ) {
+		printf $fh0 "%d,%d\n", $i,
+		  ( defined $starts[$i] ? $starts[$i] : 0 );
+	}
+	close($fh0);
+
+	my ( $fh, $filename ) = tempfile('galaxy.pause.XXXXXXX');
+	my @cmd = (
+		'Rscript', $data{location_of_rscript_file},
+		$filename0, $filename, $data{snr}
+	);
+	my ( $in, $out, $err );
+	run3 \@cmd, \$in, \$out, \$err;
+
+	# Read in R data
+	my @values;
+	while (<$fh>) {
+		chomp;
+		push( @values, $_ );
+	}
+	close($fh);
+
+	unlink($filename0);
+	unlink($filename);
+
+	return @values;
+}
+
+sub smooth {
+	my ( $self, $data_ref ) = @_;
+	my @data = @{$data_ref};
+	my @new_data;
+	my $length = scalar @data;
+	foreach ( my $i = 0 ; $i < $length ; $i++ ) {
+		my $avg =
+		  sum( @data[ $i - 20 .. $i - 1, $i + 1 .. $i + 20 ] ) / 40;
+		$new_data[$i] = $avg;
+	}
+	return \@new_data;
+}
+
+sub histogram {
+	my ( $self, %data ) = @_;
+
+	my @coverage = @{ $data{data} };
+	my @return_coverage;
+	for ( my $i = 0 ; $i < scalar(@coverage) ; $i++ ) {
+		my $size = $coverage[$i];
+		unless ($size) { $size = 0 }
+		$return_coverage[$i] = [ $i, $size, "*" x $size ];
+	}
+	my %results = (
+		'Sheet1' => {
+			headers => [qw(Base Count Plot)],
+			data    => \@return_coverage,
+		}
+	);
+	return %results;
+}
+
+sub getCoverageDensity {
+	my ( $self, %data ) = @_;
+
+	# Load the sam file
+	my $sam = Bio::DB::Sam->new(
+		-bam       => $data{bam},
+		-fasta     => $data{genome},
+		-autoindex => 1,
+	);
+
+	# Get all alignments to our indicated FASTA file
+	my @alignments = $sam->get_features_by_location(
+		-seq_id => $data{fasta_id},
+		-start  => 1,
+		-end    => $data{fasta_length}
+	);
+
+	# Set up some variables
+	my $coverage_density_max_value = 0;
+	my ( @coverage_density, @read_starts, @read_ends );
+
+	# including some for statistics
+	my $stat_start = Statistics::Descriptive::Sparse->new();
+	my $stat_end   = Statistics::Descriptive::Sparse->new();
+
+	# Looping over alignments
+	for my $a (@alignments) {
+		my $start = $a->start;
+		my $end   = $a->end;
+
+		# Increment the number of reads starting there
+		$read_starts[$start]++;
+		$read_ends[$end]++;
+
+		# And increment the coverage density
+		foreach ( $start .. $end ) {
+			$coverage_density[$_]++;
+			if ( $coverage_density[$_] >
+				$coverage_density_max_value )
+			{
+				$coverage_density_max_value =
+				  $coverage_density[$_];
+			}
+		}
+	}
+	my @start_data_for_stats;
+	my @end_data_for_stats;
+	for ( my $i = 0 ; $i < $data{fasta_length} ; $i++ ) {
+		if ( $read_starts[$i] ) {
+			push( @start_data_for_stats, $read_starts[$i] );
+		}
+		if ( $read_ends[$i] ) {
+			push( @end_data_for_stats, $read_ends[$i] );
+		}
+	}
+	$stat_start->add_data(@start_data_for_stats);
+	$stat_end->add_data(@end_data_for_stats);
+
+	# Lots of data to return
+	use CPT::Analysis::PAUSE::ParsedSam;
+	my $psam = CPT::Analysis::PAUSE::ParsedSam->new(
+		coverage_density => \@coverage_density,
+		read_starts      => \@read_starts,
+		read_ends        => \@read_ends,
+		max              => $coverage_density_max_value,
+		stats_start_max  => $stat_start->max(),
+		stats_end_max    => $stat_end->max(),
+		stats_start_mean => $stat_start->mean(),
+		stats_end_mean   => $stat_end->mean(),
+		stats_start_standard_deviation =>
+		  $stat_start->standard_deviation(),
+		stats_end_standard_deviation => $stat_end->standard_deviation(),
+	);
+	return $psam;
+}
+
+no Moose;
+1;
+
+__END__
+
+=pod
+
+=encoding UTF-8
+
+=head1 NAME
+
+CPT::Analysis::PAUSE - Library for use in PAUSE analysis
+
+=head1 VERSION
+
+version 1.96
+
+=head1 AUTHOR
+
+Eric Rasche <rasche.eric@yandex.ru>
+
+=head1 COPYRIGHT AND LICENSE
+
+This software is Copyright (c) 2014 by Eric Rasche.
+
+This is free software, licensed under:
+
+  The GNU General Public License, Version 3, June 2007
+
+=cut