damidseq_findpeaks: find

annotate find_peaks @ 10:48d9c6f9ef41 draft

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

author	mvdbeek
date	Wed, 13 Jun 2018 15:19:36 -0400
parents	be830200e987
children	7b0ca503bb95

rev	line source
0 be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	1 #!/usr/bin/perl -w
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	2
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	3 # Copyright © 2012-2015, Owen Marshall
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	4
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	5 # This program is free software; you can redistribute it and/or modify
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	6 # it under the terms of the GNU General Public License as published by
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	7 # the Free Software Foundation; either version 2 of the License, or (at
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	8 # your option) any later version.
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	9 #
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	10 # This program is distributed in the hope that it will be useful, but
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	11 # WITHOUT ANY WARRANTY; without even the implied warranty of
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	12 # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	13 # General Public License for more details.
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	14 #
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	15 # You should have received a copy of the GNU General Public License
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	16 # along with this program; if not, write to the Free Software
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	17 # Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	18 # USA
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	19
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	20 use strict;
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	21 use File::Basename;
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	22 use 5.010;
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	23 $\|++;
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	24
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	25 my $version = "1.0.1";
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	26
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	27 print STDERR "\nfind_peaks v$version\nCopyright © 2012-15, Owen Marshall\n\n";
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	28
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	29 my %vars = (
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	30 'fdr' => 0.01,
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	31 'min_count' => 2,
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	32 'n' => 100,
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	33 'frac' => 0,
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	34 'min_quant' => 0.95,
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	35 'step' => 0.01,
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	36 'unified_peaks' => 'max',
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	37 );
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	38
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	39 my %vars_details = (
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	40 'fdr' => 'False discovery rate value',
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	41 'min_count' => 'Minimum number of fragments to consider as a peak',
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	42 'n' => 'Number of iterations',
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	43 'frac' => 'Number of random fragments to consider per iteration',
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	44 'min_quant' => 'Minimum quantile for considering peaks',
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	45 'step' => 'Stepping for quantiles',
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	46 '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",
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	47 );
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	48
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	49
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	50 my @in_files;
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	51 process_cli();
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	52
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	53 # Time and date
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	54 my ($sec,$min,$hour,$mday,$mon,$year) = localtime();
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	55 my $date = sprintf("%04d-%02d-%02d.%02d-%02d-%02d",$year+1900,$mon+1,$mday,$hour,$min,$sec);
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	56
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	57 help() unless @in_files;
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	58
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	59 foreach my $fn (@in_files) {
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	60 my @in;
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	61 my @unified_peaks;
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	62 my @sig_peaks;
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	63 my @peakmins;
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	64
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	65 my %peaks;
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	66 my %peak_count;
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	67 my %peak_count_real;
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	68 my %log_scores;
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	69 my %regression;
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	70 my %peak_fdr_cutoff;
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	71 my %fdr;
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	72
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	73 # Output file names
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	74 my ($name,$dir,$ext) = fileparse($fn, qr/\.[^.]*/);
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	75
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	76 # filenames
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	77 my $fn_base_date = "peak_analysis.".$name.".$date";
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	78 my $base_dir = "$fn_base_date/";
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	79 my $out = "$base_dir"."$name-FDR$vars{'fdr'}";
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	80 my $out_peak_unified_track = $out.".peaks.gff";
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	81 my $out_peaks = $out."_FDR-data";
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	82
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	83 # Load gff data files
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	84 load_gff(FILE=>$fn, IN_REF=>\@in);
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	85
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	86 my $probes = @in;
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	87
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	88 find_quants(IN_REF=>\@in, PEAKMINS_REF=>\@peakmins);
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	89 find_randomised_peaks(IN_REF=>\@in, PEAKMINS_REF=>\@peakmins, PEAK_COUNT=>\%peak_count, PEAKS=>\%peaks);
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	90
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	91 # Make directory
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	92 mkdir($base_dir);
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	93
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	94 # Open peaks file for writing
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	95 open(OUTP, ">$out_peaks")\|\| die "Cannot open peak file for writing: $!\n";
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	96 print OUTP "FDR peak call v$version\n\n";
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	97 print OUTP "Input file: $fn\n";
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	98
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	99 calculate_regressions(IN_REF=>\@in, PEAKMINS_REF=>\@peakmins, PEAK_COUNT=>\%peak_count, PEAKS=>\%peaks, LOG_SCORES=>\%log_scores, REGRESSION=>\%regression);
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	100
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	101 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);
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	102
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	103 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);
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	104
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	105 find_significant_peaks(PEAKMINS=>\@peakmins, SIG_PEAKS=>\@sig_peaks, PEAKS=>\%peaks, PEAK_FDR_CUTOFF=>\%peak_fdr_cutoff, FDR=>\%fdr);
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	106
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	107 make_unified_peaks(SIG_PEAKS=>\@sig_peaks, UNIFIED_PEAKS=>\@unified_peaks, OUT=>$out_peak_unified_track, TYPE=>$vars{'unified_peaks'});
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	108
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	109 print STDERR "$#unified_peaks peaks found.\n\n";
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	110
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	111 close OUTP;
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	112 }
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	113
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	114 print STDERR "All done.\n\n";
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	115 exit 0;
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	116
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	117
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	118 ######################
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	119 # Subroutines start here
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	120 #
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	121
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	122 sub find_significant_peaks {
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	123 my (%opts) = @_;
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	124
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	125 my $peakmins = $opts{PEAKMINS};
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	126 my $peaks = $opts{PEAKS};
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	127 my $sig_peaks = $opts{SIG_PEAKS};
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	128 my $fdr = $opts{FDR};
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	129 my $peak_fdr_cutoff = $opts{PEAK_FDR_CUTOFF};
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	130
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	131 # Generate significant peaks and unify peaks
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	132 print STDERR "Selecting significant peaks ... \n";
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	133
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	134 foreach my $pm (@$peakmins) {
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	135 for my $i (0 .. $#{$$peaks{$pm}}) {
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	136 my ($chr, $pstart, $pend, $mean_pscore, $pscore, $count, $size) = @{ $$peaks{$pm}[$i] };
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	137 if ($count >= $$peak_fdr_cutoff{$pm}) {
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	138 push (@$sig_peaks, [ @{$$peaks{$pm}[$i]}, $$fdr{$pm}[$count] ]);
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	139 }
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	140 }
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	141 }
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	142
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	143 print OUTP "\nNumber of peaks: $#$sig_peaks\n";
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	144 }
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	145
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	146 sub calculate_fdr {
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	147 my (%opts) = @_;
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	148 my $in_ref = $opts{IN_REF};
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	149 my $peakmins = $opts{PEAKMINS_REF};
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	150 my $peak_count = $opts{PEAK_COUNT};
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	151 my $log_scores = $opts{LOG_SCORES};
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	152 my $regression = $opts{REGRESSION};
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	153 my $fdr = $opts{FDR};
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	154 my $peak_fdr_cutoff = $opts{PEAK_FDR_CUTOFF};
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	155 my $peak_count_real = $opts{PEAK_COUNT_REAL};
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	156
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	157 foreach my $pm (@$peakmins) {
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	158 # get regression variables
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	159 my ($m,$b) = @{$$regression{$pm}} if $$regression{$pm}[0];
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	160
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	161 for my $i (0 .. $#{$$peak_count_real{$pm}}) {
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	162 next unless $$peak_count_real{$pm}[$i];
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	163 my $expect = 10*($m$i + $b);
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	164
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	165 my $real_count = $$peak_count_real{$pm}[$i];
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	166 my $fdr_conservative = $expect/$real_count;
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	167 $$fdr{$pm}[$i]= $fdr_conservative;
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	168 }
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	169 }
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	170
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	171 # print FDR rates
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	172 print OUTP "\n";
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	173
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	174 foreach my $pm (@$peakmins) {
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	175 print OUTP "Peak min = $pm\n";
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	176 for my $c (0 .. $#{$$fdr{$pm}}) {
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	177 next unless defined($$fdr{$pm}[$c]);
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	178 print OUTP "Peak size: $c\tCount: $$peak_count_real{$pm}[$c]\tFDR: $$fdr{$pm}[$c]\n";
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	179 $$peak_fdr_cutoff{$pm} = $c if (($$fdr{$pm}[$c]<$vars{'fdr'}) && (!$$peak_fdr_cutoff{$pm}));
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	180 }
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	181 $$peak_fdr_cutoff{$pm}\|\|= 10**10; # clumsy hack to prevent errors
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	182 print OUTP "\n";
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	183 }
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	184
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	185 foreach my $pm (@$peakmins) {
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	186 print OUTP "Peak min $pm: peak cutoff size for alpha = $vars{'fdr'} was $$peak_fdr_cutoff{$pm}\n\n";
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	187 }
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	188 }
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	189
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	190 sub calculate_regressions {
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	191 my (%opts) = @_;
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	192 my $in_ref = $opts{IN_REF};
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	193 my $peakmins = $opts{PEAKMINS_REF};
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	194 my $peaks = $opts{PEAKS};
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	195 my $peak_count = $opts{PEAK_COUNT};
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	196 my $log_scores = $opts{LOG_SCORES};
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	197 my $regression = $opts{REGRESSION};
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	198
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	199 my $in_num = @$in_ref;
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	200
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	201 foreach my $pm (@$peakmins) {
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	202 print OUTP "Peak min = $pm\n";
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	203 for my $c (0 .. $#{$$peak_count{$pm}}) {
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	204 my $peak_count_avg = $$peak_count{$pm}[$c]/$vars{'n'} if $$peak_count{$pm}[$c];
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	205 next unless $peak_count_avg;
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	206
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	207 if ($vars{'frac'}) {
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	208 $peak_count_avg = $peak_count_avg * $in_num/$vars{'frac'};
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	209 }
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	210 $$log_scores{$pm}[$c] = log($peak_count_avg)/log(10);
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	211 print OUTP "Peak size: $c\tCount:$peak_count_avg\n";
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	212 }
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	213
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	214 # calculate exponential decay rates
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	215 # y= a+bx for log(y)
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	216 my ($sumx, $sumy, $sumxsq, $sumxy);
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	217 my $n=0;
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	218 for my $i (0 .. $#{$$peak_count{$pm}}) {
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	219 next unless $$peak_count{$pm}[$i];
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	220 $n++;
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	221 $sumx += $i;
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	222 $sumy += $$log_scores{$pm}[$i];
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	223 $sumxsq += $i ** 2;
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	224 $sumxy += $i * $$log_scores{$pm}[$i];
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	225 }
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	226
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	227 next unless $n > 1;
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	228
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	229 my $mean_x = $sumx/$n;
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	230 my $mean_y = $sumy/$n;
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	231 my $mean_xsq = $sumxsq/$n;
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	232 my $mean_xy = $sumxy/$n;
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	233
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	234 my $b = ($mean_xy - ($mean_x * $mean_y)) / ($mean_xsq - ($mean_x **2));
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	235 my $a = $mean_y - ($b * $mean_x);
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	236
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	237 # store values
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	238 $$regression{$pm}=[$b, $a];
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	239 print OUTP "regression: log(y) = $b(x) + $a\n";
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	240
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	241 for my $i (0 .. $#{$$peak_count{$pm}}) {
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	242 next unless $$peak_count{$pm}[$i];
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	243 my ($b,$a) = @{$$regression{$pm}};
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	244 my $logval = ($b*$i + $a);
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	245 my $val = 10**$logval;
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	246 print OUTP "lin regress: $i\t$$log_scores{$pm}[$i]\t$logval\t$val\n";
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	247 }
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	248
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	249 print OUTP "\n";
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	250 }
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	251 }
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	252
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	253 sub find_randomised_peaks {
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	254 my (%opts) = @_;
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	255 my $in_ref = $opts{IN_REF};
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	256 my $peakmins_ref = $opts{PEAKMINS_REF};
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	257 my $peaks = $opts{PEAKS};
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	258 my $peak_count = $opts{PEAK_COUNT};
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	259
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	260 print STDERR "Duplicating ... \n";
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	261 my @inr = @$in_ref;
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	262
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	263 # Call peaks on input file
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	264 print STDERR "Calling peaks on input file ...\n";
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	265
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	266 for my $iter (1 .. $vars{'n'}) {
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	267 #print STDERR "Iteration $iter ... \r";
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	268 print STDERR "Iteration $iter: [shuffling] \r";
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	269
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	270 if ($vars{'frac'}) {
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	271 # only use a fraction of the array per rep
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	272 my @a = inside_out(\@inr, $vars{'frac'});
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	273 call_peaks_unified_redux(ITER=>$iter, AREF=>\@a, PEAKMINS_REF=>$peakmins_ref, PEAK_COUNT=>$peak_count);
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	274 } else {
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	275 shuffle(\@inr);
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	276 call_peaks_unified_redux(ITER=>$iter, AREF=>\@inr, PEAKMINS_REF=>$peakmins_ref, PEAK_COUNT=>$peak_count);
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	277 }
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	278 }
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	279
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	280 }
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	281
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	282 sub call_peaks_unified_redux {
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	283 my (%opts) = @_;
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	284 my $iter = $opts{ITER};
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	285 my $real = $opts{REAL};
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	286 my $a = $opts{AREF};
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	287 my $peakmins_ref = $opts{PEAKMINS_REF};
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	288 my $peak_count_real = $opts{PEAK_COUNT_REAL};
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	289 my $peaks = $opts{PEAKS};
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	290 my $peak_count = $opts{PEAK_COUNT};
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	291
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	292 my ($pstart, $pend, $inpeak, $pscore, $count);
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	293 $pstart=$pend=$pscore=$inpeak=$count=0;
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	294
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	295 my @tmp_peak;
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	296 my $total = $#$a;
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	297
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	298 if ($real) {
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	299 print STDERR "Calling real peaks ... \r";
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	300 } else {
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	301 print STDERR "Iteration $iter: [processing ...] \r";
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	302 }
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	303
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	304 my $old_chr="";
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	305 foreach my $pm (@$peakmins_ref) {
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	306 for my $i (0 .. $total) {
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	307 my ($chr, $start, $end, $score) = @{ @$a[$i] };
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	308 next unless $score;
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	309
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	310 if ($real) {
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	311 unless ($chr eq $old_chr) {
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	312 # Next chromosome
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	313 # (Peaks can't carry over chromosomes, but we don't use this shortcut when randomly shuffling)
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	314 $pstart=$pend=$pscore=$inpeak=$count=0;
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	315 @tmp_peak = () if $real;
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	316 }
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	317 }
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	318 $old_chr = $chr if $real;
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	319
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	320 unless ($inpeak) {
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	321 next unless $score >= $pm;
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	322 # record new peak
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	323 $pstart = $start;
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	324 $pend = $end;
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	325 $pscore = $score * ($end-$start)/1000;
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	326 $count++;
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	327 push @tmp_peak, $score if $real;
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	328 $inpeak = 1;
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	329 } else {
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	330 if ($score >= $pm) {
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	331 # still in peak
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	332 $count++;
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	333
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	334 # Fragment score to deal with scoring peaks made from uneven sized fragments
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	335 my $fragment_score = $score * ($end-$start)/1000;
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	336
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	337 push @tmp_peak, $score if $real;
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	338 $pscore += $fragment_score;
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	339 $pend = $end;
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	340 } else {
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	341 # out of a peak
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	342 if ($count >= $vars{'min_count'}) {
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	343 # record peak
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	344 if ($real) {
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	345 $$peak_count_real{$pm}[$count]++;
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	346 my $mean_pscore = sprintf('%0.2f',($pscore/(($pend-$pstart)/1000)));
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	347 push (@{$$peaks{$pm}},[($chr, $pstart, $pend, $mean_pscore, $pscore, $count, ($pend-$pstart))]);
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	348 } else {
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	349 $$peak_count{$pm}[$count]++;
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	350 }
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	351 }
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	352
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	353 # reset
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	354 $pstart=$pend=$pscore=$inpeak=$count=0;
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	355 @tmp_peak = () if $real;
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	356 }
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	357 }
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	358 }
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	359 }
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	360 }
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	361
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	362
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	363 sub shuffle {
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	364 # Fisher-Yates shuffle (Knuth shuffle)
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	365 my ($array) = @_;
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	366 my $i = @$array;
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	367 while ( --$i ) {
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	368 my $j = int rand( $i+1 );
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	369 @$array[$i,$j] = @$array[$j,$i];
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	370 }
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	371 }
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	372
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	373 sub inside_out {
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	374 my ($array, $frac) = @_;
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	375 my @a;
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	376 for my $i (0 .. $frac-1) {
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	377 my $j = int rand( $i+1 );
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	378 if ($j != $i) {
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	379 $a[$i] = $a[$j]
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	380 }
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	381 $a[$j] = @$array[$i]
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	382 }
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	383 return @a;
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	384 }
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	385
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	386 sub load_gff {
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	387 my (%opts) = @_;
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	388 my $fn = $opts{FILE};
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	389 my $in_ref = $opts{IN_REF};
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	390
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	391 print STDERR "Reading input file: $fn ...\n";
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	392 open (IN, "<$fn") \|\| die "Unable to read $fn: $!\n";
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	393
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	394 my $i;
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	395 while (<IN>) {
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	396 $i++;
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	397 print STDERR "Read $i lines ...\r" if $i%10000 == 0;
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	398 chomp;
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	399
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	400 my @line = split('\t');
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	401
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	402 my ($chr, $start, $end, $score);
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	403 if ($#line == 3) {
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	404 # bedgraph
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	405 ($chr, $start, $end, $score) = @line;
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	406 } else {
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	407 # GFF
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	408 ($chr, $start, $end, $score) = @line[0,3,4,5];
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	409 }
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	410
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	411 next unless $start;
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	412
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	413 $score = 0 if $score eq "NA";
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	414
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	415 push (@$in_ref, [$chr, $start, $end, $score]);
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	416 }
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	417
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	418 close (IN);
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	419
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	420 print STDERR "Sorting ... \n";
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	421 @$in_ref = sort { $a->[1] <=> $b->[1] } @$in_ref;
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	422 @$in_ref = sort { $a->[0] cmp $b->[0] } @$in_ref;
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	423 }
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	424
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	425 sub find_quants {
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	426 my (%opts) = @_;
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	427
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	428 my $in_ref = $opts{IN_REF};
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	429 my $peakmins_ref = $opts{PEAKMINS_REF};
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	430
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	431 my %seg;
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	432 my @frags;
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	433
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	434 my $total_coverage;
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	435
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	436 foreach my $l (@$in_ref) {
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	437 my ($chr, $start, $end, $score) = @$l;
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	438 next unless $score;
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	439 $score = 0 if $score eq "NA";
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	440 $total_coverage += $end-$start;
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	441 push @frags, $score;
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	442 }
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	443
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	444 @frags = sort {$a <=> $b} @frags;
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	445
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	446 print STDERR "Total coverage was $total_coverage bp\n";
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	447
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	448 my @quants;
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	449 for (my $q=0;$q<=1;$q+=$vars{'step'}) {
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	450 push @quants, [$q, int($q * @frags)] if $q > $vars{'min_quant'};
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	451 }
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	452
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	453 foreach (@quants) {
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	454 my $cut_off = @{$_}[0];
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	455 my $score = $frags[@{$_}[1]];
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	456 printf(" Quantile %0.2f: %0.2f\n",$cut_off,$score);
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	457 $seg{$cut_off} = $score;
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	458 }
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	459
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	460 foreach my $c (sort {$a <=> $b} keys %seg) {
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	461 push (@$peakmins_ref, $seg{$c});
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	462 }
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	463 }
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	464
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	465 sub make_unified_peaks {
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	466 my (%opts) = @_;
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	467 my $ref = $opts{SIG_PEAKS};
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	468 my $out_peak_unified_track = $opts{OUT};
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	469 my $unified_peaks = $opts{UNIFIED_PEAKS};
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	470 my $type = $opts{TYPE};
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	471 my $total = @$ref;
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	472
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	473 # Unify overlapping peaks, and make significant peaks file
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	474 my $skipped_peaks;
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	475 print STDERR "Combining significant peaks ...\n";
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	476
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	477 # unroll chromosomes for speed
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	478 foreach my $chr (uniq( map @{$_}[0], @$ref )) {
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	479 my @c = grep {@{$_}[0] eq $chr} @$ref;
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	480
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	481 my @unified_peaks_chr;
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	482 foreach my $ar (@c) {
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	483 if (state $i++ % 100 == 0) {
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	484 my $pc = sprintf("%0.2f",($i*100)/$total);
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	485 print STDERR "$pc\% processed ...\r";
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	486 }
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	487
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	488 my ($chra, $start, $end, $score, $total_score, $count, $peaklen, $fdr) = @$ar;
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	489
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	490 # next if @unified_peaks_chr already overlaps
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	491 next if grep {
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	492 @{$_}[3] < $end
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	493 && @{$_}[4] > $start
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	494 } @unified_peaks_chr;
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	495
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	496 # Grab all elements that overlap
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	497 my @test = grep {
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	498 @{$_}[1] < $end
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	499 && @{$_}[2] > $start
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	500 } @c;
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	501
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	502 for my $j (0 .. $#test) {
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	503 my ($chr1, $start1, $end1, $score1, $total_score1, $count1, $peaklen1, $fdr1) = @{$test[$j]};
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	504
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	505 next unless $start1 < $end;
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	506 next unless $end1 > $start;
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	507
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	508 if ($type eq 'min') {
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	509 $start = max($start, $start1);
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	510 $end = min($end, $end1);
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	511 } else {
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	512 $start = min($start, $start1);
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	513 $end = max($end, $end1);
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	514 }
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	515
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	516 $score = max($score, $score1);
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	517 $fdr = min($fdr, $fdr1);
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	518 }
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	519
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	520 push @unified_peaks_chr, [($chr, '.', '.', $start, $end, $score, '.', '.', "FDR=$fdr")];
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	521 }
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	522
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	523 @$unified_peaks = (@$unified_peaks, @unified_peaks_chr);
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	524 }
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	525
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	526 $total = $#$unified_peaks;
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	527
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	528 print STDERR "Sorting unified peaks ...\n";
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	529 @$unified_peaks = sort { $a->[3] <=> $b->[3] } @$unified_peaks;
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	530 @$unified_peaks = sort { $a->[0] cmp $b->[0] } @$unified_peaks;
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	531
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	532 print STDERR "Writing unified peaks file ...\n";
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	533 open(PEAKOUTUNI, ">$out_peak_unified_track") \|\| die "Unable to open peak output track for writing: $!\n\n";
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	534 for my $j (0 .. $#$unified_peaks) {
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	535 print PEAKOUTUNI join("\t", @{$$unified_peaks[$j]}), "\n";
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	536 }
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	537 }
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	538
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	539 sub max {
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	540 my ($max, @vars) = @_;
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	541 my $index=0;
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	542 $max\|\|=0;
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	543 for my $i (0..$#vars) {
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	544 ($max, $index) = ($vars[$i], $i+1) if $vars[$i] > $max;
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	545 }
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	546 return $max;
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	547 }
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	548
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	549 sub min {
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	550 my ($min, @vars) = @_;
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	551 my $index=0;
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	552 $min\|\|=0;
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	553 for my $i (0..$#vars) {
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	554 ($min, $index) = ($vars[$i],$i+1) if $vars[$i] < $min;
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	555 }
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	556 return $min;
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	557 }
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	558
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	559 sub uniq {
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	560 my %seen;
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	561 return grep { !$seen{$_}++ } @_;
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	562 }
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	563
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	564
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	565
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	566 sub process_cli {
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	567 foreach (@ARGV) {
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	568 if (/--(.)=(.)/) {
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	569 unless (defined($vars{$1})) {
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	570 print STDERR "Did not understand $_ ...\n";
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	571 help();
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	572 }
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	573 my ($v, $opt) = ($1,$2);
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	574 $vars{$v} = $opt;
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	575 next;
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	576 } elsif (/--h[elp]*/) {
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	577 help();
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	578 } elsif (/--(.*)/) {
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	579 print STDERR "Please add a parameter to $_ ...\n\n";
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	580 exit 1;
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	581 }
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	582 push @in_files, $_;
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	583 }
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	584 }
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	585
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	586
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	587 sub help {
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	588 print STDOUT <<EOT;
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	589 Simple FDR random permutation peak caller
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	590 Usage: [options] [files in bedgraph or GFF format]
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	591
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	592 Options:
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	593 EOT
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	594
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	595 my $opt_len = 0;
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	596 foreach (keys %vars) {
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	597 my $l = length($_);
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	598 $opt_len = $l if $l > $opt_len;
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	599 }
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	600
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	601 $opt_len+=2;
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	602
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	603 my $cols= `tput cols` \|\| 80;
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	604
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	605 my ($v, $val, $def, $def_format);
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	606 my $help_format = "format STDOUT =\n"
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	607 .' '.'^'.'<'x$opt_len . ' '. '^' . '<'x($cols-$opt_len-4) . "\n"
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	608 .'$v, $def_format'."\n"
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	609 .' '.'^'.'<'x$opt_len . ' '. '^' . '<'x($cols-$opt_len-6) . "~~\n"
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	610 .'$v, $def_format'."\n"
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	611 .".\n";
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	612
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	613 eval $help_format;
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	614 die $@ if $@;
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	615
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	616 foreach my $k (sort (keys %vars)) {
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	617 ($v, $val, $def) = ($k, $vars{$k}, $vars_details{$k});
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	618 $def\|\|="";
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	619 $def_format = $val ? "$def\n\r[Current value: $val]" : $def;
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	620 $v = "--$v";
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	621 # format =
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	622 # ^<<<<<<<<<<<<<<<<<<<< ^<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	623 #$v, $def_format
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	624 # ^<<<<<<<<<<<<<<<<<<<< ^<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< ~~
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	625 #$v, $def_format
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	626 #.
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	627
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	628 write();
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	629
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	630 }
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	631 print STDOUT "\n";
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	632 exit 1;
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 mvdbeek parents: diff changeset	633 }

Mercurial > repos > mvdbeek > damidseq_findpeaks

annotate find_peaks @ 10:48d9c6f9ef41 draft