view find_peaks @ 9:8fd3191302d0 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 5bf4f4dbd82988d1612d951d69125bc5f5b439be

#!/usr/bin/perl -w

# Copyright © 2012-2015, Owen Marshall

# This program 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 2 of the License, or (at
# your option) any later version. 
# 
# This program 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 this program; if not, write to the Free Software
# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA  02111-1307 
# USA

use strict;
use File::Basename;
use 5.010;
$|++;

my $version = "1.0.1";

print STDERR "\nfind_peaks v$version\nCopyright © 2012-15, Owen Marshall\n\n";

my %vars = (
	'fdr' => 0.01,
	'min_count' => 2,
	'n' => 100,
	'frac' => 0,
	'min_quant' => 0.95,
	'step' => 0.01,
	'unified_peaks' => 'max',
);

my %vars_details = (
	'fdr' => 'False discovery rate value',
	'min_count' => 'Minimum number of fragments to consider as a peak',
	'n' => 'Number of iterations',
	'frac' => 'Number of random fragments to consider per iteration',
	'min_quant' => 'Minimum quantile for considering peaks',
	'step' => 'Stepping for quantiles',
	'unified_peaks' => "Method for calling peak overlaps (two options):\n\r'min': call minimum overlapping peak area\n\r'max': call maximum overlap as peak",
);


my @in_files;
process_cli();

# Time and date
my ($sec,$min,$hour,$mday,$mon,$year) = localtime();
my $date = sprintf("%04d-%02d-%02d.%02d-%02d-%02d",$year+1900,$mon+1,$mday,$hour,$min,$sec);

help() unless @in_files;

foreach my $fn (@in_files) {
	my @in;
	my @unified_peaks;
	my @sig_peaks;
	my @peakmins;
	
	my %peaks;
	my %peak_count;
	my %peak_count_real;
	my %log_scores;
	my %regression;
	my %peak_fdr_cutoff;
	my %fdr;
	
	# Output file names
	my ($name,$dir,$ext) = fileparse($fn, qr/\.[^.]*/);
	
	# filenames
	my $fn_base_date = "peak_analysis.".$name.".$date";
	my $base_dir = "$fn_base_date/";
	my $out = "$base_dir"."$name-FDR$vars{'fdr'}";
	my $out_peak_unified_track = $out.".peaks.gff";
	my $out_peaks = $out."_FDR-data";
	
	# Load gff data files
	load_gff(FILE=>$fn, IN_REF=>\@in);
	
	my $probes = @in;
	
	find_quants(IN_REF=>\@in, PEAKMINS_REF=>\@peakmins);
	find_randomised_peaks(IN_REF=>\@in, PEAKMINS_REF=>\@peakmins, PEAK_COUNT=>\%peak_count, PEAKS=>\%peaks);
	
	# Make directory
	mkdir($base_dir);
	
	# Open peaks file for writing
	open(OUTP, ">$out_peaks")|| die "Cannot open peak file for writing: $!\n";
	print OUTP "FDR peak call v$version\n\n";
	print OUTP "Input file: $fn\n";
	
	calculate_regressions(IN_REF=>\@in, PEAKMINS_REF=>\@peakmins, PEAK_COUNT=>\%peak_count, PEAKS=>\%peaks, LOG_SCORES=>\%log_scores, REGRESSION=>\%regression);
	
	call_peaks_unified_redux(ITER=>1, REAL=>1, AREF=>\@in, PEAKMINS_REF=>\@peakmins, PEAK_COUNT=>\%peak_count, PEAK_COUNT_REAL=>\%peak_count_real, PEAKS=>\%peaks);
	
	calculate_fdr(IN_REF=>\@in, PEAKMINS_REF=>\@peakmins, PEAK_COUNT=>\%peak_count, PEAK_COUNT_REAL=>\%peak_count_real, PEAK_FDR_CUTOFF=>\%peak_fdr_cutoff, FDR=>\%fdr, LOG_SCORES=>\%log_scores, REGRESSION=>\%regression);
	
	find_significant_peaks(PEAKMINS=>\@peakmins, SIG_PEAKS=>\@sig_peaks, PEAKS=>\%peaks, PEAK_FDR_CUTOFF=>\%peak_fdr_cutoff, FDR=>\%fdr);
	
	make_unified_peaks(SIG_PEAKS=>\@sig_peaks, UNIFIED_PEAKS=>\@unified_peaks, OUT=>$out_peak_unified_track, TYPE=>$vars{'unified_peaks'});
	
	print STDERR "$#unified_peaks peaks found.\n\n";
	
	close OUTP;
}

print STDERR "All done.\n\n";
exit 0;


######################
# Subroutines start here
#

sub find_significant_peaks {
	my (%opts) = @_;
	
	my $peakmins = $opts{PEAKMINS};
	my $peaks = $opts{PEAKS};
	my $sig_peaks = $opts{SIG_PEAKS};
	my $fdr = $opts{FDR};
	my $peak_fdr_cutoff = $opts{PEAK_FDR_CUTOFF};
	
	# Generate significant peaks and unify peaks
	print STDERR "Selecting significant peaks ...     \n";

	foreach my $pm (@$peakmins) {
		for my $i (0 .. $#{$$peaks{$pm}}) {
			my ($chr, $pstart, $pend, $mean_pscore, $pscore, $count, $size) = @{ $$peaks{$pm}[$i] };
			if ($count >= $$peak_fdr_cutoff{$pm}) {
				push (@$sig_peaks, [ @{$$peaks{$pm}[$i]}, $$fdr{$pm}[$count] ]);
			}
		}
	}
	
	print OUTP "\nNumber of peaks: $#$sig_peaks\n";
}

sub calculate_fdr {
	my (%opts) = @_;
	my $in_ref = $opts{IN_REF};
	my $peakmins = $opts{PEAKMINS_REF};
	my $peak_count = $opts{PEAK_COUNT};
	my $log_scores = $opts{LOG_SCORES};
	my $regression = $opts{REGRESSION};
	my $fdr = $opts{FDR};
	my $peak_fdr_cutoff = $opts{PEAK_FDR_CUTOFF};
	my $peak_count_real = $opts{PEAK_COUNT_REAL};
		
	foreach my $pm (@$peakmins) {
		# get regression variables
		my ($m,$b) = @{$$regression{$pm}} if $$regression{$pm}[0];
		
		for my $i (0 .. $#{$$peak_count_real{$pm}}) {
			next unless $$peak_count_real{$pm}[$i];
			my $expect = 10**($m*$i + $b);
		
			my $real_count = $$peak_count_real{$pm}[$i];
			my $fdr_conservative = $expect/$real_count;
			$$fdr{$pm}[$i]= $fdr_conservative;
		}
	}
	
	# print FDR rates
	print OUTP "\n";

	foreach my $pm (@$peakmins) {
		print OUTP "Peak min = $pm\n";
		for my $c (0 .. $#{$$fdr{$pm}}) {
			next unless defined($$fdr{$pm}[$c]);
			print OUTP "Peak size: $c\tCount: $$peak_count_real{$pm}[$c]\tFDR: $$fdr{$pm}[$c]\n";
			$$peak_fdr_cutoff{$pm} = $c if (($$fdr{$pm}[$c]<$vars{'fdr'}) && (!$$peak_fdr_cutoff{$pm}));
		}
		$$peak_fdr_cutoff{$pm}||= 10**10; # clumsy hack to prevent errors 
		print OUTP "\n";
	}
	
	foreach my $pm (@$peakmins) {
		print OUTP "Peak min $pm: peak cutoff size for alpha = $vars{'fdr'} was $$peak_fdr_cutoff{$pm}\n\n";
	}
}

sub calculate_regressions {
	my (%opts) = @_;
	my $in_ref = $opts{IN_REF};
	my $peakmins = $opts{PEAKMINS_REF};
	my $peaks = $opts{PEAKS};
	my $peak_count = $opts{PEAK_COUNT};
	my $log_scores = $opts{LOG_SCORES};
	my $regression = $opts{REGRESSION};
		
	my $in_num = @$in_ref;

	foreach my $pm (@$peakmins) {
		print OUTP "Peak min = $pm\n";
		for my $c (0 .. $#{$$peak_count{$pm}}) {
			my $peak_count_avg = $$peak_count{$pm}[$c]/$vars{'n'} if $$peak_count{$pm}[$c];
			next unless $peak_count_avg;
	
			if ($vars{'frac'}) {
				$peak_count_avg = $peak_count_avg * $in_num/$vars{'frac'};
			}
			$$log_scores{$pm}[$c] = log($peak_count_avg)/log(10);
			print OUTP "Peak size: $c\tCount:$peak_count_avg\n";
		}
		
		# calculate exponential decay rates
		# y= a+bx for log(y)	
		my ($sumx, $sumy, $sumxsq, $sumxy);
		my $n=0;
		for my $i (0 .. $#{$$peak_count{$pm}}) {
			next unless $$peak_count{$pm}[$i];
			$n++;
			$sumx   += $i;
			$sumy   += $$log_scores{$pm}[$i];
			$sumxsq += $i ** 2;
			$sumxy  += $i * $$log_scores{$pm}[$i];
		}
		
		next unless $n > 1;
		
		my $mean_x = $sumx/$n;
		my $mean_y = $sumy/$n;
		my $mean_xsq = $sumxsq/$n;
		my $mean_xy = $sumxy/$n;
		
		my $b = ($mean_xy - ($mean_x * $mean_y)) / ($mean_xsq - ($mean_x **2));
		my $a = $mean_y - ($b * $mean_x);
				
		# store values
		$$regression{$pm}=[$b, $a];
		print OUTP "regression: log(y) = $b(x) + $a\n";
		
		for my $i (0 .. $#{$$peak_count{$pm}}) {
			next unless $$peak_count{$pm}[$i];
			my ($b,$a) = @{$$regression{$pm}};
			my $logval = ($b*$i + $a);
			my $val = 10**$logval;
			print OUTP "lin regress: $i\t$$log_scores{$pm}[$i]\t$logval\t$val\n";
		}
		
		print OUTP "\n";
	}
}

sub find_randomised_peaks {
	my (%opts) = @_;
	my $in_ref = $opts{IN_REF};
	my $peakmins_ref = $opts{PEAKMINS_REF};
	my $peaks = $opts{PEAKS};
	my $peak_count = $opts{PEAK_COUNT};
	
	print STDERR "Duplicating ...               \n";
	my @inr = @$in_ref;
	
	# Call peaks on input file
	print STDERR "Calling peaks on input file ...\n";

	for my $iter (1 .. $vars{'n'}) {
		#print STDERR "Iteration $iter ...       \r";
		print STDERR "Iteration $iter: [shuffling]            \r";
		
		if ($vars{'frac'}) {
			# only use a fraction of the array per rep
			my @a = inside_out(\@inr, $vars{'frac'});
			call_peaks_unified_redux(ITER=>$iter, AREF=>\@a, PEAKMINS_REF=>$peakmins_ref, PEAK_COUNT=>$peak_count);
		} else {
			shuffle(\@inr);
			call_peaks_unified_redux(ITER=>$iter, AREF=>\@inr, PEAKMINS_REF=>$peakmins_ref, PEAK_COUNT=>$peak_count);
		}
	}
	
}

sub call_peaks_unified_redux {
	my (%opts) = @_;
	my $iter = $opts{ITER};
	my $real = $opts{REAL};
	my $a = $opts{AREF};
	my $peakmins_ref = $opts{PEAKMINS_REF};
	my $peak_count_real = $opts{PEAK_COUNT_REAL};
	my $peaks = $opts{PEAKS};
	my $peak_count = $opts{PEAK_COUNT};

	my ($pstart, $pend, $inpeak, $pscore, $count);
	$pstart=$pend=$pscore=$inpeak=$count=0;
	
	my @tmp_peak;
	my $total = $#$a;
	
	if ($real) {
		print STDERR "Calling real peaks ...            \r";
	} else {
		print STDERR "Iteration $iter: [processing ...]        \r";
	}
	
	my $old_chr="";
	foreach my $pm (@$peakmins_ref) {
		for my $i (0 .. $total) {
			my ($chr, $start, $end, $score) = @{ @$a[$i] };
			next unless $score;
			
			if ($real) {
				unless ($chr eq $old_chr) {
					# Next chromosome
					# (Peaks can't carry over chromosomes, but we don't use this shortcut when randomly shuffling)
					$pstart=$pend=$pscore=$inpeak=$count=0;
					@tmp_peak = () if $real;
				}
			}
			$old_chr = $chr if $real;
			
			unless ($inpeak) {
				next unless $score >= $pm;
				# record new peak
				$pstart = $start;
				$pend = $end;
				$pscore = $score * ($end-$start)/1000;
				$count++;
				push @tmp_peak, $score if $real;
				$inpeak = 1;
			} else {
				if ($score >= $pm) {
					# still in peak
					$count++;
					
					# Fragment score to deal with scoring peaks made from uneven sized fragments
					my $fragment_score = $score * ($end-$start)/1000;
					
					push @tmp_peak, $score if $real;
					$pscore += $fragment_score;
					$pend = $end;
				} else {
					# out of a peak
					if ($count >= $vars{'min_count'}) {
						# record peak
						if ($real) {
							$$peak_count_real{$pm}[$count]++;
							my $mean_pscore = sprintf('%0.2f',($pscore/(($pend-$pstart)/1000)));
							push (@{$$peaks{$pm}},[($chr, $pstart, $pend, $mean_pscore, $pscore, $count, ($pend-$pstart))]);
						} else {
							$$peak_count{$pm}[$count]++;
						}
					} 
					
					# reset
					$pstart=$pend=$pscore=$inpeak=$count=0;
					@tmp_peak = () if $real;
				}
			}
		}
	}
}


sub shuffle {
	# Fisher-Yates shuffle (Knuth shuffle)
	my ($array) = @_;
	my $i = @$array;
	while ( --$i ) {
		my $j = int rand( $i+1 );
		@$array[$i,$j] = @$array[$j,$i];
	}
}

sub inside_out {
	my ($array, $frac) = @_;
	my @a;
	for my $i (0 .. $frac-1) {
		my $j = int rand( $i+1 );
		if ($j != $i) {
			$a[$i] = $a[$j]
		}
		$a[$j] = @$array[$i]
	}
	return @a;
}

sub load_gff {
	my (%opts) = @_;
	my $fn = $opts{FILE};
	my $in_ref = $opts{IN_REF};

	print STDERR "Reading input file: $fn ...\n";
	open (IN, "<$fn") || die "Unable to read $fn: $!\n";
	
	my $i;
	while (<IN>) {
		$i++;
		print STDERR "Read $i lines ...\r" if $i%10000 == 0;
		chomp;
		
		my @line = split('\t');
		
		my ($chr, $start, $end, $score);
		if ($#line == 3) {
			# bedgraph
			($chr, $start, $end, $score) = @line;
		} else {
			# GFF
			($chr, $start, $end, $score) = @line[0,3,4,5];
		}
		
		next unless $start;
		
		$score = 0 if $score eq "NA";
		
		push (@$in_ref, [$chr, $start, $end, $score]);
	}
	
	close (IN);

	print STDERR "Sorting ...                 \n";
	@$in_ref = sort { $a->[1] <=> $b->[1] } @$in_ref;
	@$in_ref = sort { $a->[0] cmp $b->[0] } @$in_ref;
}

sub find_quants {
	my (%opts) = @_;
	
	my $in_ref = $opts{IN_REF};
	my $peakmins_ref = $opts{PEAKMINS_REF};
	
	my %seg;
	my @frags;

	my $total_coverage;

	foreach my $l (@$in_ref) {	
		my ($chr, $start, $end, $score) = @$l;
		next unless $score;
		$score = 0 if $score eq "NA";
		$total_coverage += $end-$start;
		push @frags, $score;
	}
	
	@frags = sort {$a <=> $b} @frags;
	
	print STDERR "Total coverage was $total_coverage bp\n";
	
	my @quants;
	for (my $q=0;$q<=1;$q+=$vars{'step'}) {
		push @quants, [$q, int($q * @frags)] if $q > $vars{'min_quant'};
	}

	foreach  (@quants) {
		my $cut_off = @{$_}[0];
		my $score = $frags[@{$_}[1]];
		printf("   Quantile %0.2f: %0.2f\n",$cut_off,$score);
		$seg{$cut_off} = $score;
	}
	
	foreach my $c (sort {$a <=> $b} keys %seg) {
		push (@$peakmins_ref, $seg{$c});
	}
}

sub make_unified_peaks {
	my (%opts) = @_;
	my $ref = $opts{SIG_PEAKS};
	my $out_peak_unified_track = $opts{OUT};
	my $unified_peaks = $opts{UNIFIED_PEAKS};
	my $type = $opts{TYPE};
	my $total = @$ref;
		
	# Unify overlapping peaks, and make significant peaks file
	my $skipped_peaks;
	print STDERR "Combining significant peaks ...\n";
	
	# unroll chromosomes for speed
	foreach my $chr (uniq( map @{$_}[0], @$ref )) {
		my @c = grep {@{$_}[0] eq $chr} @$ref;
		
		my @unified_peaks_chr;
		foreach my $ar (@c) {
			if (state $i++ % 100 == 0) {
					my $pc = sprintf("%0.2f",($i*100)/$total);
					print STDERR "$pc\% processed ...\r";
			}
			
			my ($chra, $start, $end, $score, $total_score, $count, $peaklen, $fdr) = @$ar;
			
			# next if @unified_peaks_chr already overlaps
			next if grep {
						@{$_}[3] < $end
						&& @{$_}[4] > $start
					} @unified_peaks_chr;
			
			# Grab all elements that overlap
			my @test = grep {
						@{$_}[1] < $end
						&& @{$_}[2] > $start
					} @c;
			
			for my $j (0 .. $#test) {
				my ($chr1, $start1, $end1, $score1, $total_score1, $count1, $peaklen1, $fdr1) = @{$test[$j]};
				
				next unless $start1 < $end;
				next unless $end1 > $start;
				
				if ($type eq 'min') {
					$start = max($start, $start1);
					$end = min($end, $end1);
				} else {
					$start = min($start, $start1);
					$end = max($end, $end1);
				}
				
				$score = max($score, $score1);
				$fdr = min($fdr, $fdr1);
			}
			
			push @unified_peaks_chr, [($chr, '.', '.', $start, $end, $score, '.', '.', "FDR=$fdr")];
		}
		
		@$unified_peaks = (@$unified_peaks, @unified_peaks_chr);
	}
	
	$total = $#$unified_peaks;
	
	print STDERR "Sorting unified peaks ...\n";
	@$unified_peaks = sort { $a->[3] <=> $b->[3] } @$unified_peaks;
	@$unified_peaks = sort { $a->[0] cmp $b->[0] } @$unified_peaks;
	
	print STDERR "Writing unified peaks file ...\n";
	open(PEAKOUTUNI, ">$out_peak_unified_track") || die "Unable to open peak output track for writing: $!\n\n"; 
	for my $j (0 .. $#$unified_peaks) {
		print PEAKOUTUNI join("\t", @{$$unified_peaks[$j]}), "\n";
	}
}

sub max {
    my ($max, @vars) = @_;
	my $index=0;
	$max||=0;
    for my $i (0..$#vars) {
        ($max, $index) = ($vars[$i], $i+1) if $vars[$i] > $max;
    }
    return $max;
}

sub min {
    my ($min, @vars) = @_;
	my $index=0;
	$min||=0;
    for my $i (0..$#vars) {
        ($min, $index) = ($vars[$i],$i+1) if $vars[$i] < $min;
    }
    return $min;
}

sub uniq {
	my %seen;
	return grep { !$seen{$_}++ } @_;
}



sub process_cli {
	foreach (@ARGV) {
		if (/--(.*)=(.*)/) {
			unless (defined($vars{$1})) {
				print STDERR "Did not understand $_ ...\n";
				help();
			}
			my ($v, $opt) = ($1,$2);
			$vars{$v} = $opt;
			next;
		} elsif (/--h[elp]*/) {
			help();
		} elsif (/--(.*)/) {
			print STDERR "Please add a parameter to $_ ...\n\n";
			exit 1;
		}
		push @in_files, $_;
	}
}


sub help {
	print STDOUT <<EOT;
Simple FDR random permutation peak caller
Usage: [options] [files in bedgraph or GFF format]
	
Options:
EOT
	
	my $opt_len = 0;
	foreach (keys %vars) {
		my $l = length($_);
		$opt_len = $l if $l > $opt_len;
	}
	
	$opt_len+=2;
	
	my $cols= `tput cols` || 80;
	
	my ($v, $val, $def, $def_format);
	my $help_format = "format STDOUT =\n"
		.' '.'^'.'<'x$opt_len . ' '. '^' . '<'x($cols-$opt_len-4) . "\n"
		.'$v, $def_format'."\n"
		.' '.'^'.'<'x$opt_len . '   '. '^' . '<'x($cols-$opt_len-6) . "~~\n"
		.'$v, $def_format'."\n"
		.".\n";
		
	eval $help_format;
	die $@ if $@;
	
	foreach my $k (sort (keys %vars)) {
		($v, $val, $def) = ($k, $vars{$k}, $vars_details{$k});
		$def||="";
		$def_format = $val ? "$def\n\r[Current value: $val]" : $def;
		$v = "--$v";
#		format =
# ^<<<<<<<<<<<<<<<<<<<< ^<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
#$v, $def_format
# ^<<<<<<<<<<<<<<<<<<<<   ^<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< ~~
#$v, $def_format
#.

		write();
		
	}
	print STDOUT "\n";
	exit 1;
}