# HG changeset patch
# User messersc
# Date 1418830823 18000
# Node ID d42f4d78c85eed6aa4d3b0ca3871cc43afe7a7fb
Uploaded
diff -r 000000000000 -r d42f4d78c85e JAMM.sh
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/JAMM.sh Wed Dec 17 10:40:23 2014 -0500
@@ -0,0 +1,465 @@
+#!/bin/bash
+########################################
+#### Peak finding Pipeline for NGS Data
+#### Bash script
+########################################
+
+export LC_ALL=en_US.UTF-8
+
+##Finding out the path
+sPath="`dirname \"$0\"`"
+sPath="`( cd \"$sPath\" && pwd )`"
+
+
+
+usage()
+{
+cat << EOF
+Welcome to JAMM v1.0.6rev2 (GNU GPLv3). Copyright (C) 2014 Mahmoud Ibrahim.
+
+This program comes with ABSOLUTELY NO WARRANTY; for details visit http://www.gnu.org/licenses/gpl.html. This is free software, and you are welcome to redistribute it under certain conditions; visit http://www.gnu.org/licenses/gpl.html for details.
+
+OPTIONS:
+ -s directory containing Sample files (required)
+ -g Genome size file (required)
+ -o Output directory (required)
+ -c directory containing input or Control files
+ -m Mode, normal or narrow (default: normal)
+ -r Resolution, peak or region (default: peak)
+ -f Fragment length(s) (default: estimated)
+ -w minimum Window size (default: 2 --- Note: this means minimum_window_size = bin_size x the_value_of_-w)
+ -p Number of processors used by R scripts (default: 1)
+ -b Bin Size (default: estimated)
+ -t Type, single or paired (default: single, requires BED files. paired requires BEDPE files)
+ -e window Enrichment cutoff, auto or any numeric value (default: 1 --- Set this to auto to estimate the appropriate window enrichment cutoff)
+EOF
+}
+
+
+# =========================
+# Process Input parameters
+# =========================
+
+
+#Defaults -- Change those if you want
+mode="normal"
+resol="peak"
+cores="1"
+window="2"
+type="single"
+windowe="1"
+
+
+#Defaults -- Do not change
+sdir=""
+gsize=""
+out=""
+binsize="ns"
+fraglen="ns"
+ran=$RANDOM
+wdir=$(mktemp -d)
+
+while getopts "s:g:o:c:m:r:f:p:w:b:t:e:" OPTION
+do
+ case $OPTION in
+ s) sdir=$OPTARG
+ ;;
+ g) gsize=$OPTARG
+ ;;
+ o) out=$OPTARG
+ ;;
+ c) bdir=$OPTARG
+ ;;
+ m) mode=$OPTARG
+ ;;
+ r) resol=$OPTARG
+ ;;
+ f) fraglen=$OPTARG
+ ;;
+ p) cores=$OPTARG
+ ;;
+ w) window=$OPTARG
+ ;;
+ b) binsize=$OPTARG
+ ;;
+ t) type=$OPTARG
+ ;;
+ e) windowe=$OPTARG
+ ;;
+ ?)
+ usage
+ exit
+ ;;
+ esac
+done
+if [ "$mode" == "normal" ]; then
+ clustno="2"
+fi
+if [ "$mode" == "narrow" ]; then
+ clustno="3"
+fi
+
+if [[ -z $sdir ]] || [[ -z $gsize ]] || [[ -z $out ]]
+then
+ usage
+ exit 1
+fi
+#=======================> DONE!
+
+
+
+# =============================
+# Step One: Initial Processing
+# =============================
+printf "\n\n========================================\nStarted JAMM Pipeline v1.0.6rev2...Hang on!\n========================================\n\n"
+
+if [ ! -d "$wdir" ]; then
+ mkdir $wdir #make working directory
+fi
+if [ ! -d "$out" ]; then
+ mkdir $out #make output directory
+fi
+mkdir $wdir/bkgd.$ran/ #directory to store background files
+mkdir $wdir/sizes.$ran/ #chromosomes and sizes
+mkdir $wdir/samples.$ran/ #store sample files
+
+dupnum=$(ls -1 $sdir | wc -l) #count how many sample files
+
+
+#separate chromosome sizes
+printf "Loading genome size file..."
+ext="$wdir/sizes.$ran/"
+awk -v ext="$ext" '{ print >> ext"/size." $1 ".bed" }' $gsize
+printf "Done!\n"
+
+
+printf "Processing sample files..."
+#load each chromosome from each sample file
+for i in $sdir/*.bed; do
+samplefile=$(basename $i)
+ for f in $wdir/sizes.$ran/*; do
+ sizefile=$(basename $f)
+ chr=$(echo $sizefile | awk -F"." '{print $2}' | awk -F"." '{print $1}');
+ awk -v chr="$chr" -v ext="$wdir/samples.$ran/" -v samplefile="$samplefile" -F"\t" '$1 == chr { print $2"\t"$6 >> ext"sample."chr"."samplefile }' "$i"
+ done
+done
+printf "Done!\n"
+
+
+if [ ! -z $bdir ]; then
+#concatenate all background files into one file
+printf "Processing control files..."
+cat $bdir/*.bed > $wdir/bkgd.$ran/ctrl.bed
+
+for f in $wdir/sizes.$ran/*; do
+ sizefile=$(basename $f)
+ chr=$(echo $sizefile | awk -F"." '{print $2}' | awk -F"." '{print $1}');
+ awk -v chr="$chr" -v ext="$wdir/bkgd.$ran/" -F"\t" '$1 == chr { print $2"\t"$6 >> ext"bkgd."chr".ctrl.bed" }' "$wdir/bkgd.$ran/ctrl.bed"
+done
+
+printf "Done!\n"
+fi
+
+#determine average read lengths
+printf "Getting average read lengths..."
+ if [ ! -z $bdir ]; then
+ readC=$(awk '{a=$3-$2;print a;}' "$wdir/bkgd.$ran/ctrl.bed" | perl -lane '$a+=$_;END{print $a/$.}' | awk '{a=$1+0.5;print a;}' | cut -d"." -f1)
+ fi
+ readL=""
+ for s in $sdir/*.bed; do #and for each sample file
+ read=$(awk '{a=$3-$2;print a;}' "$s" | perl -lane '$a+=$_;END{print $a/$.}' | awk '{a=$1+0.5;print a;}' | cut -d"." -f1)
+ readL="$readL,$read"
+ done
+ readL=${readL#","}
+printf "Done!\n"
+#=======================> DONE!
+
+
+
+# =============================
+# Step Two: Fragment Length
+# =============================
+#single-end
+if [ $type == "single" ]; then
+
+if [ $fraglen == "ns" ]; then
+
+ ##Counting Where Reads Start and Calculating Cross Correlation
+ mkdir $wdir/stats.$ran/ #store count files
+ mkdir $out/xcorr #final xcorr results
+
+
+ printf "Calculating Fragment Length(s)...\n"
+ for f in $wdir/sizes.$ran/*; do #for each chromosome
+ samplelist=""
+ readlist=""
+ sizefile=$(basename $f)
+ chr=$(echo $sizefile | awk -F"." '{print $2}' | awk -F"." '{print $1}');
+
+ #list of sample bed files and read lengths
+ for s in $wdir/samples.$ran/*.bed; do #and for each sample file
+ samplefile=$(basename $s)
+ chr2=$(echo $samplefile | awk -F"." '{print $2}');
+ if [ $chr == $chr2 ] #belonging to this chromosome
+ then
+ samplelist="$samplelist,$wdir/samples.$ran/$samplefile"
+ fi
+ done
+ readlist="$readL"
+
+ #list of control bed files and read lengths
+ if [ ! -z $bdir ]; then
+ for s in $wdir/bkgd.$ran/*.bed; do #and for each sample file
+ samplefile=$(basename $s)
+ chr2=$(echo $samplefile | awk -F"." '{print $2}');
+ if [ $chr == $chr2 ] #belonging to this chromosome
+ then
+ samplelist="$samplelist,$wdir/bkgd.$ran/$samplefile"
+ readlist="$readL,$readC"
+ fi
+ done
+ fi
+
+ #remove leading comma
+ samplelist=${samplelist#","}
+
+ #call R script for xcorr calculation
+ Rscript "$sPath/xcorr.r" -ibed="$samplelist" -s="$wdir/sizes.$ran/size.$chr.bed" -rl="$readlist" -d="$wdir/stats.$ran" -p="$cores"
+ done
+
+ #report xcorr results (samples)
+ for f in $sdir/*.bed; do
+ file=$(basename $f)
+ samplefile=$(echo $file | awk -F"." '{print $1}');
+ mkdir "$out/xcorr/$samplefile" #final xcorr results
+ if [ -f "$wdir/stats.$ran/xc.$samplefile.tab" ]; then
+ cp $wdir/stats.$ran/xc.$samplefile.tab $out/xcorr/$samplefile/shifts.txt
+ fi
+ Rscript "$sPath/xcorrhelper.r" -infile="$out/xcorr/$samplefile/shifts.txt" -out="$out/xcorr/$samplefile"
+ done
+ #report xcorr results (control)
+ if [ ! -z $bdir ]; then
+ mkdir "$out/xcorr/ctrl" #final xcorr results
+ if [ -f "$wdir/stats.$ran/xc.ctrl.tab" ]; then
+ cp $wdir/stats.$ran/xc.ctrl.tab $out/xcorr/ctrl/shifts.txt
+ fi
+ Rscript "$sPath/xcorrhelper.r" -infile="$out/xcorr/ctrl/shifts.txt" -out="$out/xcorr/ctrl"
+ fi
+
+fi
+fi
+
+#paired-end
+if [ $type == "paired" ]; then
+ printf "Getting Average Fragment Length(s)...\n"
+ mkdir $out/xcorr #final xcorr results
+
+ for f in $sdir/*.bed; do
+ file=$(basename $f)
+ samplefile=$(echo $file | awk -F"." '{print $1}');
+ mkdir "$out/xcorr/$samplefile"
+ frag=$(awk '{a=$6-$2;print a;}' $f | perl -lane '$a+=$_;END{print $a/$.}' | awk '{a=$1+0.5;print a;}' | cut -d"." -f1)
+ echo "Average_from_paired $frag" > $out/xcorr/$samplefile/shifts.txt
+ Rscript "$sPath/xcorrhelper.r" -infile="$out/xcorr/$samplefile/shifts.txt" -out="$out/xcorr/$samplefile"
+ done
+fi
+#=======================> DONE!
+
+
+
+# =================================
+# Step Three: Calculating Bin Size
+# =================================
+if [ $binsize == "ns" ]; then
+ printf "Getting Bin Size: "
+
+ chr=$(sort -nr -k2 $gsize | head -n 1 | awk -F"\t" '{print $1}');
+ samplelist=""
+ frag=""
+ if [ $fraglen != "ns" ]; then
+ frag=$fraglen
+ k=1
+ fi
+
+ #list of sample bed files and read lengths
+ for s in $wdir/samples.$ran/*.bed; do
+ samplefile=$(basename $s)
+ chr2=$(echo $samplefile | awk -F"." '{print $2}');
+ if [ $chr == $chr2 ]
+ then
+ samplelist="$samplelist,$wdir/samples.$ran/$samplefile"
+ samplename=$(echo $samplefile | awk -F"." '{ print $3 }')
+ samplefilename=$(echo $samplefile | cut -d'.' -f 3-)
+ if [ $fraglen == "ns" ]; then
+ shift=$(awk -F":" '$1 == "Fragment Length" { print $2 }' "$out/xcorr/$samplename/xcorrsummary.txt")
+ frag="$frag,$shift"
+ fi
+ fi
+ done
+ #remove leading comma
+ samplelist=${samplelist#","}
+ frag=${frag#","}
+
+ Rscript "$sPath/bincalculator.r" -ibed="$samplelist" -s="$gsize" -rl="$readL" -d="$wdir" -p="$cores" -f="$frag" -type="$type"
+fi
+if [ $binsize != "ns" ]; then
+ printf "You set a Bin Size: $binsize \n"
+fi
+#=======================> DONE!
+
+
+
+# ===========================
+# Step Four: Calling Peaks
+# ===========================
+mkdir $wdir/peaks.$ran/ #store count files
+mkdir $out/peaks #store peak files
+
+printf "Calling Peaks...(mode: $mode, resolution: $resol)\n"
+
+
+#single-end reads
+if [ $type == "single" ]; then
+
+if [ $binsize == "ns" ]; then
+ binsize=$(cat "$wdir/binsize.txt")
+fi
+
+counting=1;
+for f in $wdir/sizes.$ran/*; do #for each chromosome
+ samplelist=""
+ frag=""
+ k=1
+ if [ $fraglen != "ns" ]; then
+ frag=$fraglen
+ fi
+
+
+ sizefile=$(basename $f)
+ chr=$(echo $sizefile | awk -F"." '{print $2}' | awk -F"." '{print $1}');
+
+ printf "Chromosome $chr: "
+
+ #list of sample bed files and fragment lengths
+ for s in $wdir/samples.$ran/*.bed; do #and for each sample file
+ samplefile=$(basename $s)
+ chr2=$(echo $samplefile | awk -F"." '{print $2}');
+ if [ $chr == $chr2 ] #belonging to this chromosome
+ then
+ samplelist="$samplelist,$wdir/samples.$ran/ext.$samplefile"
+ samplename=$(echo $samplefile | awk -F"." '{ print $3 }')
+ samplefilename=$(echo $samplefile | cut -d'.' -f 3-)
+ if [ $fraglen == "ns" ]; then
+ shift=$(awk -F":" '$1 == "Fragment Length" { print $2 }' "$out/xcorr/$samplename/xcorrsummary.txt")
+ frag="$frag,$shift"
+ read=$(echo $readL | cut -f "$k" -d ",")
+ k=$(($k+1))
+ fi
+ if [ $fraglen != "ns" ]; then
+ shift=$(echo $frag | cut -f "$k" -d ",")
+ read=$(echo $readL | cut -f "$k" -d ",")
+ k=$(($k+1))
+ fi
+ perl "$sPath/readshifter.pl" "$wdir/samples.$ran/$samplefile" $shift $read > "$wdir/samples.$ran/ext.$samplefile"
+ fi
+ done
+
+ #control file
+ bkgdfile="None"
+ if [ ! -z $bdir ]; then
+ if [ $fraglen == "ns" ]; then
+ bshift=$(awk -F":" '$1 == "Fragment Length" { print $2 }' "$out/xcorr/ctrl/xcorrsummary.txt")
+ frag="$frag,$bshift"
+ fi
+ if [ $fraglen != "ns" ]; then
+ l=$(($dupnum+1))
+ bshift=$(echo $frag | cut -f "$l" -d ",")
+ fi
+ perl "$sPath/readshifter.pl" "$wdir/bkgd.$ran/bkgd.$chr.ctrl.bed" $bshift $readC > "$wdir/bkgd.$ran/ext.bkgd.$chr.ctrl.bed"
+ bkgdfile="$wdir/bkgd.$ran/ext.bkgd.$chr.ctrl.bed"
+ fi
+
+ #remove leading comma
+ samplelist=${samplelist#","}
+ frag=${frag#","}
+
+ #call the peak calling R script
+ Rscript "$sPath/peakfinder.r" -sfile="$f" -bednames="$samplelist" -frag="$frag" -bkgd=$bkgdfile -out="$wdir/peaks.$ran/" -clustnummer="$clustno" -resolution="$resol" -window="$window" -p="$cores" -bin="$binsize" -type="$type" -chrcount="$counting" -windowe="$windowe"
+ counting=$(($counting+1));
+ cp "$wdir/peaks.$ran/$chr.peaks.bed" "$out/peaks/$chr.peaks.bed"
+ rm "$wdir/peaks.$ran/$chr.peaks.bed"
+done
+counting=1;
+fi
+
+
+#paired-end reads
+if [ $type == "paired" ]; then
+
+if [ $binsize == "ns" ]; then
+ binsize=$(cat "$wdir/binsize.txt")
+fi
+
+
+counting=1;
+for f in $wdir/sizes.$ran/*; do #for each chromosome
+ samplelist=""
+
+ sizefile=$(basename $f)
+ chr=$(echo $sizefile | awk -F"." '{print $2}' | awk -F"." '{print $1}');
+
+ printf "Chromosome $chr: "
+
+ #list of sample bed files and fragment lengths
+ for s in $wdir/samples.$ran/*.bed; do #and for each sample file
+ samplefile=$(basename $s)
+ chr2=$(echo $samplefile | awk -F"." '{print $2}');
+ if [ $chr == $chr2 ] #belonging to this chromosome
+ then
+ samplelist="$samplelist,$wdir/samples.$ran/$samplefile"
+ samplename=$(echo $samplefile | awk -F"." '{ print $3 }')
+ samplefilename=$(echo $samplefile | cut -d'.' -f 3-)
+ x="$sdir/$samplefilename"
+ fi
+ done
+
+ #control file
+ bkgdfile="None"
+ if [ ! -z $bdir ]; then
+ bkgdfile="$wdir/bkgd.$ran/bkgd.$chr.ctrl.bed"
+ fi
+
+ #remove leading comma
+ samplelist=${samplelist#","}
+ frag=${frag#","}
+
+ #call the peak calling R script
+ Rscript "$sPath/peakfinder.r" -sfile=$f -bednames=$samplelist -frag="NA" -bkgd=$bkgdfile -out="$wdir/peaks.$ran/" -clustnummer="$clustno" -resolution="$resol" -window="$window" -p="$cores" -bin="$binsize" -type="$type" -chrcount="$counting" -windowe="$windowe"
+ counting=$(($counting+1));
+ cp "$wdir/peaks.$ran/$chr.peaks.bed" "$out/peaks/$chr.peaks.bed"
+ rm "$wdir/peaks.$ran/$chr.peaks.bed"
+done
+counting=1;
+fi
+
+
+cp $wdir/peaks.$ran/min.peaksize $out/peaks/min.peaksize
+
+
+#concatenate, sort and filter
+cat $out/peaks/*.bed > $out/peaks/all.narrowPeak
+Rscript "$sPath/peakhelper.r" -filelist="$out/peaks/all.narrowPeak"
+perl "$sPath/peakfilter.pl" $out/peaks/all.narrowPeak | sort -nr -k7 > $out/peaks/filtered.peaks.narrowPeak
+cut -f1-10 $out/peaks/all.narrowPeak | awk -F"\t" -v j=0 '$7 > j' | sort -nr -k7 > $out/peaks/all.peaks.narrowPeak
+rm $out/peaks/all.narrowPeak
+rm $out/peaks/*.bed
+rm $out/peaks/min.peaksize
+#=======================> DONE!
+
+
+
+rm -rf $wdir
+
+
+
+printf "\n\n========================================\nWe're done...Congratulations!\n========================================\n\n"
diff -r 000000000000 -r d42f4d78c85e README.md
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/README.md Wed Dec 17 10:40:23 2014 -0500
@@ -0,0 +1,13 @@
+JAMM: a peak finder for joint analysis of NGS replicates
+====
+doi: 10.1093/bioinformatics/btu568
+
+JAMM (Joint Analysis of NGS replicates via Mixture Model clustering):
+a peak finder that can integrate information from biological replicates,
+determine enrichment site widths accurately and resolve neighboring narrow peaks.
+JAMM is a universal peak finder that is applicable to different types of datasets
+
+Galaxy
+====
+
+This is a wrapper for JAMM for use in Galaxy (usegalaxy.org)
diff -r 000000000000 -r d42f4d78c85e SignalGenerator.sh
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/SignalGenerator.sh Wed Dec 17 10:40:23 2014 -0500
@@ -0,0 +1,220 @@
+#!/usr/bin/bash
+
+
+
+
+##Finding out the path
+sPath="`dirname \"$0\"`"
+sPath="`( cd \"$sPath\" && pwd )`"
+
+
+
+usage()
+{
+cat << EOF
+Welcome to JAMM v1.0.6rev2 Signal Generator Script (GNU GPLv3). Copyright (C) 2014 Mahmoud Ibrahim.
+
+This program comes with ABSOLUTELY NO WARRANTY; for details visit http://www.gnu.org/licenses/gpl.html. This is free software, and you are welcome to redistribute it under certain conditions; visit http://www.gnu.org/licenses/gpl.html for details.
+
+OPTIONS:
+ -s Directory containing sample files (required)
+ -g Genome size file (required)
+ -o Output Directory (required)
+ -c directory containing input or Control files
+ -r file with Regions to get signal for (required)
+ -b Bin size for signal generation (default: 10)
+ -f Fragment lengths (required)
+ -p Number of processors used by R scripts (default: 1)
+
+EOF
+}
+
+
+# =========================
+# Process Input parameters
+# =========================
+
+
+sdir=""
+gsize=""
+out=""
+signal="10"
+regs=""
+fraglen=""
+wdir=$(mktemp -d)
+ran=$RANDOM
+cores="1"
+
+
+while getopts "s:o:c:r:b:f:g:p:" OPTION
+do
+ case $OPTION in
+ s) sdir=$OPTARG
+ ;;
+ g) gsize=$OPTARG
+ ;;
+ o) out=$OPTARG
+ ;;
+ c) bdir=$OPTARG
+ ;;
+ r) regs=$OPTARG
+ ;;
+ b) signal=$OPTARG
+ ;;
+ f) fraglen=$OPTARG
+ ;;
+ p) cores=$OPTARG
+ ;;
+ ?)
+ usage
+ exit
+ ;;
+ esac
+done
+
+
+if [[ -z $fraglen ]] || [[ -z $sdir ]] || [[ -z $regs ]] || [[ -z $out ]]
+then
+ usage
+ exit 1
+fi
+#=======================> DONE!
+
+
+
+# =============================
+# Step One: Initial Processing
+# =============================
+printf "\n\n============================================\nStarted JAMM Signal Generator Pipeline...Hang on!\n============================================\n\n"
+
+if [ ! -d "$wdir" ]; then
+ mkdir $wdir #make working directory
+fi
+if [ ! -d "$out" ]; then
+ mkdir $out #make working directory
+fi
+mkdir $wdir/bkgd.$ran/ #directory to store background files
+mkdir $wdir/sizes.$ran/ #chromosomes and sizes
+mkdir $wdir/samples.$ran/ #store sample files
+
+dupnum=$(ls -1 $sdir | wc -l) #count how many sample files
+
+
+#separate chromosome sizes
+printf "Loading genome size file..."
+ext="$wdir/sizes.$ran/"
+awk -v ext="$ext" '{ print >> ext"/size." $1 ".bed" }' $gsize
+printf "Done!\n"
+
+
+printf "Processing sample files..."
+#load each chromosome from each sample file
+for i in $sdir/*.bed; do
+samplefile=$(basename $i)
+ for f in $wdir/sizes.$ran/*; do
+ sizefile=$(basename $f)
+ chr=$(echo $sizefile | awk -F"." '{print $2}' | awk -F"." '{print $1}');
+ awk -v chr="$chr" -v ext="$wdir/samples.$ran/" -v samplefile="$samplefile" -F"\t" '$1 == chr { print $2"\t"$6 >> ext"sample."chr"."samplefile }' "$i"
+ done
+done
+printf "Done!\n"
+
+
+if [ ! -z $bdir ]; then
+#concatenate all background files into one file
+printf "Processing control files..."
+cat $bdir/*.bed > $wdir/bkgd.$ran/ctrl.bed
+
+for f in $wdir/sizes.$ran/*; do
+ sizefile=$(basename $f)
+ chr=$(echo $sizefile | awk -F"." '{print $2}' | awk -F"." '{print $1}');
+ awk -v chr="$chr" -v ext="$wdir/bkgd.$ran/" -F"\t" '$1 == chr { print $2"\t"$6 >> ext"bkgd."chr".ctrl.bed" }' "$wdir/bkgd.$ran/ctrl.bed"
+done
+
+rm $wdir/bkgd.$ran/ctrl.bed
+
+printf "Done!\n"
+fi
+
+
+#determine average read lengths
+printf "Getting average read lengths..."
+ if [ ! -z $bdir ]; then
+ readC=$(awk '{a=$3-$2;print a;}' "$wdir/bkgd.$ran/ctrl.bed" | perl -lane '$a+=$_;END{print $a/$.}' | awk '{print int($1)}')
+ fi
+ readL=""
+ for s in $sdir/*.bed; do #and for each sample file
+ read=$(awk '{a=$3-$2;print a;}' "$s" | perl -lane '$a+=$_;END{print $a/$.}' | awk '{print int($1)}')
+ readL="$readL,$read"
+ done
+ readL=${readL#","}
+printf "Done!\n"
+#=======================> DONE!
+
+
+
+
+
+
+# ===========================
+# Step Three: Getting Signal
+# ===========================
+mkdir $wdir/signal.$ran/
+mkdir $out/signal #store signal
+
+
+printf "Generating Signal...(bin size: $signal)\n"
+
+counting=1;
+for f in $wdir/sizes.$ran/*; do #for each chromosome
+ samplelist=""
+ frag=""
+ frag=$fraglen
+ k=1
+
+ sizefile=$(basename $f)
+ chr=$(echo $sizefile | awk -F"." '{print $2}' | awk -F"." '{print $1}');
+ chrSize=$(cat $f | cut -f2);
+ printf "Chromosome $chr: "
+
+ #list of sample bed files and fragment lengths
+ for s in $wdir/samples.$ran/*.bed; do #and for each sample file
+ samplefile=$(basename $s)
+ chr2=$(echo $samplefile | awk -F"." '{print $2}');
+ if [ $chr == $chr2 ] #belonging to this chromosome
+ then
+ samplelist="$samplelist,$wdir/samples.$ran/ext.$samplefile"
+ samplename=$(echo $samplefile | awk -F"." '{ print $3 }')
+ samplefilename=$(echo $samplefile | cut -d'.' -f 3-)
+ shift=$(echo "$frag" | cut -f "$k" -d ",")
+ read=$(echo "$readL" | cut -f "$k" -d ",")
+ k=$(($k+1))
+ perl "$sPath/readshifter.pl" "$wdir/samples.$ran/$samplefile" $shift $read > "$wdir/samples.$ran/ext.$samplefile"
+ fi
+ done
+
+ #control file
+ bkgdfile="None"
+ if [ ! -z $bdir ]; then
+ l=$(($dupnum+1))
+ bshift=$(echo $frag | cut -f "$l" -d ",")
+ perl "$sPath/readshifter.pl" "$wdir/bkgd.$ran/bkgd.$chr.ctrl.bed" $bshift $readC > "$wdir/bkgd.$ran/ext.bkgd.$chr.ctrl.bed"
+ bkgdfile="$wdir/bkgd.$ran/ext.bkgd.$chr.ctrl.bed"
+ fi
+
+ #remove leading comma
+ samplelist=${samplelist#","}
+ frag=${frag#","}
+
+ #call the peak calling R script
+ Rscript "$sPath/signalmaker.r" -chromoS="$chrSize" -chromo="$chr" -bednames=$samplelist -frag=$frag -bkgd=$bkgdfile -out="$wdir/signal.$ran/" -sig="$signal" -regions="$regs" -p="$cores" -chrcount="$counting"
+ cat $wdir/signal.$ran/*.bedSignal | awk -F"\t" -v j=0 '$4 > j' > "$out/signal/$chr.bedGraph"
+ rm $wdir/signal.$ran/*.bedSignal
+ counting=$(($counting+1));
+done
+counting=1;
+#=======================> DONE!
+
+rm -rf $wdir
+
+printf "\n\n========================================\nWe're done...Congratulations!\n========================================\n\n"
diff -r 000000000000 -r d42f4d78c85e bincalculator.r
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/bincalculator.r Wed Dec 17 10:40:23 2014 -0500
@@ -0,0 +1,196 @@
+#############################################################
+#### Bin Size Calculator after Shimazaki and Shinomoto 2007
+#### R script
+#############################################################
+
+
+# =======================
+# User-defined variables
+# =======================
+defaultBins = seq(50, 50*15, by = 50) # default binsize search space, used when fragment length is equal or less than read length
+#=======================> DONE!
+
+
+
+
+# ================================
+# Required Libraries check & load
+# ================================
+if ((is.element('parallel', installed.packages()[,1]) == FALSE)) {
+ stop("R package'parallel' is required. Please install it!")
+}
+suppressPackageStartupMessages(library("parallel"))
+#=======================> DONE!
+
+
+
+
+# =================
+# Custom Functions
+# =================
+#Implements the Shimazaki procedure
+shimazaki = function(bedfile, rl, bins, maxIter, filelist, chromSize, type) {
+
+ #read in the file data
+ if (type == "single") {
+ reads = read.table(bedfile, header = FALSE)
+ reads = cbind(as.character(reads[[1]]), as.character(reads[[2]]))
+ }
+ if (type == "paired") {
+ #reads = sqldf("SELECT V1 As 'start', V2 As 'end' FROM readsFile", file.format=list(header = FALSE, sep = "\t"))
+ reads = read.table(bedfile, header = FALSE)
+ reads = cbind(as.numeric(reads[[1]]), as.numeric(reads[[2]]))
+ }
+ readnum = length(reads[[1]])
+ o = which(filelist == bedfile)
+ readlen = rl[o]
+ jack = o - 1
+ bins = bins[(1+(jack*15)):(15+(jack*15))]
+
+ costs = vector(mode = "numeric", length = length(bins))
+ #Shimazaki procedure
+ for (i in 1:length(bins)) {
+ #construct the counting breaks vector
+ genomevec = seq(0, chromSize, by = bins[i]);
+ if (max(genomevec) < chromSize) {
+ genomevec = append(genomevec, chromSize);
+ }
+
+ #create a vector of read counts
+ if (type == "single") {
+ ameirah = sort(c((as.numeric(reads[reads[,2] == "+",,drop = FALSE][,1])), ((as.numeric(reads[reads[,2] == "-",,drop = FALSE][,1])) + readlen - 1)))
+ }
+ if (type == "paired") {
+ ameirah = sort(c((reads[[1]]), (reads[[2]])))
+ }
+ ameirah = hist(ameirah, breaks = genomevec, plot = FALSE)
+ ameirah = ameirah$counts
+
+ #get cost function
+ m = mean(ameirah)
+ v = (sum((ameirah - m)^2)) / (length(ameirah))
+ num = ((2*m) - v)
+ den = ((bins[i]) * readnum)^2
+ cost = -(log(abs(num)) - log(den))
+ costs[i] = cost
+ }
+
+index = which.min(costs)
+finbin = bins[index]
+
+return(finbin)
+}
+#=======================> DONE!
+
+
+
+
+# ==========================
+# Parse-in System Variables
+# ==========================
+args = commandArgs(trailingOnly = TRUE) # Read Arguments from command line
+
+
+#Set arguments to default values
+ibed = NA # input bed file
+sFile = NA # chromosome size
+storeFile = NA # file to store result
+cornum = 1 # number of processors to use
+rl = NA # read length
+frags = NA # fragment lengths
+bins = NA
+
+#Parsing arguments and storing values
+for (each.arg in args) {
+ if (grepl('^-ibed=',each.arg)) {
+ arg.split <- strsplit(each.arg,'=',fixed=TRUE)[[1]]
+ if (! is.na(arg.split[2]) ) {
+ ibed <- arg.split[2]
+ } else {
+ stop('No input bed file')
+ }
+ }
+ if (grepl('^-s=',each.arg)) {
+ arg.split <- strsplit(each.arg,'=',fixed=TRUE)[[1]]
+ if (! is.na(arg.split[2]) ) {
+ sFile <- arg.split[2]
+ } else {
+ stop('No chromosome size file')
+ }
+ }
+ if (grepl('^-rl=',each.arg)) {
+ arg.split <- strsplit(each.arg,'=',fixed=TRUE)[[1]]
+ if (! is.na(arg.split[2]) ) {
+ rl <- arg.split[2]
+ }
+ }
+ if (grepl('^-d=',each.arg)) {
+ arg.split <- strsplit(each.arg,'=',fixed=TRUE)[[1]]
+ if (! is.na(arg.split[2]) ) {
+ storeFile <- arg.split[2]
+ } else {
+ stop('No file to store result')
+ }
+ }
+ if (grepl('^-p=',each.arg)) {
+ arg.split <- strsplit(each.arg,'=',fixed=TRUE)[[1]]
+ if (! is.na(arg.split[2]) ) {
+ cornum <- as.numeric(arg.split[2])
+ } else {
+ stop('No number of cores given')
+ }
+ }
+ if (grepl('^-f=',each.arg)) {
+ arg.split <- strsplit(each.arg,'=',fixed=TRUE)[[1]]
+ if (! is.na(arg.split[2]) ) {
+ frags <- arg.split[2]
+ } else {
+ stop('No Fragment lengths given')
+ }
+ }
+ if (grepl('^-type=',each.arg)) {
+ arg.split <- strsplit(each.arg,'=',fixed=TRUE)[[1]]
+ if (! is.na(arg.split[2]) ) {
+ type <- arg.split[2]
+ } else {
+ stop('No type given')
+ }
+ }
+}
+
+#Read in variables
+chromosomes = read.table(sFile, header=FALSE)
+chromSize = as.numeric(chromosomes$V2) #chromosome size
+chromSize = max(chromSize) #get maximum chrom size
+rm(chromosomes)
+
+ibed = strsplit(ibed, ",", fixed = TRUE)[[1]]
+rl = as.numeric(strsplit(rl, ",", fixed = TRUE)[[1]])
+frags = as.numeric(strsplit(frags, ",", fixed = TRUE)[[1]])
+#=======================> DONE!
+
+
+
+# =====================
+# Shimazaki Procedure
+# =====================
+for (i in 1:length(ibed)) {
+ if (frags[i] > rl[i]) {
+ minbin = floor(frags[i] / 2)
+ bins = c(bins, seq(minbin, minbin*15, by = minbin))
+ } else {
+ bins = c(bins, defaultBins)
+ }
+}
+bins = bins[!is.na(bins)]
+bins = mclapply(ibed, shimazaki, rl, bins, maxIter, ibed, chromSize, type = type, mc.cores = cornum)
+bins = min(unlist(bins))
+#=======================> DONE!
+
+
+# ==================
+# Write Information
+# ==================
+write(paste0(bins), file = paste0(storeFile, "/binsize.txt"))
+message(bins)
+#=======================> DONE!
diff -r 000000000000 -r d42f4d78c85e changelog
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/changelog Wed Dec 17 10:40:23 2014 -0500
@@ -0,0 +1,6 @@
+===================
+Version 1.0.6rev2
+===================
+
+- fixed various bugs in v1.0.6rev1 that caused paired-end runs to malfunction.
+
diff -r 000000000000 -r d42f4d78c85e countwins.r
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/countwins.r Wed Dec 17 10:40:23 2014 -0500
@@ -0,0 +1,680 @@
+###############################
+#### Peak finder for NGS Data
+#### R script
+###############################
+
+
+
+
+# =======================
+# User-defined variables
+# =======================
+cutoff = NA #To enforce an SNR cutoff ratio, delete NA and enter the number you want
+strict = 1 #to make peak calling more / less strict, increase / decrease this number - Only use this if you are getting an unusually large or small number of peaks.
+options(warn = -1, scipen = 1000) #R will not report any warnings (warn = -1), R will not use scientific notation (scipen = 1000)
+#=======================> DONE!
+
+
+
+
+# ================================
+# Required Libraries check & load
+# ================================
+if ((is.element('mclust', installed.packages()[,1]) == FALSE) || (is.element('signal', installed.packages()[,1]) == FALSE) || (is.element('sqldf', installed.packages()[,1]) == FALSE) || (is.element('parallel', installed.packages()[,1]) == FALSE)) {
+ stop("R package 'Mclust', 'signal', 'sqldf' and 'parallel' are required. Please install them!")
+}
+suppressPackageStartupMessages(library("mclust"))
+suppressPackageStartupMessages(library("signal"))
+suppressPackageStartupMessages(library("sqldf"))
+suppressPackageStartupMessages(library("tcltk"))
+suppressPackageStartupMessages(library("parallel"))
+#=======================> DONE!
+
+
+
+
+
+# =================
+# Custom Functions
+# =================
+#Get per-row Geometric mean (takes list, returns vectors, not lists!)
+geomeanL <- function(mat){
+ n = length(mat)
+ if (n > 1) {
+ mult = (mat[[1]])*(mat[[2]])
+ if (n > 2) {
+ for (i in 3:n) {
+ mult = mult*(mat[[i]])
+ }
+ }
+ mult = mult^(1/n)
+ mat = mult
+ return(mat)
+ } else {
+ return(mat[[1]])
+ }
+}
+
+
+
+#Get per-row Geometric mean (takes matrix, returns vectors, not lists!)
+geomean <- function(mat){
+ n = NCOL(mat)
+ if (n > 1) {
+ mult = (mat[,1])*(mat[,2])
+ if (n > 2) {
+ for (i in 3:n) {
+ mult = mult*(mat[,i])
+ }
+ }
+ mult = mult^(1/n)
+ mat = mult
+ }
+return(mat)
+}
+
+
+
+#Read in bed(st2) file
+parsein = function(bedfile) {
+ l = sqldf()
+ readsFile = file(bedfile)
+ return(sqldf("SELECT V1 + 1 As 'start' FROM readsFile", file.format=list(header = FALSE, sep = "\t"))$start)
+ l = sqldf()
+ close(readsFile)
+}
+
+
+#Read in bedpe(st2) file
+parseinpe = function(bedfile) {
+ l = sqldf()
+ readsFile = file(bedfile)
+ sebastian = sqldf("SELECT * FROM readsFile", file.format=list(header = FALSE, sep = "\t"))
+ return(cbind(sebastian[[1]]+1, sebastian[[2]]))
+ l = sqldf()
+ close(readsFile)
+}
+
+
+#Produces normalized extended read counts (takes output of parsein(), return a vector of floats)
+countreads = function(bedfile, reads, frag, chromsize, filelist) {
+
+ o = which(filelist == bedfile)
+
+ counts = vector(mode = "numeric", length = chromsize)
+
+ for (j in 1:length(reads[[o]])) {
+ if ((reads[[o]][j]+frag[o]-1) <= chromsize) {
+ counts[(reads[[o]][j]):(reads[[o]][j]+frag[o]-1)] = counts[(reads[[o]][j]):(reads[[o]][j]+frag[o]-1)] + 1
+ }
+ }
+ counts = counts/(mean(counts))
+ return(counts)
+}
+
+
+
+#Produces normalized extended read counts (takes output of parsein(), return a vector of floats)
+countreadspe = function(bedfile, reads, chromsize, filelist) {
+
+ o = which(filelist == bedfile)
+
+ counts = vector(mode = "numeric", length = chromsize)
+
+ for (j in 1:length(reads[[o]][,1])) {
+ counts[(reads[[o]][j,1]):(reads[[o]][j,2])] = counts[(reads[[o]][j,1]):(reads[[o]][j,2])] + 1
+ }
+ counts = counts/(mean(counts))
+ return(counts)
+}
+
+
+
+#find enriched bins
+pickbins = function(winStart, counts, binSize, chromSize, numdup, C, cutoff, strict, mCs, dCs, bkgd) {
+
+ if ((winStart + binSize) <= chromSize) {
+ winEnd = winStart + binSize
+ } else {
+ winEnd = chromSize
+ }
+ binSizeTemp = winEnd - winStart
+ tempend = winEnd - 1
+
+ #extract subset of the background
+ if (bkgd != "None") {
+ Cs = counts[[numdup+1]][winStart:tempend]
+ mCs = mean(Cs)
+ dCs = sd(Cs)
+ } else {
+ Cs = sample(C, binSizeTemp, replace = TRUE)
+ }
+
+
+ #find out whether it's enriched
+ go = rep(0, numdup)
+ for (g in 1:numdup) {
+ mS = (mean(counts[[g]][winStart:tempend]))
+ ratio = mS/dCs
+ if ((mS > (mCs * strict)) && (ratio > cutoff)) {
+ go[g] = 1
+ }
+ }
+ veep = sum(go)
+
+ #get counts when enriched
+ if (veep == numdup) {
+ mS = rep(0, numdup)
+ for (g in 1:numdup) {
+ mS[g] = (mean(counts[[g]][winStart:winEnd]))
+ }
+ cairo = mean(mS)
+ } else {
+ mS = rep(0, numdup)
+ for (g in 1:numdup) {
+ mS[g] = (mean(counts[[g]][winStart:winEnd]))
+ }
+ cairo = -(mean(mS))
+ }
+ return(cairo)
+}
+
+
+
+#find enriched wins
+pickwins = function(winStart, coffeeshopSud, counts, numdup, startlist, winSize) {
+
+ plz = which(startlist == winStart)
+ winEnd = coffeeshopSud[plz]
+ rWinSize = winEnd - winStart + 1
+
+
+ if(rWinSize >= winSize) {
+ mS = rep(0, numdup)
+ for (g in 1:numdup) {
+ mS[g] = (sum(counts[[g]][winStart:winEnd]))
+ }
+ veep = sum(mS)
+ } else {
+ veep = FALSE
+ }
+
+ return(veep)
+}
+
+
+
+#Initialize MClust clustering parameters
+smoothcounts = function(winStart, coffeeshopSud, numdup, counts, startlist) { #helper function1
+
+ plz = which(startlist == winStart)
+ winEnd = coffeeshopSud[plz]
+
+ #extract subset of the IP
+ Rs = matrix(0, nrow = (winEnd - winStart + 1), ncol = numdup)
+ for (j in 1:numdup) {
+ Rs[,j] = counts[[j]][winStart:winEnd]
+ }
+ #smooth extended read counts
+ for (j in 1:numdup) {
+ Rs[,j] = filtfilt(rep(1,80)/80,1,Rs[,j])
+ }
+ return(Rs)
+}
+cluster = function(model, sig, init, clustnummer, noise) { #helper function2
+ noisy = sample(noise, length(sig[,1]), replace = TRUE)
+ clust = me(model, sig+noisy, init)
+ bicc = bic(model, clust$loglik, length(sig[,1]), length(sig[1,]), clustnummer)
+ out = list(bicc = bicc, param = clust$parameters)
+ return(out)
+}
+initparam = function(coffeeshopNord, coffeeshopSud, numdup, counts, cornum, clustnummer, modelnames, noise) { #main function
+
+ n = length(coffeeshopNord)
+ #smooth extended read counts
+ if (cornum > 1) {
+ sig = mclapply(coffeeshopNord, smoothcounts, coffeeshopSud, numdup, counts, startlist = coffeeshopNord, mc.cores = cornum, mc.preschedule = TRUE)
+ } else {
+ sig = lapply(coffeeshopNord, smoothcounts, coffeeshopSud, numdup, counts, startlist = coffeeshopNord)
+ }
+ sig = do.call(rbind, sig)
+
+ #kmeans initialization
+ init = kmeans(sig, clustnummer)
+ init = unmap(init$cluster)
+
+
+ if (cornum > 1) {
+ param = mclapply(modelnames, cluster, sig, init, clustnummer, noise, mc.cores = cornum, mc.preschedule = TRUE)
+ } else {
+ param = lapply(modelnames, cluster, sig, init, clustnummer, noise)
+ }
+
+ bicc = vector(mode = "numeric", length = length(modelnames))
+ for (i in 1:length(modelnames)) {
+ bicc[i] = as.numeric(param[[i]]$bicc)
+ }
+ bicc = which.max(bicc)
+
+ out = list(initparam = param[[bicc]]$param, modelname = modelnames[bicc])
+ return(out)
+}
+
+
+
+
+#find peaks
+findpeak = function(winStart, coffeeshopSud, numdup, C, param, bkgd, resol, counts, noise, startlist) {
+
+
+ plz = which(startlist == winStart)
+ winEnd = coffeeshopSud[plz]
+
+
+ #will store peak information
+ writethis = list()
+
+
+ rWinSizeTemp = winEnd - winStart + 1
+
+ #extract subset of the IP
+ Rs = matrix(nrow = rWinSizeTemp, ncol = numdup)
+ Rsr = Rs
+ for (j in 1:numdup) {
+ Rsr[,j] = counts[[j]][winStart:winEnd]
+ Rs[,j] = filtfilt(rep(1,80)/80,1,Rsr[,j])
+ }
+
+
+ ####CLUSTERING START HERE#####
+ noisy = sample(noise, rWinSizeTemp, replace = TRUE)
+ clust = em(param$modelname, Rs+noisy, param$initparam)
+ clust$classification = map(clust$z)
+ ####CLUSTERING DONE####
+
+ #check whether clutering succeeded
+ if((any(diff(clust$classification)) != 0) && (!(any(is.na(clust$classification))))) {
+
+
+ #check whether all components replicates agreed on clustering assignments
+ ccx = 1
+ if (numdup > 1) {
+ cc = vector(mode = "numeric", length = numdup)
+ for (g in 1:numdup) {
+ cc[g] = which.max(clust$parameters$mean[g,]) #which cluster has the largest mean (this is the peak cluster, hopefully!)
+ }
+ ccx = sum(diff(cc))
+ cluster = cc[1]
+ rm(cc)
+ } else {
+ cluster = which.max(clust$parameters$mean) #which cluster has the largest mean (this is the peak cluster, hopefully!)
+ ccx = 0
+ }
+ if (ccx == 0) {
+
+ #extract subset of the background
+ if (bkgd != "None") {
+ Cs = counts[[numdup+1]][winStart:winEnd]
+ Cs = filtfilt(rep(1,80)/80,1,Cs)
+ } else {
+ Cs = sample(C, rWinSizeTemp, replace = TRUE)
+ Cs = filtfilt(rep(1,80)/80,1,Cs)
+ }
+
+ #find region boundaries
+ loc = 1:length(clust$classification)
+ gmclass = cbind(loc, clust$classification)
+ locPeak = gmclass[gmclass[,2] == cluster,,drop=FALSE]
+ rStart = locPeak[1] #start position of the region
+ rEnd = locPeak[length(locPeak[,1]),1] #end position of the region
+
+ #peak resolution check
+ if (resol == "region") {
+ pSize = rEnd - rStart
+ signal = (geomean(Rs[rStart:rEnd,]))
+ signal2 = (signal) - (Cs[rStart:rEnd])
+ gm = mean(signal2)
+ summit = which.max(geomean(Rsr[rStart:rEnd,])) - 1
+ will2k = wilcox.test(signal, Cs[rStart:rEnd])
+
+ #Is there signal in the region above background
+ if (gm > 0) {
+ writethis[[1]] = rStart + winStart - 1
+ writethis[[2]] = rEnd + winStart
+ writethis[[3]] = paste0(chromName, ".", rStart+winStart -1)
+ writethis[[4]] = "1000"
+ writethis[[5]] = "."
+ writethis[[6]] = gm
+ writethis[[7]] = will2k$p.value
+ writethis[[8]] = "-1"
+ writethis[[9]] = summit
+ }
+ } else if (resol == "peak") {
+ #find out where separate peaks are
+ d = diff(locPeak[,1])
+ d[length(d)+1] = 0
+ locPeak = cbind(locPeak, d)
+ bound1 = which(locPeak[,3] > 1, arr.in=TRUE)
+ bound2 = bound1 + 1
+ bound = locPeak[sort(c(bound1,bound2))]
+ bound = c(rStart, bound, rEnd)
+ w = 1
+ warum = 0
+ while (w < length(bound)) {
+ pStart = bound[w] + winStart - 1
+ pEnd = bound[w+1] + winStart
+ pSize = pEnd - pStart
+ signal = (geomean(Rs[(bound[w]):(bound[w+1]),]))
+ signal2 = (signal) - (Cs[bound[w]:bound[w+1]])
+ gm = mean(signal2)
+ summit = which.max(geomean(Rsr[(bound[w]):(bound[w+1]),])) - 1
+ will2k = wilcox.test(signal, Cs[(bound[w]):(bound[w+1])])
+
+ weil = warum * 9
+ #Is there signal in the region above background
+ if (gm > 0) {
+ writethis[[1+weil]] = pStart
+ writethis[[2+weil]] = pEnd
+ writethis[[3+weil]] = paste0(chromName, ".", pStart)
+ writethis[[4+weil]] = "1000"
+ writethis[[5+weil]] = "."
+ writethis[[6+weil]] = gm
+ writethis[[7+weil]] = will2k$p.value
+ writethis[[8+weil]] = "-1"
+ writethis[[9+weil]] = summit
+ }
+ w = w + 2
+ warum = warum + 1
+ }
+
+ } #peak resolution check
+ } #all replicates agree on clustering assignments?
+ } #clustering worked?
+return(writethis)
+}
+
+
+#filter return value of findpeak()
+processPeaks = function(peaks) {
+ peaks = matrix(unlist(peaks), ncol=9, byrow=TRUE)
+ peaks = peaks[peaks[,1] != FALSE,,drop=FALSE]
+ peaks = data.frame(peaks)
+ return(peaks)
+}
+#=======================> DONE!
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+# ==========================
+# Parse-in System Variables
+# ==========================
+args = commandArgs(trailingOnly = TRUE) # Read Arguments from command line
+
+#Parsing arguments and storing values
+for (each.arg in args) {
+ #chormosome size file
+ if (grepl('^-sfile=',each.arg)) {
+ arg.split <- strsplit(each.arg,'=',fixed=TRUE)[[1]] # split on =
+ if (! is.na(arg.split[2]) ) {
+ size.file <- arg.split[2]
+ } else {
+ stop('No genome size file')
+ }
+ }
+ #bed file names
+ if (grepl('^-bednames=',each.arg)) {
+ arg.split <- strsplit(each.arg,'=',fixed=TRUE)[[1]] # split on =
+ if (! is.na(arg.split[2]) ) {
+ bednames <- arg.split[2]
+ } else {
+ stop('No bed file names')
+ }
+ }
+ #bed files directory
+ if (grepl('^-frag=',each.arg)) {
+ arg.split <- strsplit(each.arg,'=',fixed=TRUE)[[1]] # split on =
+ if (! is.na(arg.split[2]) ) {
+ frag <- arg.split[2]
+ } else {
+ stop('No fragment length given')
+ }
+ }
+ #bakcground files directory
+ if (grepl('^-bkgd=',each.arg)) {
+ arg.split <- strsplit(each.arg,'=',fixed=TRUE)[[1]] # split on =
+ if (! is.na(arg.split[2]) ) {
+ bkgd <- arg.split[2]
+ } else {
+ stop('No background file')
+ }
+ }
+ #bakcground files directory
+ if (grepl('^-out=',each.arg)) {
+ arg.split <- strsplit(each.arg,'=',fixed=TRUE)[[1]] # split on =
+ if (! is.na(arg.split[2]) ) {
+ out <- arg.split[2]
+ } else {
+ stop('No output directory given')
+ }
+ }
+ #Cluster number
+ if (grepl('^-clustnummer=',each.arg)) {
+ arg.split <- strsplit(each.arg,'=',fixed=TRUE)[[1]] # split on =
+ if (! is.na(arg.split[2]) ) {
+ clustnummer <- as.numeric(arg.split[2])
+ }
+ }
+ #resolution
+ if (grepl('^-resolution=',each.arg)) {
+ arg.split <- strsplit(each.arg,'=',fixed=TRUE)[[1]] # split on =
+ if (! is.na(arg.split[2]) ) {
+ resol <- arg.split[2]
+ }
+ }
+ #processor cores
+ if (grepl('^-p=',each.arg)) {
+ arg.split <- strsplit(each.arg,'=',fixed=TRUE)[[1]] # split on =
+ if (! is.na(arg.split[2]) ) {
+ cornum <- as.numeric(arg.split[2])
+ }
+ }
+ #minimum window size
+ if (grepl('^-window=',each.arg)) {
+ arg.split <- strsplit(each.arg,'=',fixed=TRUE)[[1]] # split on =
+ if (! is.na(arg.split[2]) ) {
+ winSize <- arg.split[2]
+ }
+ }
+ #window size
+ if (grepl('^-bin=',each.arg)) {
+ arg.split <- strsplit(each.arg,'=',fixed=TRUE)[[1]] # split on =
+ if (! is.na(arg.split[2]) ) {
+ binsize <- arg.split[2]
+ }
+ }
+ #type (paired / single)
+ if (grepl('^-type=',each.arg)) {
+ arg.split <- strsplit(each.arg,'=',fixed=TRUE)[[1]] # split on =
+ if (! is.na(arg.split[2]) ) {
+ type <- arg.split[2]
+ }
+ }
+}
+
+##Parse in variables
+chromosomes = read.table(size.file, header=FALSE)
+chromName = chromosomes$V1; #which chromosome
+chromSize = chromosomes$V2; #chromosomes size
+rm(chromosomes)
+
+readsFiles = as.list(strsplit(bednames, ",", fixed = TRUE)[[1]])
+numdup = length(readsFiles) #number of replicates
+if (bkgd != "None") {
+ readsFiles[[numdup+1]] = bkgd
+}
+winSize = as.numeric(winSize)
+binSize = as.numeric(binsize)
+winSize = binSize * winSize
+
+if (type == "single") {
+ frags = as.numeric(strsplit(frag, ",", fixed = TRUE)[[1]])
+}
+rm(bednames)
+
+if (numdup > 1) {
+ modelnames = c("VVV","VEV")
+} else {
+ modelnames = "V"
+}
+
+options(stringsAsFactors = FALSE)
+#=======================> DONE!
+
+
+
+
+# =======================
+# Some preliminary stuff
+# =======================
+if (type == "single") {
+ if (cornum > 1) {
+ datain = mclapply(readsFiles, parsein, mc.cores = cornum, mc.preschedule = TRUE) #read in all bed files (samples and control)
+ } else {
+ datain = lapply(readsFiles, parsein) #read in all bed files (samples and control)
+ }
+}
+
+if (type == "paired") {
+ if (cornum > 1) {
+ datain = mclapply(readsFiles, parseinpe, mc.cores = cornum, mc.preschedule = TRUE) #read in all bed files (samples and control)
+ } else {
+ datain = lapply(readsFiles, parseinpe) #read in all bed files (samples and control)
+ }
+}
+
+#minimum peak size (only a recommendation)
+minpeak = floor(binSize / 4)
+
+#make bins vector
+bins = seq(from = 1, to = (chromSize - 1), by = binSize)
+#=======================> DONE!
+
+
+
+
+# ===============
+# Counting Reads
+# ===============
+if (type == "single") {
+ if (cornum > 1) {
+ counts = mclapply(readsFiles, countreads, reads = datain, frag = frags, chromsize = chromSize, filelist = readsFiles, mc.cores = cornum, mc.preschedule = TRUE)
+ } else {
+ counts = lapply(readsFiles, countreads, reads = datain, frag = frags, chromsize = chromSize, filelist = readsFiles)
+ }
+}
+
+if (type == "paired") {
+ if (cornum > 1) {
+ counts = mclapply(readsFiles, countreadspe, reads = datain, chromsize = chromSize, filelist = readsFiles, mc.cores = cornum, mc.preschedule = TRUE)
+ } else {
+ counts = lapply(readsFiles, countreadspe, reads = datain, chromsize = chromSize, filelist = readsFiles)
+ }
+}
+
+rm(datain)
+
+#get total counts
+mS = vector(mode = "numeric", length = numdup)
+for (g in 1:numdup) {
+ mS[g] = sum(counts[[g]])
+}
+totalCounts = sum(mS)
+rm(mS)
+#=======================> DONE!
+
+
+
+# ===================
+# Estimating Cutoff
+# ===================
+if (is.na(cutoff)) {
+ if (bkgd != "None") {
+ cutoff = vector(length = numdup)
+ sdC = sd(counts[[numdup+1]])
+ for (x in 1:numdup) {
+ cutoff[x] = (mean(counts[[x]]))/(sdC)
+ }
+ cutoff = max(cutoff)
+ C = NULL
+ mCs = NULL
+ } else {
+ cutoff = vector(length = numdup)
+ mmV = var(geomeanL(counts))
+ mmM = mean(geomeanL(counts))
+ sigma = log(1+((mmV) / ((mmM)^2)))
+ mu = (log(mmM)) - (0.5 * (sigma))
+ C = rlnorm(100000, mu, sqrt(sigma))
+ for (x in 1:numdup) {
+ cutoff[x] = (mean(counts[[x]]))/(sd(C))
+ }
+ cutoff = max(cutoff)
+ mCs = (mean(sample(C, binSize*5, replace = TRUE)))
+ dCs = (sd(sample(C, binSize*5, replace = TRUE)))
+ }
+}
+#=======================> DONE!
+
+
+
+
+# ========================
+# Picking Enriched Windows
+# ========================
+binNum = vector(mode = "numeric", length = 41)
+binTotalSize = vector(mode = "numeric", length = 41)
+binTotalSizeRatio = vector(mode = "numeric", length = 41)
+binTotalCount = vector(mode = "numeric", length = 41)
+binTotalCountNO = vector(mode = "numeric", length = 41)
+binTotalCountRatio = vector(mode = "numeric", length = 41)
+maxiFun = vector(mode = "numeric", length = 41)
+ggg = seq(1,5, by = 0.1)
+for (i in 1:41) {
+ if (cornum > 1) {
+ coffeeshop = mclapply(bins, pickbins, counts, binSize, chromSize, numdup, C, cutoff, ggg[i], mCs, dCs, bkgd, mc.cores = cornum, mc.preschedule = TRUE)
+ } else {
+ coffeeshop = lapply(bins, pickbins, counts, binSize, chromSize, numdup, C, cutoff, ggg[i], mCs, dCs, bkgd)
+ }
+ coffeeshop = as.numeric(unlist(coffeeshop))
+ coffeeshopYES = coffeeshop[coffeeshop > 0]
+ coffeeshopNO = -(coffeeshop[coffeeshop <= 0])
+
+ binNum[i] = length(coffeeshopYES)
+ binTotalSize[i] = binNum[i] * binSize
+ binTotalSizeRatio[i] = binTotalSize[i] / chromSize
+
+ binTotalCount[i] = sum(coffeeshopYES)
+ binTotalCountNO[i] = sum(coffeeshopNO)
+ binTotalCountRatio[i] = binTotalCount[i] / binTotalCountNO[i]
+
+ maxiFun[i] = binTotalCountRatio[i] / binTotalSizeRatio[i]
+}
+rm(bins)
+#=======================> DONE!
+
+
+write(paste(ggg, binNum, binTotalSize, binTotalSizeRatio, binTotalCount, binTotalCountNO, binTotalCountRatio, maxiFun, sep = " "), file = paste0(file = paste0("/home/mibrahim/Documents/", chromName, ".GOYEAH"), ncolumns = 1))
diff -r 000000000000 -r d42f4d78c85e jamm.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/jamm.xml Wed Dec 17 10:40:23 2014 -0500
@@ -0,0 +1,76 @@
+
+Calls peaks on NGS data
+
+
+
+
+jammwrapper.py -i
+ #for $x in $replicate
+ ${x.input.file_name}
+ #end for
+ -g ${genomeSizeFile}
+ -z $output
+ -m $mode
+ -r $resolution
+ -p $processes
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ 10.1093/bioinformatics/btu568
+
+
+.. class:: infomark
+
+This tool requires files in *bed* format.
+
+----
+
+**What it does**
+JAMM calls peaks on NGS data, i.e. for finding binding sites.
+
+
diff -r 000000000000 -r d42f4d78c85e jammwrapper.py
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/jammwrapper.py Wed Dec 17 10:40:23 2014 -0500
@@ -0,0 +1,88 @@
+# This is a wrapper for JAMM to use it in Galaxy
+# It will be accompanied with a jamm.xml file, which specifies the interface that Galaxy is showing to the user
+# as well as the JAMM software including JAMM.sh, the bash script that is actually called.
+
+# This wrapper does the following things:
+# map the files (from Galaxy history) to a directory
+# pass the parameters from the GUI to JAMM.sh
+# call JAMM.sh
+# maybe map the resulting tabular files back to history items, the XML could take care of that if output is fixed
+
+#import optparse
+import argparse, os, shutil, subprocess, sys, tempfile
+import shlex
+# importing some of the modules used, especially for symlinking, dir manipulation and tool calling.
+# since python2.7, argparse is preferred over optparse.
+
+# for reference wrappers, see
+# https://bitbucket.org/fubar/rossdev/src/4a91f99b5e1953270c9b35d2ca70c325a10fcfcb/rgdev/bwa_wrapper.py?at=default
+# https://www.e-biogenouest.org/wiki/WrapperpythonforGalaxy:Asyntaxexample
+
+def main():
+
+ #Read command line arguments
+ parser = argparse.ArgumentParser()
+ parser.add_argument('-i', dest = 'input', nargs='+')
+ parser.add_argument('-g', dest = 'gsize')
+ parser.add_argument('-z', dest = 'peakfile')
+
+ parser.add_argument('-m', dest = 'mode')
+ parser.add_argument('-r', dest = 'resolution')
+ parser.add_argument('-p', dest = 'processes')
+ #parser.add_argument('-b', dest = 'binSize')
+
+ args = parser.parse_args()
+
+ print "\n"
+ print "Wrapper debugging"
+ print "Files to be used:"
+ for j in args.input:
+ print j
+
+ print "output file:"
+ print args.peakfile
+
+ # depracted, can still be found in may of the example wrappers
+ #parser = optparse.OptionParser()
+ #parser.add_option( '-i', dest='input', help='input bed files' )
+ #parser.add_option( '-c', dest='csize', help='chr sizes' )
+ #(options, args) = parser.parse_args()
+
+ # create temp dir
+ tmp_dir = tempfile.mkdtemp()
+ os.chdir(tmp_dir)
+ # symlink creation
+ for file in args.input:
+ filen = tmp_dir + "/" + os.path.basename(os.path.splitext(file)[0])+".bed"
+ os.symlink(file, filen)
+
+ # in case temp files should have random names
+ # ref_file = tempfile.NamedTemporaryFile( dir=tmp_dir )
+ # ref_file_name = ref_file.name
+ # ref_file.close()
+ # os.symlink( file, ref_file_name )
+
+ command = ( "/home/cmesser/galaxy/tools/jamm/JAMM.sh -s %s -g %s -o results -m %s -r %s -p %s"
+ % ( tmp_dir, args.gsize, args.mode, args.resolution, args.processes ) )
+ print command
+ # depending on how your programm is called, it may be necessary to use shlex.split on the command string before
+ # in this case, this was actually harmful. idk why
+# command = shlex.split(command)
+ # Please read the docs for subprocess.Popen. You can't just pass as string as variables need to be extended
+ # Note that shell = True can be a security hazard.
+# proc = subprocess.Popen( command, executable = '/bin/bash', shell=True )
+ proc = subprocess.Popen( command, shell=True)
+ returncode = proc.wait()
+
+ #mv files to a place where galaxy wrapper can find them
+ mvcommand = "mv %s/results/peaks/all.peaks.narrowPeak %s" % ( tmp_dir, args.peakfile )
+ os.system(mvcommand)
+
+# clean up temp dir
+ if os.path.exists( tmp_dir ):
+ shutil.rmtree( tmp_dir )
+
+
+if __name__ == "__main__":
+ main()
+
diff -r 000000000000 -r d42f4d78c85e license.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/license.txt Wed Dec 17 10:40:23 2014 -0500
@@ -0,0 +1,190 @@
+
+GNU GENERAL PUBLIC LICENSE
+
+Version 3, 29 June 2007
+
+Copyright © 2007 Free Software Foundation, Inc.
+
+Everyone is permitted to copy and distribute verbatim copies of this license document, but changing it is not allowed.
+Preamble
+
+The GNU General Public License is a free, copyleft license for software and other kinds of works.
+
+The licenses for most software and other practical works are designed to take away your freedom to share and change the works. By contrast, the GNU General Public License is intended to guarantee your freedom to share and change all versions of a program--to make sure it remains free software for all its users. We, the Free Software Foundation, use the GNU General Public License for most of our software; it applies also to any other work released this way by its authors. You can apply it to your programs, too.
+
+When we speak of free software, we are referring to freedom, not price. Our General Public Licenses are designed to make sure that you have the freedom to distribute copies of free software (and charge for them if you wish), that you receive source code or can get it if you want it, that you can change the software or use pieces of it in new free programs, and that you know you can do these things.
+
+To protect your rights, we need to prevent others from denying you these rights or asking you to surrender the rights. Therefore, you have certain responsibilities if you distribute copies of the software, or if you modify it: responsibilities to respect the freedom of others.
+
+For example, if you distribute copies of such a program, whether gratis or for a fee, you must pass on to the recipients the same freedoms that you received. You must make sure that they, too, receive or can get the source code. And you must show them these terms so they know their rights.
+
+Developers that use the GNU GPL protect your rights with two steps: (1) assert copyright on the software, and (2) offer you this License giving you legal permission to copy, distribute and/or modify it.
+
+For the developers' and authors' protection, the GPL clearly explains that there is no warranty for this free software. For both users' and authors' sake, the GPL requires that modified versions be marked as changed, so that their problems will not be attributed erroneously to authors of previous versions.
+
+Some devices are designed to deny users access to install or run modified versions of the software inside them, although the manufacturer can do so. This is fundamentally incompatible with the aim of protecting users' freedom to change the software. The systematic pattern of such abuse occurs in the area of products for individuals to use, which is precisely where it is most unacceptable. Therefore, we have designed this version of the GPL to prohibit the practice for those products. If such problems arise substantially in other domains, we stand ready to extend this provision to those domains in future versions of the GPL, as needed to protect the freedom of users.
+
+Finally, every program is threatened constantly by software patents. States should not allow patents to restrict development and use of software on general-purpose computers, but in those that do, we wish to avoid the special danger that patents applied to a free program could make it effectively proprietary. To prevent this, the GPL assures that patents cannot be used to render the program non-free.
+
+The precise terms and conditions for copying, distribution and modification follow.
+TERMS AND CONDITIONS
+0. Definitions.
+
+“This License” refers to version 3 of the GNU General Public License.
+
+“Copyright” also means copyright-like laws that apply to other kinds of works, such as semiconductor masks.
+
+“The Program” refers to any copyrightable work licensed under this License. Each licensee is addressed as “you”. “Licensees” and “recipients” may be individuals or organizations.
+
+To “modify” a work means to copy from or adapt all or part of the work in a fashion requiring copyright permission, other than the making of an exact copy. The resulting work is called a “modified version” of the earlier work or a work “based on” the earlier work.
+
+A “covered work” means either the unmodified Program or a work based on the Program.
+
+To “propagate” a work means to do anything with it that, without permission, would make you directly or secondarily liable for infringement under applicable copyright law, except executing it on a computer or modifying a private copy. Propagation includes copying, distribution (with or without modification), making available to the public, and in some countries other activities as well.
+
+To “convey” a work means any kind of propagation that enables other parties to make or receive copies. Mere interaction with a user through a computer network, with no transfer of a copy, is not conveying.
+
+An interactive user interface displays “Appropriate Legal Notices” to the extent that it includes a convenient and prominently visible feature that (1) displays an appropriate copyright notice, and (2) tells the user that there is no warranty for the work (except to the extent that warranties are provided), that licensees may convey the work under this License, and how to view a copy of this License. If the interface presents a list of user commands or options, such as a menu, a prominent item in the list meets this criterion.
+1. Source Code.
+
+The “source code” for a work means the preferred form of the work for making modifications to it. “Object code” means any non-source form of a work.
+
+A “Standard Interface” means an interface that either is an official standard defined by a recognized standards body, or, in the case of interfaces specified for a particular programming language, one that is widely used among developers working in that language.
+
+The “System Libraries” of an executable work include anything, other than the work as a whole, that (a) is included in the normal form of packaging a Major Component, but which is not part of that Major Component, and (b) serves only to enable use of the work with that Major Component, or to implement a Standard Interface for which an implementation is available to the public in source code form. A “Major Component”, in this context, means a major essential component (kernel, window system, and so on) of the specific operating system (if any) on which the executable work runs, or a compiler used to produce the work, or an object code interpreter used to run it.
+
+The “Corresponding Source” for a work in object code form means all the source code needed to generate, install, and (for an executable work) run the object code and to modify the work, including scripts to control those activities. However, it does not include the work's System Libraries, or general-purpose tools or generally available free programs which are used unmodified in performing those activities but which are not part of the work. For example, Corresponding Source includes interface definition files associated with source files for the work, and the source code for shared libraries and dynamically linked subprograms that the work is specifically designed to require, such as by intimate data communication or control flow between those subprograms and other parts of the work.
+
+The Corresponding Source need not include anything that users can regenerate automatically from other parts of the Corresponding Source.
+
+The Corresponding Source for a work in source code form is that same work.
+2. Basic Permissions.
+
+All rights granted under this License are granted for the term of copyright on the Program, and are irrevocable provided the stated conditions are met. This License explicitly affirms your unlimited permission to run the unmodified Program. The output from running a covered work is covered by this License only if the output, given its content, constitutes a covered work. This License acknowledges your rights of fair use or other equivalent, as provided by copyright law.
+
+You may make, run and propagate covered works that you do not convey, without conditions so long as your license otherwise remains in force. You may convey covered works to others for the sole purpose of having them make modifications exclusively for you, or provide you with facilities for running those works, provided that you comply with the terms of this License in conveying all material for which you do not control copyright. Those thus making or running the covered works for you must do so exclusively on your behalf, under your direction and control, on terms that prohibit them from making any copies of your copyrighted material outside their relationship with you.
+
+Conveying under any other circumstances is permitted solely under the conditions stated below. Sublicensing is not allowed; section 10 makes it unnecessary.
+3. Protecting Users' Legal Rights From Anti-Circumvention Law.
+
+No covered work shall be deemed part of an effective technological measure under any applicable law fulfilling obligations under article 11 of the WIPO copyright treaty adopted on 20 December 1996, or similar laws prohibiting or restricting circumvention of such measures.
+
+When you convey a covered work, you waive any legal power to forbid circumvention of technological measures to the extent such circumvention is effected by exercising rights under this License with respect to the covered work, and you disclaim any intention to limit operation or modification of the work as a means of enforcing, against the work's users, your or third parties' legal rights to forbid circumvention of technological measures.
+4. Conveying Verbatim Copies.
+
+You may convey verbatim copies of the Program's source code as you receive it, in any medium, provided that you conspicuously and appropriately publish on each copy an appropriate copyright notice; keep intact all notices stating that this License and any non-permissive terms added in accord with section 7 apply to the code; keep intact all notices of the absence of any warranty; and give all recipients a copy of this License along with the Program.
+
+You may charge any price or no price for each copy that you convey, and you may offer support or warranty protection for a fee.
+5. Conveying Modified Source Versions.
+
+You may convey a work based on the Program, or the modifications to produce it from the Program, in the form of source code under the terms of section 4, provided that you also meet all of these conditions:
+
+ a) The work must carry prominent notices stating that you modified it, and giving a relevant date.
+ b) The work must carry prominent notices stating that it is released under this License and any conditions added under section 7. This requirement modifies the requirement in section 4 to “keep intact all notices”.
+ c) You must license the entire work, as a whole, under this License to anyone who comes into possession of a copy. This License will therefore apply, along with any applicable section 7 additional terms, to the whole of the work, and all its parts, regardless of how they are packaged. This License gives no permission to license the work in any other way, but it does not invalidate such permission if you have separately received it.
+ d) If the work has interactive user interfaces, each must display Appropriate Legal Notices; however, if the Program has interactive interfaces that do not display Appropriate Legal Notices, your work need not make them do so.
+
+A compilation of a covered work with other separate and independent works, which are not by their nature extensions of the covered work, and which are not combined with it such as to form a larger program, in or on a volume of a storage or distribution medium, is called an “aggregate” if the compilation and its resulting copyright are not used to limit the access or legal rights of the compilation's users beyond what the individual works permit. Inclusion of a covered work in an aggregate does not cause this License to apply to the other parts of the aggregate.
+6. Conveying Non-Source Forms.
+
+You may convey a covered work in object code form under the terms of sections 4 and 5, provided that you also convey the machine-readable Corresponding Source under the terms of this License, in one of these ways:
+
+ a) Convey the object code in, or embodied in, a physical product (including a physical distribution medium), accompanied by the Corresponding Source fixed on a durable physical medium customarily used for software interchange.
+ b) Convey the object code in, or embodied in, a physical product (including a physical distribution medium), accompanied by a written offer, valid for at least three years and valid for as long as you offer spare parts or customer support for that product model, to give anyone who possesses the object code either (1) a copy of the Corresponding Source for all the software in the product that is covered by this License, on a durable physical medium customarily used for software interchange, for a price no more than your reasonable cost of physically performing this conveying of source, or (2) access to copy the Corresponding Source from a network server at no charge.
+ c) Convey individual copies of the object code with a copy of the written offer to provide the Corresponding Source. This alternative is allowed only occasionally and noncommercially, and only if you received the object code with such an offer, in accord with subsection 6b.
+ d) Convey the object code by offering access from a designated place (gratis or for a charge), and offer equivalent access to the Corresponding Source in the same way through the same place at no further charge. You need not require recipients to copy the Corresponding Source along with the object code. If the place to copy the object code is a network server, the Corresponding Source may be on a different server (operated by you or a third party) that supports equivalent copying facilities, provided you maintain clear directions next to the object code saying where to find the Corresponding Source. Regardless of what server hosts the Corresponding Source, you remain obligated to ensure that it is available for as long as needed to satisfy these requirements.
+ e) Convey the object code using peer-to-peer transmission, provided you inform other peers where the object code and Corresponding Source of the work are being offered to the general public at no charge under subsection 6d.
+
+A separable portion of the object code, whose source code is excluded from the Corresponding Source as a System Library, need not be included in conveying the object code work.
+
+A “User Product” is either (1) a “consumer product”, which means any tangible personal property which is normally used for personal, family, or household purposes, or (2) anything designed or sold for incorporation into a dwelling. In determining whether a product is a consumer product, doubtful cases shall be resolved in favor of coverage. For a particular product received by a particular user, “normally used” refers to a typical or common use of that class of product, regardless of the status of the particular user or of the way in which the particular user actually uses, or expects or is expected to use, the product. A product is a consumer product regardless of whether the product has substantial commercial, industrial or non-consumer uses, unless such uses represent the only significant mode of use of the product.
+
+“Installation Information” for a User Product means any methods, procedures, authorization keys, or other information required to install and execute modified versions of a covered work in that User Product from a modified version of its Corresponding Source. The information must suffice to ensure that the continued functioning of the modified object code is in no case prevented or interfered with solely because modification has been made.
+
+If you convey an object code work under this section in, or with, or specifically for use in, a User Product, and the conveying occurs as part of a transaction in which the right of possession and use of the User Product is transferred to the recipient in perpetuity or for a fixed term (regardless of how the transaction is characterized), the Corresponding Source conveyed under this section must be accompanied by the Installation Information. But this requirement does not apply if neither you nor any third party retains the ability to install modified object code on the User Product (for example, the work has been installed in ROM).
+
+The requirement to provide Installation Information does not include a requirement to continue to provide support service, warranty, or updates for a work that has been modified or installed by the recipient, or for the User Product in which it has been modified or installed. Access to a network may be denied when the modification itself materially and adversely affects the operation of the network or violates the rules and protocols for communication across the network.
+
+Corresponding Source conveyed, and Installation Information provided, in accord with this section must be in a format that is publicly documented (and with an implementation available to the public in source code form), and must require no special password or key for unpacking, reading or copying.
+7. Additional Terms.
+
+“Additional permissions” are terms that supplement the terms of this License by making exceptions from one or more of its conditions. Additional permissions that are applicable to the entire Program shall be treated as though they were included in this License, to the extent that they are valid under applicable law. If additional permissions apply only to part of the Program, that part may be used separately under those permissions, but the entire Program remains governed by this License without regard to the additional permissions.
+
+When you convey a copy of a covered work, you may at your option remove any additional permissions from that copy, or from any part of it. (Additional permissions may be written to require their own removal in certain cases when you modify the work.) You may place additional permissions on material, added by you to a covered work, for which you have or can give appropriate copyright permission.
+
+Notwithstanding any other provision of this License, for material you add to a covered work, you may (if authorized by the copyright holders of that material) supplement the terms of this License with terms:
+
+ a) Disclaiming warranty or limiting liability differently from the terms of sections 15 and 16 of this License; or
+ b) Requiring preservation of specified reasonable legal notices or author attributions in that material or in the Appropriate Legal Notices displayed by works containing it; or
+ c) Prohibiting misrepresentation of the origin of that material, or requiring that modified versions of such material be marked in reasonable ways as different from the original version; or
+ d) Limiting the use for publicity purposes of names of licensors or authors of the material; or
+ e) Declining to grant rights under trademark law for use of some trade names, trademarks, or service marks; or
+ f) Requiring indemnification of licensors and authors of that material by anyone who conveys the material (or modified versions of it) with contractual assumptions of liability to the recipient, for any liability that these contractual assumptions directly impose on those licensors and authors.
+
+All other non-permissive additional terms are considered “further restrictions” within the meaning of section 10. If the Program as you received it, or any part of it, contains a notice stating that it is governed by this License along with a term that is a further restriction, you may remove that term. If a license document contains a further restriction but permits relicensing or conveying under this License, you may add to a covered work material governed by the terms of that license document, provided that the further restriction does not survive such relicensing or conveying.
+
+If you add terms to a covered work in accord with this section, you must place, in the relevant source files, a statement of the additional terms that apply to those files, or a notice indicating where to find the applicable terms.
+
+Additional terms, permissive or non-permissive, may be stated in the form of a separately written license, or stated as exceptions; the above requirements apply either way.
+8. Termination.
+
+You may not propagate or modify a covered work except as expressly provided under this License. Any attempt otherwise to propagate or modify it is void, and will automatically terminate your rights under this License (including any patent licenses granted under the third paragraph of section 11).
+
+However, if you cease all violation of this License, then your license from a particular copyright holder is reinstated (a) provisionally, unless and until the copyright holder explicitly and finally terminates your license, and (b) permanently, if the copyright holder fails to notify you of the violation by some reasonable means prior to 60 days after the cessation.
+
+Moreover, your license from a particular copyright holder is reinstated permanently if the copyright holder notifies you of the violation by some reasonable means, this is the first time you have received notice of violation of this License (for any work) from that copyright holder, and you cure the violation prior to 30 days after your receipt of the notice.
+
+Termination of your rights under this section does not terminate the licenses of parties who have received copies or rights from you under this License. If your rights have been terminated and not permanently reinstated, you do not qualify to receive new licenses for the same material under section 10.
+9. Acceptance Not Required for Having Copies.
+
+You are not required to accept this License in order to receive or run a copy of the Program. Ancillary propagation of a covered work occurring solely as a consequence of using peer-to-peer transmission to receive a copy likewise does not require acceptance. However, nothing other than this License grants you permission to propagate or modify any covered work. These actions infringe copyright if you do not accept this License. Therefore, by modifying or propagating a covered work, you indicate your acceptance of this License to do so.
+10. Automatic Licensing of Downstream Recipients.
+
+Each time you convey a covered work, the recipient automatically receives a license from the original licensors, to run, modify and propagate that work, subject to this License. You are not responsible for enforcing compliance by third parties with this License.
+
+An “entity transaction” is a transaction transferring control of an organization, or substantially all assets of one, or subdividing an organization, or merging organizations. If propagation of a covered work results from an entity transaction, each party to that transaction who receives a copy of the work also receives whatever licenses to the work the party's predecessor in interest had or could give under the previous paragraph, plus a right to possession of the Corresponding Source of the work from the predecessor in interest, if the predecessor has it or can get it with reasonable efforts.
+
+You may not impose any further restrictions on the exercise of the rights granted or affirmed under this License. For example, you may not impose a license fee, royalty, or other charge for exercise of rights granted under this License, and you may not initiate litigation (including a cross-claim or counterclaim in a lawsuit) alleging that any patent claim is infringed by making, using, selling, offering for sale, or importing the Program or any portion of it.
+11. Patents.
+
+A “contributor” is a copyright holder who authorizes use under this License of the Program or a work on which the Program is based. The work thus licensed is called the contributor's “contributor version”.
+
+A contributor's “essential patent claims” are all patent claims owned or controlled by the contributor, whether already acquired or hereafter acquired, that would be infringed by some manner, permitted by this License, of making, using, or selling its contributor version, but do not include claims that would be infringed only as a consequence of further modification of the contributor version. For purposes of this definition, “control” includes the right to grant patent sublicenses in a manner consistent with the requirements of this License.
+
+Each contributor grants you a non-exclusive, worldwide, royalty-free patent license under the contributor's essential patent claims, to make, use, sell, offer for sale, import and otherwise run, modify and propagate the contents of its contributor version.
+
+In the following three paragraphs, a “patent license” is any express agreement or commitment, however denominated, not to enforce a patent (such as an express permission to practice a patent or covenant not to sue for patent infringement). To “grant” such a patent license to a party means to make such an agreement or commitment not to enforce a patent against the party.
+
+If you convey a covered work, knowingly relying on a patent license, and the Corresponding Source of the work is not available for anyone to copy, free of charge and under the terms of this License, through a publicly available network server or other readily accessible means, then you must either (1) cause the Corresponding Source to be so available, or (2) arrange to deprive yourself of the benefit of the patent license for this particular work, or (3) arrange, in a manner consistent with the requirements of this License, to extend the patent license to downstream recipients. “Knowingly relying” means you have actual knowledge that, but for the patent license, your conveying the covered work in a country, or your recipient's use of the covered work in a country, would infringe one or more identifiable patents in that country that you have reason to believe are valid.
+
+If, pursuant to or in connection with a single transaction or arrangement, you convey, or propagate by procuring conveyance of, a covered work, and grant a patent license to some of the parties receiving the covered work authorizing them to use, propagate, modify or convey a specific copy of the covered work, then the patent license you grant is automatically extended to all recipients of the covered work and works based on it.
+
+A patent license is “discriminatory” if it does not include within the scope of its coverage, prohibits the exercise of, or is conditioned on the non-exercise of one or more of the rights that are specifically granted under this License. You may not convey a covered work if you are a party to an arrangement with a third party that is in the business of distributing software, under which you make payment to the third party based on the extent of your activity of conveying the work, and under which the third party grants, to any of the parties who would receive the covered work from you, a discriminatory patent license (a) in connection with copies of the covered work conveyed by you (or copies made from those copies), or (b) primarily for and in connection with specific products or compilations that contain the covered work, unless you entered into that arrangement, or that patent license was granted, prior to 28 March 2007.
+
+Nothing in this License shall be construed as excluding or limiting any implied license or other defenses to infringement that may otherwise be available to you under applicable patent law.
+12. No Surrender of Others' Freedom.
+
+If conditions are imposed on you (whether by court order, agreement or otherwise) that contradict the conditions of this License, they do not excuse you from the conditions of this License. If you cannot convey a covered work so as to satisfy simultaneously your obligations under this License and any other pertinent obligations, then as a consequence you may not convey it at all. For example, if you agree to terms that obligate you to collect a royalty for further conveying from those to whom you convey the Program, the only way you could satisfy both those terms and this License would be to refrain entirely from conveying the Program.
+13. Use with the GNU Affero General Public License.
+
+Notwithstanding any other provision of this License, you have permission to link or combine any covered work with a work licensed under version 3 of the GNU Affero General Public License into a single combined work, and to convey the resulting work. The terms of this License will continue to apply to the part which is the covered work, but the special requirements of the GNU Affero General Public License, section 13, concerning interaction through a network will apply to the combination as such.
+14. Revised Versions of this License.
+
+The Free Software Foundation may publish revised and/or new versions of the GNU General Public License from time to time. Such new versions will be similar in spirit to the present version, but may differ in detail to address new problems or concerns.
+
+Each version is given a distinguishing version number. If the Program specifies that a certain numbered version of the GNU General Public License “or any later version” applies to it, you have the option of following the terms and conditions either of that numbered version or of any later version published by the Free Software Foundation. If the Program does not specify a version number of the GNU General Public License, you may choose any version ever published by the Free Software Foundation.
+
+If the Program specifies that a proxy can decide which future versions of the GNU General Public License can be used, that proxy's public statement of acceptance of a version permanently authorizes you to choose that version for the Program.
+
+Later license versions may give you additional or different permissions. However, no additional obligations are imposed on any author or copyright holder as a result of your choosing to follow a later version.
+15. Disclaimer of Warranty.
+
+THERE IS NO WARRANTY FOR THE PROGRAM, TO THE EXTENT PERMITTED BY APPLICABLE LAW. EXCEPT WHEN OTHERWISE STATED IN WRITING THE COPYRIGHT HOLDERS AND/OR OTHER PARTIES PROVIDE THE PROGRAM “AS IS” WITHOUT WARRANTY OF ANY KIND, EITHER EXPRESSED OR IMPLIED, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE. THE ENTIRE RISK AS TO THE QUALITY AND PERFORMANCE OF THE PROGRAM IS WITH YOU. SHOULD THE PROGRAM PROVE DEFECTIVE, YOU ASSUME THE COST OF ALL NECESSARY SERVICING, REPAIR OR CORRECTION.
+16. Limitation of Liability.
+
+IN NO EVENT UNLESS REQUIRED BY APPLICABLE LAW OR AGREED TO IN WRITING WILL ANY COPYRIGHT HOLDER, OR ANY OTHER PARTY WHO MODIFIES AND/OR CONVEYS THE PROGRAM AS PERMITTED ABOVE, BE LIABLE TO YOU FOR DAMAGES, INCLUDING ANY GENERAL, SPECIAL, INCIDENTAL OR CONSEQUENTIAL DAMAGES ARISING OUT OF THE USE OR INABILITY TO USE THE PROGRAM (INCLUDING BUT NOT LIMITED TO LOSS OF DATA OR DATA BEING RENDERED INACCURATE OR LOSSES SUSTAINED BY YOU OR THIRD PARTIES OR A FAILURE OF THE PROGRAM TO OPERATE WITH ANY OTHER PROGRAMS), EVEN IF SUCH HOLDER OR OTHER PARTY HAS BEEN ADVISED OF THE POSSIBILITY OF SUCH DAMAGES.
+17. Interpretation of Sections 15 and 16.
+
+If the disclaimer of warranty and limitation of liability provided above cannot be given local legal effect according to their terms, reviewing courts shall apply local law that most closely approximates an absolute waiver of all civil liability in connection with the Program, unless a warranty or assumption of liability accompanies a copy of the Program in return for a fee.
+
+END OF TERMS AND CONDITIONS
diff -r 000000000000 -r d42f4d78c85e peakfilter.pl
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/peakfilter.pl Wed Dec 17 10:40:23 2014 -0500
@@ -0,0 +1,43 @@
+#!/usr/bin/perl
+########################################
+#### Filters peaks by p-value and width
+#### Perl script
+#######################################
+
+
+use feature qw(say);
+
+
+# ==================
+# Parsing Arguments
+# ==================
+#initialize to NULL
+my $bed_file = NULL; #bed file
+
+#Parse the arguments
+$bed_file = $ARGV[0]; #bed file
+#=======================> DONE!
+
+
+
+
+# ========================================
+# Parse the bed file and extend the reads
+# ========================================
+#open the file
+open(DATA, $bed_file) || die("Can't open the bed file, probably you gave me the wrong path!");
+
+while () {
+ my ($chr, $start, $end, $name, $score, $strand, $signal, $pvalue, $qvalue, $summit, $minpeak, $geom) = split(/\t/,$_,12);
+
+ my $size = $end - $start;
+
+ if($size >= $minpeak) {
+ if($signal > $geom) {
+ #Now write the new line
+ $summit =~ s/\015?\012?$//;
+ say join "\t", $chr, $start, $end, $name, $score, $strand, $signal, $pvalue, $qvalue, $summit;
+ }
+ }
+}
+#=======================> DONE!
diff -r 000000000000 -r d42f4d78c85e peakfinder.r
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/peakfinder.r Wed Dec 17 10:40:23 2014 -0500
@@ -0,0 +1,914 @@
+###############################
+#### Peak finder for NGS Data
+#### R script
+###############################
+
+
+# =======================
+# User-defined variables
+# =======================
+cutoff = NA #To enforce an SNR cutoff ratio, delete NA and enter the number you want
+strict = 1 #to make peak calling more / less strict, increase / decrease this number
+meanAdjust = "n" #adjust the initialization mean vector for each window before clustering? If you want to do so, change this to "y".
+options(warn = -1, scipen = 1000) #R will not report any warnings (warn = -1), R will not use scientific notation (scipen = 1000)
+#=======================> DONE!
+
+
+
+
+# ================================
+# Required Libraries check & load
+# ================================
+if ((is.element('mclust', installed.packages()[,1]) == FALSE) || (is.element('signal', installed.packages()[,1]) == FALSE) || (is.element('parallel', installed.packages()[,1]) == FALSE)) {
+ stop("R package 'mclust', 'signal' and 'parallel' are required. Please install them!")
+}
+suppressPackageStartupMessages(library("mclust"))
+suppressPackageStartupMessages(library("signal"))
+suppressPackageStartupMessages(library("parallel"))
+#=======================> DONE!
+
+
+
+
+
+# =================
+# Custom Functions
+# =================
+#Get per-row Geometric mean (takes list, returns vectors, not lists!)
+geomeanL <- function(mat){
+ n = length(mat)
+ if (n > 1) {
+ mult = (mat[[1]])*(mat[[2]])
+ if (n > 2) {
+ for (i in 3:n) {
+ mult = mult*(mat[[i]])
+ }
+ }
+ mult = mult^(1/n)
+ mat = mult
+ return(mat)
+ } else {
+ return(mat[[1]])
+ }
+}
+
+
+
+#Get per-row Geometric mean (takes matrix, returns vectors, not lists!)
+geomean <- function(mat){
+ n = NCOL(mat)
+ if (n > 1) {
+ mult = (mat[,1])*(mat[,2])
+ if (n > 2) {
+ for (i in 3:n) {
+ mult = mult*(mat[,i])
+ }
+ }
+ mult = mult^(1/n)
+ mat = mult
+ }
+return(mat)
+}
+
+
+
+#Read in bed(st2) file
+parsein = function(bedfile) {
+ l = read.table(bedfile, header = FALSE)[[1]]
+ l = l + 1
+ return(l)
+}
+
+
+#Read in bedpe(st2) file
+parseinpe = function(bedfile) {
+ l = read.table(bedfile, header = FALSE)
+ l = cbind((l[[1]] + 1), l[[2]])
+ return(l)
+}
+
+
+#Produces normalized extended read counts (takes output of parsein(), return a vector of floats)
+countreads = function(bedfile, reads, frag, chromsize, filelist, chrcount) {
+
+ o = which(filelist == bedfile)
+
+ counts = vector(mode = "numeric", length = chromsize)
+
+ for (j in 1:length(reads[[o]])) {
+ if ((reads[[o]][j]+frag[o]-1) <= chromsize) {
+ counts[(reads[[o]][j]):(reads[[o]][j]+frag[o]-1)] = counts[(reads[[o]][j]):(reads[[o]][j]+frag[o]-1)] + 1
+ }
+ }
+
+ mCount = mean(counts)
+
+ if (chrcount == 1) {
+ counts = counts/mCount
+ write(paste(mCount), file = paste0(out, "/norma.", o, ".info"))
+ } else {
+ meanCounts = mean(as.numeric(read.table(paste0(out, "/norma.", o, ".info"))[[1]]))
+ if ((mCount > (5*meanCounts)) || (mCount < (0.2*meanCounts))) {
+ mCount = meanCounts
+ } else {
+ write(paste(mCount), file = paste0(out, "/norma.", o, ".info"), append = TRUE)
+ }
+ counts = counts/mCount
+ }
+
+ return(counts)
+}
+
+
+
+#Produces normalized extended read counts (takes output of parsein(), return a vector of floats)
+countreadspe = function(bedfile, reads, chromsize, filelist, chrcount) {
+
+ o = which(filelist == bedfile)
+
+ counts = vector(mode = "numeric", length = chromsize)
+
+ for (j in 1:length(reads[[o]][,1])) {
+ counts[(reads[[o]][j,1]):(reads[[o]][j,2])] = counts[(reads[[o]][j,1]):(reads[[o]][j,2])] + 1
+ }
+
+ mCount = mean(counts)
+
+ if (chrcount == 1) {
+ counts = counts/mCount
+ write(paste(mCount), file = paste0(out, "/norma.", o, ".info"))
+ } else {
+ meanCounts = mean(as.numeric(read.table(paste0(out, "/norma.", o, ".info"))[[1]]))
+ if ((mCount > (5*meanCounts)) || (mCount < (0.2*meanCounts))) {
+ mCount = meanCounts
+ } else {
+ write(paste(mCount), file = paste0(out, "/norma.", o, ".info"), append = TRUE)
+ }
+ counts = counts/mCount
+ }
+
+ return(counts)
+}
+
+
+
+#find enriched bins
+pickbins = function(winStart, counts, binSize, chromSize, numdup, C, cutoff, strict, mCs, dCs, bkgd) {
+
+ if ((winStart + binSize) <= chromSize) {
+ winEnd = winStart + binSize
+ } else {
+ winEnd = chromSize
+ }
+ binSizeTemp = winEnd - winStart
+ tempend = winEnd - 1
+
+ #extract subset of the background
+ if (bkgd != "None") {
+ Cs = counts[[numdup+1]][winStart:tempend]
+ mCs = mean(Cs)
+ dCs = sd(Cs)
+ } else {
+ Cs = sample(C, binSizeTemp, replace = TRUE)
+ }
+
+
+ go = rep(0, numdup)
+ for (g in 1:numdup) {
+ mS = (mean(counts[[g]][winStart:tempend]))
+ ratio = mS/dCs
+ if ((mS > (mCs * strict)) && (ratio > cutoff)) {
+ go[g] = 1
+ }
+ }
+ veep = sum(go)
+ return(veep)
+}
+
+
+
+
+#find enriched wins
+pickwins = function(winStart, coffeeshopSud, counts, numdup, startlist, winSize) {
+
+ plz = which(startlist == winStart)
+ winEnd = coffeeshopSud[plz]
+ rWinSize = winEnd - winStart + 1
+
+
+ if(rWinSize >= winSize) {
+ mS = rep(0, numdup)
+ for (g in 1:numdup) {
+ mS[g] = (mean(counts[[g]][winStart:winEnd]))
+ }
+ veep = mean(mS)
+ } else {
+ veep = FALSE
+ }
+
+ return(veep)
+}
+
+
+
+#score windows for fast analysis
+scorewindow = function(winStart, coffeeshopSud, numdup, C, bkgd, counts, startlist) {
+
+ plz = which(startlist == winStart)
+ winEnd = coffeeshopSud[plz]
+
+ #will store peak information
+ writethis = list()
+
+ rWinSizeTemp = winEnd - winStart + 1
+
+ #extract subset of the IP
+ Rs = matrix(nrow = rWinSizeTemp, ncol = numdup)
+ Rsr = Rs
+ for (j in 1:numdup) {
+ Rsr[,j] = counts[[j]][winStart:winEnd]
+ Rs[,j] = filtfilt(rep(1,80)/80,1,Rsr[,j])
+ }
+ #extract subset of the background
+ if (bkgd != "None") {
+ Cs = counts[[numdup+1]]
+ Cmin = min(Cs[Cs > 0])
+ Cs = Cs[winStart:winEnd]
+ Cs = filtfilt(rep(1,80)/80,1,Cs) + Cmin #gets rid of Inf in the fold change
+ } else {
+ Cs = sample(C, rWinSizeTemp, replace = TRUE)
+ Cs = filtfilt(rep(1,80)/80,1,Cs)
+ }
+
+ #start scoring
+ signal = (geomean(Rs))
+ cairo = (mean(signal)) / (mean(Cs))
+ return(cairo)
+}
+
+
+#Initialize MClust clustering parameters
+smoothcounts = function(winStart, coffeeshopSud, numdup, counts, startlist) { #helper function1
+
+ plz = which(startlist == winStart)
+ winEnd = coffeeshopSud[plz]
+
+ #extract subset of the IP
+ Rs = matrix(0, nrow = (winEnd - winStart + 1), ncol = numdup)
+ for (j in 1:numdup) {
+ Rs[,j] = counts[[j]][winStart:winEnd]
+ }
+ #smooth extended read counts
+ for (j in 1:numdup) {
+ Rs[,j] = filtfilt(rep(1,80)/80,1,Rs[,j])
+ }
+ return(Rs)
+}
+cluster = function(model, sig, init, clustnummer, noise) { #helper function2
+ noisy = sample(noise, length(sig[,1]), replace = TRUE)
+ clust = me(model, sig+noisy, init)
+ bicc = bic(model, clust$loglik, length(sig[,1]), length(sig[1,]), clustnummer)
+ out = list(bicc = bicc, param = clust$parameters)
+ return(out)
+}
+initparam = function(coffeeshopNord, coffeeshopSud, numdup, counts, cornum, clustnummer, modelnames, noise) { #main function
+
+ n = length(coffeeshopNord)
+ #smooth extended read counts
+ if (cornum > 1) {
+ sig = mclapply(coffeeshopNord, smoothcounts, coffeeshopSud, numdup, counts, startlist = coffeeshopNord, mc.cores = cornum, mc.preschedule = TRUE)
+ } else {
+ sig = lapply(coffeeshopNord, smoothcounts, coffeeshopSud, numdup, counts, startlist = coffeeshopNord)
+ }
+ sig = do.call(rbind, sig)
+
+ #kmeans initialization
+ init = kmeans(sig, clustnummer)
+ init = unmap(init$cluster)
+
+
+ if (cornum > 1) {
+ param = mclapply(modelnames, cluster, sig, init, clustnummer, noise, mc.cores = cornum, mc.preschedule = TRUE)
+ } else {
+ param = lapply(modelnames, cluster, sig, init, clustnummer, noise)
+ }
+
+ bicc = vector(mode = "numeric", length = length(modelnames))
+ for (i in 1:length(modelnames)) {
+ bicc[i] = as.numeric(param[[i]]$bicc)
+ }
+ bicc = which.max(bicc)
+
+ out = list(initparam = param[[bicc]]$param, modelname = modelnames[bicc])
+ return(out)
+}
+
+
+
+
+#find peaks
+findpeak = function(winStart, coffeeshopSud, numdup, C, param, bkgd, resol, counts, noise, startlist, meanAdjust) {
+
+
+ plz = which(startlist == winStart)
+ winEnd = coffeeshopSud[plz]
+
+
+ #will store peak information
+ writethis = list()
+
+
+ rWinSizeTemp = winEnd - winStart + 1
+
+ #extract subset of the IP
+ Rs = matrix(nrow = rWinSizeTemp, ncol = numdup)
+ Rsr = Rs
+ if (meanAdjust == "y") {
+ for (j in 1:numdup) {
+ Rsr[,j] = counts[[j]][winStart:winEnd]
+ Rs[,j] = filtfilt(rep(1,80)/80,1,Rsr[,j])
+ kabel = which.max(param$init$mean[j,])
+ param$initparam$mean[j,kabel] = mean(Rs[,j])
+ }
+ } else {
+ for (j in 1:numdup) {
+ Rsr[,j] = counts[[j]][winStart:winEnd]
+ Rs[,j] = filtfilt(rep(1,80)/80,1,Rsr[,j])
+ }
+ }
+
+ if (resol != "window") {
+
+ ####CLUSTERING START HERE#####
+ noisy = sample(noise, rWinSizeTemp, replace = TRUE)
+ clust = em(param$modelname, Rs+noisy, param$initparam)
+ clust$classification = map(clust$z)
+ ####CLUSTERING DONE####
+
+ #check whether clutering succeeded
+ if((any(diff(clust$classification)) != 0) && (!(any(is.na(clust$classification))))) {
+
+
+ #check whether all components replicates agreed on clustering assignments
+ ccx = 1
+ if (numdup > 1) {
+ cc = vector(mode = "numeric", length = numdup)
+ for (g in 1:numdup) {
+ cc[g] = which.max(clust$parameters$mean[g,]) #which cluster has the largest mean (this is the peak cluster, hopefully!)
+ }
+ ccx = sum(diff(cc))
+ cluster = cc[1]
+ rm(cc)
+ } else {
+ cluster = which.max(clust$parameters$mean) #which cluster has the largest mean (this is the peak cluster, hopefully!)
+ ccx = 0
+ }
+ if (ccx == 0) {
+
+ #extract subset of the background
+ if (bkgd != "None") {
+ Cs = counts[[numdup+1]][winStart:winEnd]
+ Cs = filtfilt(rep(1,80)/80,1,Cs)
+ } else {
+ Cs = sample(C, rWinSizeTemp, replace = TRUE)
+ Cs = filtfilt(rep(1,80)/80,1,Cs)
+ }
+
+ #find region boundaries
+ loc = 1:length(clust$classification)
+ gmclass = cbind(loc, clust$classification)
+ locPeak = gmclass[gmclass[,2] == cluster,,drop=FALSE]
+ rStart = locPeak[1] #start position of the region
+ rEnd = locPeak[length(locPeak[,1]),1] #end position of the region
+
+ #peak resolution check
+ if (resol == "region") {
+ pSize = rEnd - rStart
+ signal = (geomean(Rs[rStart:rEnd,]))
+ signal2 = (signal) - (Cs[rStart:rEnd])
+ gm = mean(signal2)
+ summit = which.max(geomean(Rsr[rStart:rEnd,])) - 1
+ will2k = wilcox.test(signal, Cs[rStart:rEnd])
+
+ #Is there signal in the region above background
+ if (gm > 0) {
+ writethis[[1]] = rStart + winStart - 1
+ writethis[[2]] = rEnd + winStart
+ writethis[[3]] = paste0(chromName, ".", rStart+winStart -1)
+ writethis[[4]] = "1000"
+ writethis[[5]] = "."
+ writethis[[6]] = gm
+ writethis[[7]] = will2k$p.value
+ writethis[[8]] = "-1"
+ writethis[[9]] = summit
+ }
+ } else if (resol == "peak") {
+ #find out where separate peaks are
+ d = diff(locPeak[,1])
+ d[length(d)+1] = 0
+ locPeak = cbind(locPeak, d)
+ bound1 = which(locPeak[,3] > 1, arr.in=TRUE)
+ bound2 = bound1 + 1
+ bound = locPeak[sort(c(bound1,bound2))]
+ bound = c(rStart, bound, rEnd)
+ w = 1
+ warum = 0
+ while (w < length(bound)) {
+ pStart = bound[w] + winStart - 1
+ pEnd = bound[w+1] + winStart
+ pSize = pEnd - pStart
+ signal = (geomean(Rs[(bound[w]):(bound[w+1]),]))
+ signal2 = (signal) - (Cs[bound[w]:bound[w+1]])
+ gm = mean(signal2)
+ summit = which.max(geomean(Rsr[(bound[w]):(bound[w+1]),])) - 1
+ will2k = wilcox.test(signal, Cs[(bound[w]):(bound[w+1])])
+
+ weil = warum * 9
+ #Is there signal in the region above background
+ if (gm > 0) {
+ writethis[[1+weil]] = pStart
+ writethis[[2+weil]] = pEnd
+ writethis[[3+weil]] = paste0(chromName, ".", pStart)
+ writethis[[4+weil]] = "1000"
+ writethis[[5+weil]] = "."
+ writethis[[6+weil]] = gm
+ writethis[[7+weil]] = will2k$p.value
+ writethis[[8+weil]] = "-1"
+ writethis[[9+weil]] = summit
+ }
+ w = w + 2
+ warum = warum + 1
+ }
+
+ } #peak resolution check
+ } #all replicates agree on clustering assignments?
+ } #clustering worked?
+
+ } else if (resol == "window") { #window resolution check
+
+ #extract subset of the background
+ if (bkgd != "None") {
+ Cs = counts[[numdup+1]][winStart:winEnd]
+ Cs = filtfilt(rep(1,80)/80,1,Cs)
+ } else {
+ Cs = sample(C, rWinSizeTemp, replace = TRUE)
+ Cs = filtfilt(rep(1,80)/80,1,Cs)
+ }
+
+ #calculate scores
+ pSize = rWinSizeTemp
+ signal = geomean(Rs)
+ signal2 = (signal) - (Cs)
+ gm = mean(signal2)
+ summit = which.max(geomean(Rsr)) - 1
+ will2k = wilcox.test(signal, Cs)
+
+ #Is there signal in the region above background
+ if (gm > 0) {
+ writethis[[1]] = winStart - 1
+ writethis[[2]] = winEnd
+ writethis[[3]] = paste0(chromName, ".", winStart -1)
+ writethis[[4]] = "1000"
+ writethis[[5]] = "."
+ writethis[[6]] = gm
+ writethis[[7]] = will2k$p.value
+ writethis[[8]] = "-1"
+ writethis[[9]] = summit
+ }
+ } #window clustering
+
+return(writethis)
+}
+
+
+#filter return value of findpeak()
+processPeaks = function(peaks) {
+ peaks = matrix(unlist(peaks), ncol=9, byrow=TRUE)
+ peaks = peaks[peaks[,1] != FALSE,,drop=FALSE]
+ peaks = data.frame(peaks)
+ return(peaks)
+}
+#=======================> DONE!
+
+
+
+
+
+
+
+
+
+# ==========================
+# Parse-in System Variables
+# ==========================
+args = commandArgs(trailingOnly = TRUE) # Read Arguments from command line
+
+#Parsing arguments and storing values
+for (each.arg in args) {
+ #chormosome size file
+ if (grepl('^-sfile=',each.arg)) {
+ arg.split <- strsplit(each.arg,'=',fixed=TRUE)[[1]]
+ if (! is.na(arg.split[2]) ) {
+ size.file <- arg.split[2]
+ } else {
+ stop('No genome size file')
+ }
+ }
+ #bed file names
+ if (grepl('^-bednames=',each.arg)) {
+ arg.split <- strsplit(each.arg,'=',fixed=TRUE)[[1]]
+ if (! is.na(arg.split[2]) ) {
+ bednames <- arg.split[2]
+ } else {
+ stop('No bed file names')
+ }
+ }
+ #bed files directory
+ if (grepl('^-frag=',each.arg)) {
+ arg.split <- strsplit(each.arg,'=',fixed=TRUE)[[1]]
+ if (! is.na(arg.split[2]) ) {
+ frag <- arg.split[2]
+ } else {
+ stop('No fragment length given')
+ }
+ }
+ #bakcground files directory
+ if (grepl('^-bkgd=',each.arg)) {
+ arg.split <- strsplit(each.arg,'=',fixed=TRUE)[[1]]
+ if (! is.na(arg.split[2]) ) {
+ bkgd <- arg.split[2]
+ } else {
+ stop('No background file')
+ }
+ }
+ #bakcground files directory
+ if (grepl('^-out=',each.arg)) {
+ arg.split <- strsplit(each.arg,'=',fixed=TRUE)[[1]]
+ if (! is.na(arg.split[2]) ) {
+ out <- arg.split[2]
+ } else {
+ stop('No output directory given')
+ }
+ }
+ #Cluster number
+ if (grepl('^-clustnummer=',each.arg)) {
+ arg.split <- strsplit(each.arg,'=',fixed=TRUE)[[1]]
+ if (! is.na(arg.split[2]) ) {
+ clustnummer <- as.numeric(arg.split[2])
+ }
+ }
+ #resolution
+ if (grepl('^-resolution=',each.arg)) {
+ arg.split <- strsplit(each.arg,'=',fixed=TRUE)[[1]]
+ if (! is.na(arg.split[2]) ) {
+ resol <- arg.split[2]
+ }
+ }
+ #processor cores
+ if (grepl('^-p=',each.arg)) {
+ arg.split <- strsplit(each.arg,'=',fixed=TRUE)[[1]]
+ if (! is.na(arg.split[2]) ) {
+ cornum <- as.numeric(arg.split[2])
+ }
+ }
+ #minimum window size
+ if (grepl('^-window=',each.arg)) {
+ arg.split <- strsplit(each.arg,'=',fixed=TRUE)[[1]]
+ if (! is.na(arg.split[2]) ) {
+ winSize <- arg.split[2]
+ }
+ }
+ #window size
+ if (grepl('^-bin=',each.arg)) {
+ arg.split <- strsplit(each.arg,'=',fixed=TRUE)[[1]]
+ if (! is.na(arg.split[2]) ) {
+ binsize <- arg.split[2]
+ }
+ }
+ #type (paired / single)
+ if (grepl('^-type=',each.arg)) {
+ arg.split <- strsplit(each.arg,'=',fixed=TRUE)[[1]]
+ if (! is.na(arg.split[2]) ) {
+ type <- arg.split[2]
+ }
+ }
+ #chromosome number
+ if (grepl('^-chrcount=',each.arg)) {
+ arg.split <- strsplit(each.arg,'=',fixed=TRUE)[[1]]
+ if (! is.na(arg.split[2]) ) {
+ chrcount <- as.numeric(arg.split[2])
+ }
+ }
+ #window enrichment cutoff
+ if (grepl('^-windowe=',each.arg)) {
+ arg.split <- strsplit(each.arg,'=',fixed=TRUE)[[1]]
+ if (! is.na(arg.split[2]) ) {
+ windowe <- arg.split[2]
+ }
+ }
+}
+
+##Parse in variables
+chromosomes = read.table(size.file, header=FALSE)
+chromName = chromosomes$V1; #which chromosome
+chromSize = chromosomes$V2; #chromosomes size
+rm(chromosomes)
+
+readsFiles = as.list(strsplit(bednames, ",", fixed = TRUE)[[1]])
+numdup = length(readsFiles) #number of replicates
+if (bkgd != "None") {
+ readsFiles[[numdup+1]] = bkgd
+}
+winSize = as.numeric(winSize)
+binSize = as.numeric(binsize)
+winSize = binSize * winSize
+
+if (type == "single") {
+ frags = as.numeric(strsplit(frag, ",", fixed = TRUE)[[1]])
+}
+rm(bednames)
+
+if (numdup > 1) {
+ modelnames = c("VVV","VEV")
+} else {
+ modelnames = "V"
+}
+
+if (windowe != "auto") {
+ windowe = as.numeric(windowe)
+}
+
+nothing = FALSE #default is we found some peaks
+options(stringsAsFactors = FALSE)
+#=======================> DONE!
+
+
+
+
+
+# =======================
+# Some preliminary stuff
+# =======================
+if (type == "single") {
+ if (cornum > 1) {
+ datain = mclapply(readsFiles, parsein, mc.cores = cornum, mc.preschedule = TRUE) #read in all bed files (samples and control)
+ } else {
+ datain = lapply(readsFiles, parsein) #read in all bed files (samples and control)
+ }
+}
+
+if (type == "paired") {
+ if (cornum > 1) {
+ datain = mclapply(readsFiles, parseinpe, mc.cores = cornum, mc.preschedule = TRUE) #read in all bed files (samples and control)
+ } else {
+ datain = lapply(readsFiles, parseinpe) #read in all bed files (samples and control)
+ }
+}
+
+#minimum peak size (only a recommendation)
+minpeak = floor(binSize / 4)
+
+#make bins vector
+bins = seq(from = 1, to = (chromSize - 1), by = binSize)
+#=======================> DONE!
+
+
+
+
+# ===============
+# Counting Reads
+# ===============
+if (type == "single") {
+ if (cornum > 1) {
+ counts = mclapply(readsFiles, countreads, reads = datain, frag = frags, chromsize = chromSize, filelist = readsFiles, chrcount = chrcount, mc.cores = cornum, mc.preschedule = TRUE)
+ } else {
+ counts = lapply(readsFiles, countreads, reads = datain, frag = frags, chromsize = chromSize, filelist = readsFiles, chrcount = chrcount)
+ }
+}
+
+if (type == "paired") {
+ if (cornum > 1) {
+ counts = mclapply(readsFiles, countreadspe, reads = datain, chromsize = chromSize, filelist = readsFiles, chrcount = chrcount, mc.cores = cornum, mc.preschedule = TRUE)
+ } else {
+ counts = lapply(readsFiles, countreadspe, reads = datain, chromsize = chromSize, filelist = readsFiles, chrcount = chrcount)
+ }
+}
+
+rm(datain)
+#=======================> DONE!
+
+
+
+
+# ============================
+# Estimating Background Model
+# ============================
+
+if (chrcount == 1){ #first chromosome, estimate bkgd (includes SNR cutoff)
+ if (is.na(cutoff)) {
+ if (bkgd != "None") {
+ cutoff = vector(length = numdup)
+ sdC = sd(counts[[numdup+1]])
+ for (x in 1:numdup) {
+ cutoff[x] = (mean(counts[[x]]))/(sdC)
+ }
+ cutoff = max(cutoff)
+ C = NULL
+ mCs = NULL
+ write(paste(c(cutoff,NA,NA)), file = paste0(out, "/bkgd.info"), append = TRUE)
+ } else {
+ cutoff = vector(length = numdup)
+ mmV = var(geomeanL(counts))
+ mmM = mean(geomeanL(counts))
+ sigma = log(1+((mmV) / ((mmM)^2)))
+ mu = (log(mmM)) - (0.5 * (sigma))
+ C = rlnorm(100000, mu, sqrt(sigma))
+ for (x in 1:numdup) {
+ cutoff[x] = (mean(counts[[x]]))/(sd(C))
+ }
+ cutoff = max(cutoff)
+ mCs = (mean(sample(C, binSize*5, replace = TRUE)))
+ dCs = (sd(sample(C, binSize*5, replace = TRUE)))
+ write(paste(c(cutoff,sigma,mu)), file = paste0(out, "/bkgd.info"), append = TRUE)
+ }
+ }
+} else { #bkgd estiamted from before
+ bkgdInfo = read.table(paste0(out, "/bkgd.info"), header = FALSE)
+ if (is.na(cutoff)) {
+ cutoff = as.numeric(bkgdInfo[[1]][1])
+ }
+
+ if (bkgd != "None") {
+ C = NULL
+ mCs = NULL
+ } else {
+ sigma = as.numeric(bkgdInfo[[1]][2])
+ mu = as.numeric(bkgdInfo[[1]][3])
+ C = rlnorm(100000, mu, sqrt(sigma))
+ mCs = (mean(sample(C, binSize*5, replace = TRUE)))
+ dCs = (sd(sample(C, binSize*5, replace = TRUE)))
+ }
+}
+#=======================> DONE!
+
+
+
+
+# ========================
+# Picking Enriched Windows
+# ========================
+if (cornum > 1) {
+ coffeeshop = mclapply(bins, pickbins, counts, binSize, chromSize, numdup, C, cutoff, strict, mCs, dCs, bkgd, mc.cores = cornum, mc.preschedule = TRUE)
+} else {
+ coffeeshop = lapply(bins, pickbins, counts, binSize, chromSize, numdup, C, cutoff, strict, mCs, dCs, bkgd)
+}
+coffeeshop = as.numeric(unlist(coffeeshop))
+coffeeshop[coffeeshop != numdup] = 0
+coffeeshop = c(0, diff(coffeeshop))
+coffeeshop = cbind(coffeeshop, bins)
+coffeeshopNord = coffeeshop[coffeeshop[,1] == numdup,,drop=FALSE]
+coffeeshopSud = coffeeshop[coffeeshop[,1] == -numdup,,drop=FALSE]
+coffeeshopNord = coffeeshopNord[,2]
+coffeeshopSud = coffeeshopSud[,2] - 1
+if (length(coffeeshopSud) < length(coffeeshopNord)) {
+ coffeeshopSud = c(coffeeshopSud, chromSize)
+} else if (length(coffeeshopSud) > length(coffeeshopNord)) {
+ coffeeshopNord = c(1, coffeeshopNord)
+}
+if (coffeeshopSud[length(coffeeshopSud)] > chromSize) {
+ coffeeshopSud[length(coffeeshopSud)] = chromSize
+}
+
+
+if (cornum > 1) {
+ coffeeshop = mclapply(coffeeshopNord, pickwins, coffeeshopSud, counts, numdup, startlist = coffeeshopNord, winSize, mc.cores = cornum, mc.preschedule = TRUE)
+} else {
+ coffeeshop = lapply(coffeeshopNord, pickwins, coffeeshopSud, counts, numdup, startlist = coffeeshopNord, winSize)
+}
+coffeeshop = as.numeric(unlist(coffeeshop))
+coffeeshop = cbind(coffeeshopNord, coffeeshopSud, coffeeshop)
+coffeeshop = coffeeshop[coffeeshop[,3] != FALSE,,drop=FALSE]
+coffeeshop = coffeeshop[order(coffeeshop[,3], decreasing = TRUE),]
+rm(bins)
+#=======================> DONE!
+
+
+
+
+# ===================================
+# Initializing Clustering Parameters
+# ===================================
+if (length(coffeeshop[,1]) > 0) { #any enriched windows detected?
+
+yummy = ceiling(length(coffeeshop[,1]) / 4)
+if (yummy > 20) {
+ yummy = sample(1:yummy, 20)
+} else if (yummy > 0) {
+ yummy = 1:yummy
+} else {
+ yummy = 1
+}
+coffeeshopNord = coffeeshop[yummy,1]
+coffeeshopSud = coffeeshop[yummy,2]
+noise = rnorm(100000, mean=0, sd=0.1)
+param = initparam(coffeeshopNord, coffeeshopSud, numdup, counts, cornum, clustnummer, modelnames, noise)
+#=======================> DONE!
+
+
+
+
+
+# ==========================
+# Enriched Window Filtering
+# ==========================
+if (windowe != 1) { #do it only if window fold enrichment filtering is required
+ if (cornum > 1) {
+ scores = mclapply(coffeeshop[,1], scorewindow, coffeeshop[,2], numdup, C, bkgd, counts, startlist = coffeeshop[,1], mc.cores = cornum, mc.preschedule = TRUE)
+ } else {
+ scores = lapply(coffeeshop[,1], scorewindow, coffeeshop[,2], numdup, C, bkgd, counts, startlist = coffeeshop[,1])
+ }
+ scores = unlist(scores)
+ #scores = scores[is.finite(scores)] #just a sanity check
+
+ if (windowe == "auto") {
+ lscores = log(scores)
+ if (length(scores) > 0) {
+ if (chrcount == 1) {
+ cutthisTEMP = ((mean(lscores)) + (sd(lscores)*1))
+ write(paste(cutthisTEMP), file = paste0(out, "/bkgd.info"), append = TRUE)
+ } else {
+ cutthisTEMP = as.numeric(bkgdInfo[[1]][4])
+ }
+ finalwins = which(lscores > cutthisTEMP)
+ cutthisW = min(scores[finalwins])
+ coffeeshop = coffeeshop[finalwins,]
+ } else {
+ if (chrcount == 1) {
+ cutthisTEMP = 0
+ cutthisW = "Not Applicable, All Windows Analyzed!"
+ write(paste(cutthisTEMP), file = paste0(out, "/bkgd.info"), append = TRUE)
+ }
+ }
+ } else {
+ cutthisW = windowe
+ if (length(scores) > 0) {
+ finalwins = which(scores >= windowe)
+ coffeeshop = coffeeshop[finalwins,]
+ }
+ }
+}
+else { cutthisW = 1 }
+#=======================> DONE!
+
+
+
+
+
+# ==============
+# Finding Peaks
+# ==============
+#if (length(coffeeshop[,1]) > 0) { #any enriched windows left after filtering?, just a sanity check!
+coffeeshop = coffeeshop[,-3]
+if (cornum > 1) {
+ peaks = mclapply(coffeeshop[,1], findpeak, coffeeshop[,2], numdup, C, param, bkgd, resol, counts, noise, startlist = coffeeshop[,1], meanAdjust, mc.cores = cornum, mc.preschedule = TRUE)
+} else {
+ peaks = lapply(coffeeshop[,1], findpeak, coffeeshop[,2], numdup, C, param, bkgd, resol, counts, noise, startlist = coffeeshop[,1], meanAdjust)
+}
+if (!(is.null(peaks))) { #any peaks discovered?
+writethis = processPeaks(peaks)
+#=======================> DONE!
+
+
+
+
+
+# =========================
+# Writing Peak Information
+# =========================
+} else { nothing = TRUE } #no peaks
+#} else { nothing = TRUE } #no enriched windows left after filtering, just a sanity check (at least one window should still be there)
+} else { nothing = TRUE } #no enriched widnows discovered
+
+if (isTRUE(nothing)) {
+ file.create(paste0(out, "/", chromName, ".peaks.bed"))
+ write(paste(chromName, minpeak, sep = " "), file = paste0(out, "/min.peaksize"), append=TRUE)
+
+ if (chrcount == 1) {
+ message(paste0("No peaks found! - Window Fold Enrichment: ", round(cutthisW,2)))
+ } else {
+ message("No peaks found!")
+ }
+} else {
+ write(paste(chromName, writethis$X1, writethis$X2, writethis$X3, writethis$X4, writethis$X5, writethis$X6, writethis$X7, writethis$X8, writethis$X9, minpeak, sep = " "), file = paste0(out, "/", chromName, ".peaks.bed"), ncolumns = 1)
+ write(paste(chromName, minpeak, sep = " "), file = paste0(out, "/min.peaksize"), append=TRUE)
+
+
+ if (chrcount == 1) {
+ message(paste0("Done! - Window Fold Enrichment: ", round(cutthisW,2)))
+ } else {
+ message("Done!")
+ }
+}
+#=======================> DONE!
+
+
diff -r 000000000000 -r d42f4d78c85e peakhelper.r
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/peakhelper.r Wed Dec 17 10:40:23 2014 -0500
@@ -0,0 +1,110 @@
+#########################################################################################
+#### Fixes output of peakfinder.r to produce proper narrowPeak format with proper scores
+#### R script
+########################################################################################
+
+
+
+
+# =======================
+# User-defined variables
+# =======================
+options(warn = -1, scipen = 1000) #R will not report any warnings (warn = -1), R will not use scientific notation (scipen = 1000)
+#=======================> DONE!
+
+
+
+
+# ==============================================
+# Parsing Arguments (source: phantom SPP script)
+# ==============================================
+args = commandArgs(trailingOnly = TRUE) # Read Arguments from command line
+
+
+#Parsing arguments and storing values
+for (each.arg in args) {
+ #bed file names
+ if (grepl('^-filelist=',each.arg)) {
+ arg.split <- strsplit(each.arg,'=',fixed=TRUE)[[1]] # split on =
+ if (! is.na(arg.split[2]) ) {
+ bednames <- arg.split[2]
+ } else {
+ stop('No bed file names')
+ }
+ }
+}
+options(stringsAsFactors = FALSE)
+#=======================> DONE!
+
+
+
+
+# ==============================================
+# Required Libraries check (Source: http://r.789695.n4.nabble.com/test-if-a-package-is-installed-td1750671.htm)
+# ==============================================
+if ((is.element('sqldf', installed.packages()[,1]) == FALSE)) {
+ stop("R package 'sqldf' is required. Please install it!")
+}
+suppressPackageStartupMessages(library("sqldf"))
+suppressPackageStartupMessages(library("tcltk"))
+#=======================> DONE!
+
+
+
+
+# =================
+# Custom Functions
+# =================
+score <- function(x){
+ x = ((x-min(x))/(max(x)-min(x)))*10000
+ return(x)
+}
+
+fixnpf = function(bedfile) {
+
+ writethis = read.table(bedfile, header=FALSE)
+
+
+ message(paste0("Minimum Peak Width Used to Produce Filtered List: ", writethis$V11[1]))
+ writethis$V9 = p.adjust(writethis$V8, method = "BH")
+ writethis$V8[writethis$V8 == 0] = 10
+ writethis$V8[writethis$V8 == 10] = min(writethis$V8)
+ writethis$V8 = -(log10(writethis$V8))
+ writethis$V9[writethis$V9 == 0] = 10
+ writethis$V9[writethis$V9 == 10] = min(writethis$V9)
+ writethis$V9 = -(log10(writethis$V9))
+ writethis$V7 = as.numeric(writethis$V7) * writethis$V9
+ writethis$V5 = score(as.numeric(writethis$V7))
+
+
+ #find peak score cutoff (pareto distribution)
+ sizes = writethis$V3 - writethis$V2
+ scores = writethis$V7
+ ss = cbind(sizes, scores)
+ ss = ss[ss[,1] > writethis$V11[1],,drop=FALSE]
+ scores = ss[,2]
+ scores = scores[scores > 0]
+ num = length(scores)
+ if (length(scores) > 300000) {
+ scores = scores[1:300000]
+ num = 300000
+ }
+ den = log(min(scores))
+ den = sum(log(scores) - den)
+ alpha = num / den
+ geom = (exp(1/alpha)) * (min(scores))
+ message(paste0("Minimum Peak Score Used to Produce Filtered List: ", geom))
+
+ #done now write something
+ write(paste(writethis$V1, writethis$V2, writethis$V3, writethis$V4, writethis$V5, ".", writethis$V7, writethis$V8, writethis$V9, writethis$V10, writethis$V11, geom, sep = "\t"), file = bedfile, ncolumns = 1)
+ return(bedfile)
+}
+#=======================> DONE!
+
+
+
+# ==================
+# Fixing narrowpeak
+# ==================
+bedfiles = fixnpf(bednames) #read in all bed files (samples and control)
+#=======================> DONE!
diff -r 000000000000 -r d42f4d78c85e readshifter.pl
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/readshifter.pl Wed Dec 17 10:40:23 2014 -0500
@@ -0,0 +1,61 @@
+#!/usr/bin/perl
+##############################################
+#### Shifts minus strand reads by read length
+#### Perl script
+#############################################
+
+
+
+use feature qw(say);
+
+
+# ==================
+# Parsing Arguments
+# ==================
+
+#initialize to NULL
+my $bed_file = NULL; #bed file
+my $shift_size = NULL; #shift size
+my $read_length = NULL; #read length
+
+#Parse the arguments
+$bed_file = $ARGV[0]; #bed file
+$shift_size = $ARGV[1]; #shift size
+$read_length = $ARGV[2]; #read length
+
+#=======================> DONE!
+
+
+
+# ========================================
+# Parse the bed file and extend the reads
+# ========================================
+
+#open the file
+open(DATA, $bed_file) || die("Can't open the bed file, probably you gave me the wrong path!");
+
+#loop through the rest of the file line by line (To do: look for a faster way)
+while () {
+ my ($start, $strand) = split(/\t/,$_,2);
+ $strand =~ s/\015?\012?$//;
+
+
+
+ #plus strand
+ if ($strand eq '+') {
+ #do nothing
+ }
+ #minus strand
+ elsif ($strand eq '-') {
+ $start = $start - $shift_size + $read_length; #difference between $start and $end should be equal to fragment length ($shift_size)
+ }
+ #bad format
+ else {
+ die("It appears the bed file is not formatted properly. Specifically, I expect to find either + or - in the second column, but I found something else!");
+ }
+ if ($start >= 0) {
+ #Now write the new line
+ say join "\t", $start, $strand;
+ }
+}
+#=======================> DONE!
diff -r 000000000000 -r d42f4d78c85e signalmaker.r
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/signalmaker.r Wed Dec 17 10:40:23 2014 -0500
@@ -0,0 +1,312 @@
+###############################
+#### Signal Maker for NGS Data
+#### R script
+###############################
+
+
+
+
+# =======================
+# User-defined variables
+# =======================
+options(warn = -1, scipen = 1000) #R will not report any warnings (warn = -1), R will not use scientific notation (scipen = 1000)
+#=======================> DONE!
+
+
+
+
+# ================================
+# Required Libraries check & load
+# ================================
+if ((is.element('signal', installed.packages()[,1]) == FALSE) || (is.element('parallel', installed.packages()[,1]) == FALSE)) {
+ stop("R packages 'signal'and 'parallel' are required. Please install them!")
+}
+suppressPackageStartupMessages(library("signal"))
+suppressPackageStartupMessages(library("parallel"))
+#=======================> DONE!
+
+
+
+
+
+# =================
+# Custom Functions
+# =================
+#Get per-row Geometric mean (takes list, returns vectors, not lists!)
+geomeanL <- function(mat){
+ n = length(mat)
+ if (n > 1) {
+ mult = (mat[[1]])*(mat[[2]])
+ if (n > 2) {
+ for (i in 3:n) {
+ mult = mult*(mat[[i]])
+ }
+ }
+ mult = mult^(1/n)
+ mat = mult
+ return(mat)
+ } else {
+ return(mat[[1]])
+ }
+}
+
+
+
+#Get per-row Geometric mean (takes matrix, returns vectors, not lists!)
+geomean <- function(mat){
+ n = NCOL(mat)
+ if (n > 1) {
+ mult = (mat[,1])*(mat[,2])
+ if (n > 2) {
+ for (i in 3:n) {
+ mult = mult*(mat[,i])
+ }
+ }
+ mult = mult^(1/n)
+ mat = mult
+ }
+return(mat)
+}
+
+
+
+#Read in bed(st2) file
+parsein = function(bedfile) {
+ reads = read.table(bedfile, header = FALSE)[[1]]
+ return(reads)
+}
+
+
+
+#Produces normalized extended read counts (takes output of parsein(), return a vector of floats)
+countreads = function(bedfile, reads, frag, chromsize, filelist) {
+
+ o = which(filelist == bedfile)
+
+ counts = vector(mode = "numeric", length = chromsize)
+
+ for (j in 1:length(reads[[o]])) {
+ if ((reads[[o]][j]+frag[o]-1) <= chromsize) {
+ counts[(reads[[o]][j]):(reads[[o]][j]+frag[o]-1)] = counts[(reads[[o]][j]):(reads[[o]][j]+frag[o]-1)] + 1
+ }
+ }
+
+ mCount = mean(counts)
+
+ if (chrcount == 1) {
+ counts = counts/mCount
+ write(paste(mCount), file = paste0(out, "/norma.", o, ".info"))
+ } else {
+ meanCounts = mean(as.numeric(read.table(paste0(out, "/norma.", o, ".info"))[[1]]))
+ if ((mCount > (5*meanCounts)) || (mCount < (0.2*meanCounts))) {
+ mCount = meanCounts
+ } else {
+ write(paste(mCount), file = paste0(out, "/norma.", o, ".info"), append = TRUE)
+ }
+ counts = counts/mCount
+ }
+
+ return(counts)
+}
+
+
+
+
+#generate signal
+getsig = function(winStart, winEnds, startList, stepSize, chromName) {
+
+
+ plz = which(startList == winStart)
+ winEnd = winEnds[plz]
+ rWinSizeTemp = winEnd - winStart + 1
+
+ #extract subset of the IP
+ Rs = matrix(nrow = rWinSizeTemp, ncol = numdup)
+ for (j in 1:numdup) {
+ Rs[,j] = counts[[j]][winStart:winEnd]
+ Rs[,j] = filtfilt(rep(1,80)/80,1,Rs[,j])
+ }
+
+ #extract subset of the background and initial signal
+ if (bkgd != "None") {
+ Cs = counts[[numdup+1]][winStart:winEnd]
+ Cs = filtfilt(rep(1,80)/80,1,Cs)
+ signal = (geomean(Rs)) - (Cs)
+ } else {
+ signal = geomean(Rs)
+ }
+
+
+ #get binned signal
+ signal = round(colMeans(matrix(c(signal, rep(0, stepSize - length(signal) %% stepSize)), stepSize)), digits = 2)
+ steps = seq(winStart, winEnd, by = stepSize)
+ starts = steps - 1
+ ends = steps + stepSize - 1
+ if (ends[length(ends)] > winEnd) {
+ ends[length(ends)] = winEnd
+ }
+
+ #write to file
+ write(paste(chromName, starts, ends, signal, sep = " "), file = paste0(out, "/", chromName, plz, ".bedSignal"), ncolumns = 1)
+
+
+return(NULL)
+}
+#=======================> DONE!
+
+
+
+
+
+# ==========================
+# Parse-in System Variables
+# ==========================
+args = commandArgs(trailingOnly = TRUE) # Read Arguments from command line
+
+#Parsing arguments and storing values
+for (each.arg in args) {
+ #bed file names
+ if (grepl('^-bednames=',each.arg)) {
+ arg.split <- strsplit(each.arg,'=',fixed=TRUE)[[1]]
+ if (! is.na(arg.split[2]) ) {
+ bednames <- arg.split[2]
+ } else {
+ stop('No bed file names')
+ }
+ }
+ #bed file names
+ if (grepl('^-chromo=',each.arg)) {
+ arg.split <- strsplit(each.arg,'=',fixed=TRUE)[[1]]
+ if (! is.na(arg.split[2]) ) {
+ chromName <- arg.split[2]
+ } else {
+ stop('No bed file names')
+ }
+ }
+ #bed files directory
+ if (grepl('^-frag=',each.arg)) {
+ arg.split <- strsplit(each.arg,'=',fixed=TRUE)[[1]]
+ if (! is.na(arg.split[2]) ) {
+ frag <- arg.split[2]
+ } else {
+ stop('No fragment length given')
+ }
+ }
+ #bakcground files directory
+ if (grepl('^-bkgd=',each.arg)) {
+ arg.split <- strsplit(each.arg,'=',fixed=TRUE)[[1]]
+ if (! is.na(arg.split[2]) ) {
+ bkgd <- arg.split[2]
+ } else {
+ stop('No background file')
+ }
+ }
+ #bakcground files directory
+ if (grepl('^-out=',each.arg)) {
+ arg.split <- strsplit(each.arg,'=',fixed=TRUE)[[1]]
+ if (! is.na(arg.split[2]) ) {
+ out <- arg.split[2]
+ } else {
+ stop('No output directory given')
+ }
+ }
+ #Cluster number
+ if (grepl('^-clustnummer=',each.arg)) {
+ arg.split <- strsplit(each.arg,'=',fixed=TRUE)[[1]]
+ if (! is.na(arg.split[2]) ) {
+ clustnummer <- as.numeric(arg.split[2])
+ }
+ }
+ #regions
+ if (grepl('^-regions=',each.arg)) {
+ arg.split <- strsplit(each.arg,'=',fixed=TRUE)[[1]]
+ if (! is.na(arg.split[2]) ) {
+ regions <- arg.split[2]
+ }
+ }
+ #processor cores
+ if (grepl('^-p=',each.arg)) {
+ arg.split <- strsplit(each.arg,'=',fixed=TRUE)[[1]]
+ if (! is.na(arg.split[2]) ) {
+ cornum <- as.numeric(arg.split[2])
+ }
+ }
+ #chromSize
+ if (grepl('^-chromoS=',each.arg)) {
+ arg.split <- strsplit(each.arg,'=',fixed=TRUE)[[1]]
+ if (! is.na(arg.split[2]) ) {
+ chromSize <- as.numeric(arg.split[2])
+ }
+ }
+ #stepsize
+ if (grepl('^-sig=',each.arg)) {
+ arg.split <- strsplit(each.arg,'=',fixed=TRUE)[[1]]
+ if (! is.na(arg.split[2]) ) {
+ sigstep <- as.numeric(arg.split[2])
+ }
+ }
+ #chrcount
+ if (grepl('^-chrcount=',each.arg)) {
+ arg.split <- strsplit(each.arg,'=',fixed=TRUE)[[1]]
+ if (! is.na(arg.split[2]) ) {
+ chrcount <