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run_pd_diffbind.sh
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executable file
·276 lines (213 loc) · 11.9 KB
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NAME=$1
SET=$2
TOOL=$3
mkdir -p results/$TOOL results/$TOOL/$SET
mkdir -p log/$TOOL
files=$(ls results/$TOOL/$SET/*.bed 2> /dev/null | wc -l)
if [ "$files" = "0" ]; then
echo "running $TOOL with: $1 $2 $3" #$4 $5 $6 $7 $8 $9 $10 $11 $12 $13"
NAME11=$(basename $4 _mm.bam)
NAME12=$(basename $5 _mm.bam)
NAME21=$(basename $7 _mm.bam)
NAME22=$(basename $8 _mm.bam)
SCRIPT="script.R"
LOG="../../../log/$TOOL/$SET.log"
DBMETHODS="DBA_EDGER DBA_DESEQ2"
cd results/$TOOL/$SET/
STARTTIME=`date +%s.%N`
PREPDONE=`date +%s.%N`
TIMEDIFFPREP=`echo "$PREPDONE - $STARTTIME" | bc | awk -F"." '{print}'`
echo "prep $TIMEDIFFPREP" > time.txt
for PCALLER in ../../../results_peaks/*; do
for PMODE in $PCALLER/$SET/*; do
echo "using $(basename $PCALLER) mode: $(basename $PMODE)"
cat $PMODE/s11_peaks.bed > s11_peaks.bed
cat $PMODE/s12_peaks.bed > s12_peaks.bed
cat $PMODE/s21_peaks.bed > s21_peaks.bed
cat $PMODE/s22_peaks.bed > s22_peaks.bed
for DBMETHOD in $DBMETHODS; do #loop through DB methods
# in R: bFullLibrarySize=F bSubControl=F
echo "library(DiffBind)" > $SCRIPT
echo "library(locfit)" >> $SCRIPT
echo "SampleID=c(\"1_1\",\"1_2\",\"2_1\",\"2_2\")" >> $SCRIPT
echo "Tissue=c(\"NA\",\"NA\",\"NA\",\"NA\")" >> $SCRIPT
echo "Factor=c(\"sim\",\"sim\",\"sim\",\"sim\")" >> $SCRIPT
echo "Condition=c(1,1,2,2)" >> $SCRIPT
echo "Treatment=c(\"sim\",\"sim\",\"sim\",\"sim\")" >> $SCRIPT
echo "Replicate=c(1,2,1,2)" >> $SCRIPT
echo "bamReads=c(\"$4\",\"$5\",\"$7\",\"$8\")" >> $SCRIPT
echo "ControlID=c(\"c1\",\"c1\",\"c2\",\"c2\")" >> $SCRIPT
echo "bamControl=c(\"$6\",\"$6\",\"$8\",\"$8\")" >> $SCRIPT
echo "Peaks=c(\"s11_peaks.bed\",\"s12_peaks.bed\",\"s21_peaks.bed\",\"s22_peaks.bed\")" >> $SCRIPT
echo "PeakCaller=c(\"raw\",\"raw\",\"raw\",\"raw\")" >> $SCRIPT
echo "myinputdata <- data.frame(SampleID,Tissue,Factor,Condition,Treatment,Replicate,bamReads,ControlID,bamControl,Peaks,PeakCaller)" >> $SCRIPT
echo "mydata = dba(sampleSheet=myinputdata)" >> $SCRIPT
echo "mydata = dba.count(mydata, minOverlap=1)" >> $SCRIPT
echo "mydata = dba.contrast(mydata, categories=DBA_CONDITION,minMembers=2)" >> $SCRIPT
echo "mydata = dba.analyze(mydata,method=$DBMETHOD,bFullLibrarySize=F,bSubControl=F)" >> $SCRIPT
#save as csv..
echo "options(scipen = 999)" >> $SCRIPT
echo "rep = dba.report(mydata, bCounts=T, bCalled=T, bCalledDetail=T, th=1, method=$DBMETHOD, file=\"diff_peaks\")" >> $SCRIPT
STARTTIME=`date +%s.%N`
#run it...
/usr/bin/time -o mem.txt -f "%K %M" R CMD BATCH --vanilla $SCRIPT
#save result
PSHORT=$(basename $PCALLER)
MSHORT=$(basename $PMODE)
OUT_NAME=$(basename $NAME _sample1-rep1_mm)"_"$PSHORT"_"$MSHORT"_"$DBMETHOD"_1.bed"
ENDTIME=`date +%s.%N`
TIMEDIFF=`echo "$ENDTIME - $STARTTIME" | bc | awk -F"." '{print}'`
echo $PSHORT"_"$MSHORT"_"$DBMETHOD"_1 $TIMEDIFF" >> time.txt
MEMUSAGE=$(sed '/non-zero status/d' mem.txt )
echo $PSHORT"_"$MSHORT"_"$DBMETHOD"_1 $MEMUSAGE" >> memory.txt
if [ -e DBA_diff_peaks.csv ]; then
#reformat for eval
cut -f1,2,3,7,9 -d, DBA_diff_peaks.csv | grep -v "^\"Chr\",\"Start\"" | sed "s/\"//g" | sed "s/,/\t/g" | awk '{print $1"\t"$2"\t"$3"\t"$5"\t"$4}' | sort -k1,1 -k2,2n > $OUT_NAME
else
#create empty file
touch $OUT_NAME
fi
#save log
cat script.Rout >> $LOG
#clean up
rm -f $SCRIPT script.Rout .RData DBA_diff_peaks.csv mem.txt
echo "library(DiffBind)" > $SCRIPT
echo "library(locfit)" >> $SCRIPT
echo "SampleID=c(\"1_1\",\"1_2\",\"2_1\",\"2_2\")" >> $SCRIPT
echo "Tissue=c(\"NA\",\"NA\",\"NA\",\"NA\")" >> $SCRIPT
echo "Factor=c(\"sim\",\"sim\",\"sim\",\"sim\")" >> $SCRIPT
echo "Condition=c(1,1,2,2)" >> $SCRIPT
echo "Treatment=c(\"sim\",\"sim\",\"sim\",\"sim\")" >> $SCRIPT
echo "Replicate=c(1,2,1,2)" >> $SCRIPT
echo "bamReads=c(\"$4\",\"$5\",\"$7\",\"$8\")" >> $SCRIPT
echo "ControlID=c(\"c1\",\"c1\",\"c2\",\"c2\")" >> $SCRIPT
echo "bamControl=c(\"$6\",\"$6\",\"$8\",\"$8\")" >> $SCRIPT
echo "Peaks=c(\"s11_peaks.bed\",\"s12_peaks.bed\",\"s21_peaks.bed\",\"s22_peaks.bed\")" >> $SCRIPT
echo "PeakCaller=c(\"raw\",\"raw\",\"raw\",\"raw\")" >> $SCRIPT
echo "myinputdata <- data.frame(SampleID,Tissue,Factor,Condition,Treatment,Replicate,bamReads,ControlID,bamControl,Peaks,PeakCaller)" >> $SCRIPT
echo "mydata = dba(sampleSheet=myinputdata)" >> $SCRIPT
echo "mydata = dba.count(mydata, minOverlap=1)" >> $SCRIPT
echo "mydata = dba.contrast(mydata, categories=DBA_CONDITION,minMembers=2)" >> $SCRIPT
echo "mydata = dba.analyze(mydata,method=$DBMETHOD,bFullLibrarySize=T,bSubControl=F)" >> $SCRIPT
#save as csv..
echo "options(scipen = 999)" >> $SCRIPT
echo "rep = dba.report(mydata, bCounts=T, bCalled=T, bCalledDetail=T, th=1, method=$DBMETHOD, file=\"diff_peaks\")" >> $SCRIPT
STARTTIME=`date +%s.%N`
#run it...
/usr/bin/time -o mem.txt -f "%K %M" R CMD BATCH --vanilla $SCRIPT
#save result
PSHORT=$(basename $PCALLER)
MSHORT=$(basename $PMODE)
OUT_NAME=$(basename $NAME _sample1-rep1_mm)"_"$PSHORT"_"$MSHORT"_"$DBMETHOD"_2.bed"
ENDTIME=`date +%s.%N`
TIMEDIFF=`echo "$ENDTIME - $STARTTIME" | bc | awk -F"." '{print}'`
echo $PSHORT"_"$MSHORT"_"$DBMETHOD"_2 $TIMEDIFF" >> time.txt
MEMUSAGE=$(sed '/non-zero status/d' mem.txt )
echo $PSHORT"_"$MSHORT"_"$DBMETHOD"_2 $MEMUSAGE" >> memory.txt
if [ -e DBA_diff_peaks.csv ]; then
#reformat for eval
cut -f1,2,3,7,9 -d, DBA_diff_peaks.csv | grep -v "^\"Chr\",\"Start\"" | sed "s/\"//g" | sed "s/,/\t/g" | awk '{print $1"\t"$2"\t"$3"\t"$5"\t"$4}' | sort -k1,1 -k2,2n > $OUT_NAME
else
#create empty file
touch $OUT_NAME
fi
#save log
cat script.Rout >> $LOG
#clean up
rm -f $SCRIPT script.Rout .RData DBA_diff_peaks.csv mem.txt
echo "library(DiffBind)" > $SCRIPT
echo "library(locfit)" >> $SCRIPT
echo "SampleID=c(\"1_1\",\"1_2\",\"2_1\",\"2_2\")" >> $SCRIPT
echo "Tissue=c(\"NA\",\"NA\",\"NA\",\"NA\")" >> $SCRIPT
echo "Factor=c(\"sim\",\"sim\",\"sim\",\"sim\")" >> $SCRIPT
echo "Condition=c(1,1,2,2)" >> $SCRIPT
echo "Treatment=c(\"sim\",\"sim\",\"sim\",\"sim\")" >> $SCRIPT
echo "Replicate=c(1,2,1,2)" >> $SCRIPT
echo "bamReads=c(\"$4\",\"$5\",\"$7\",\"$8\")" >> $SCRIPT
echo "ControlID=c(\"c1\",\"c1\",\"c2\",\"c2\")" >> $SCRIPT
echo "bamControl=c(\"$6\",\"$6\",\"$8\",\"$8\")" >> $SCRIPT
echo "Peaks=c(\"s11_peaks.bed\",\"s12_peaks.bed\",\"s21_peaks.bed\",\"s22_peaks.bed\")" >> $SCRIPT
echo "PeakCaller=c(\"raw\",\"raw\",\"raw\",\"raw\")" >> $SCRIPT
echo "myinputdata <- data.frame(SampleID,Tissue,Factor,Condition,Treatment,Replicate,bamReads,ControlID,bamControl,Peaks,PeakCaller)" >> $SCRIPT
echo "mydata = dba(sampleSheet=myinputdata)" >> $SCRIPT
echo "mydata = dba.count(mydata, minOverlap=1)" >> $SCRIPT
echo "mydata = dba.contrast(mydata, categories=DBA_CONDITION,minMembers=2)" >> $SCRIPT
echo "mydata = dba.analyze(mydata,method=$DBMETHOD,bFullLibrarySize=F,bSubControl=T)" >> $SCRIPT
#save as csv..
echo "options(scipen = 999)" >> $SCRIPT
echo "rep = dba.report(mydata, bCounts=T, bCalled=T, bCalledDetail=T, th=1, method=$DBMETHOD, file=\"diff_peaks\")" >> $SCRIPT
STARTTIME=`date +%s.%N`
#run it...
/usr/bin/time -o mem.txt -f "%K %M" R CMD BATCH --vanilla $SCRIPT
#save result
PSHORT=$(basename $PCALLER)
MSHORT=$(basename $PMODE)
OUT_NAME=$(basename $NAME _sample1-rep1_mm)"_"$PSHORT"_"$MSHORT"_"$DBMETHOD"_3.bed"
ENDTIME=`date +%s.%N`
TIMEDIFF=`echo "$ENDTIME - $STARTTIME" | bc | awk -F"." '{print}'`
echo $PSHORT"_"$MSHORT"_"$DBMETHOD"_3 $TIMEDIFF" >> time.txt
MEMUSAGE=$(sed '/non-zero status/d' mem.txt )
echo $PSHORT"_"$MSHORT"_"$DBMETHOD"_3 $MEMUSAGE" >> memory.txt
if [ -e DBA_diff_peaks.csv ]; then
#reformat for eval
cut -f1,2,3,7,9 -d, DBA_diff_peaks.csv | grep -v "^\"Chr\",\"Start\"" | sed "s/\"//g" | sed "s/,/\t/g" | awk '{print $1"\t"$2"\t"$3"\t"$5"\t"$4}' | sort -k1,1 -k2,2n > $OUT_NAME
else
#create empty file
touch $OUT_NAME
fi
#save log
cat script.Rout >> $LOG
#clean up
rm -f $SCRIPT script.Rout .RData DBA_diff_peaks.csv mem.txt
echo "library(DiffBind)" > $SCRIPT
echo "library(locfit)" >> $SCRIPT
echo "SampleID=c(\"1_1\",\"1_2\",\"2_1\",\"2_2\")" >> $SCRIPT
echo "Tissue=c(\"NA\",\"NA\",\"NA\",\"NA\")" >> $SCRIPT
echo "Factor=c(\"sim\",\"sim\",\"sim\",\"sim\")" >> $SCRIPT
echo "Condition=c(1,1,2,2)" >> $SCRIPT
echo "Treatment=c(\"sim\",\"sim\",\"sim\",\"sim\")" >> $SCRIPT
echo "Replicate=c(1,2,1,2)" >> $SCRIPT
echo "bamReads=c(\"$4\",\"$5\",\"$7\",\"$8\")" >> $SCRIPT
echo "ControlID=c(\"c1\",\"c1\",\"c2\",\"c2\")" >> $SCRIPT
echo "bamControl=c(\"$6\",\"$6\",\"$8\",\"$8\")" >> $SCRIPT
echo "Peaks=c(\"s11_peaks.bed\",\"s12_peaks.bed\",\"s21_peaks.bed\",\"s22_peaks.bed\")" >> $SCRIPT
echo "PeakCaller=c(\"raw\",\"raw\",\"raw\",\"raw\")" >> $SCRIPT
echo "myinputdata <- data.frame(SampleID,Tissue,Factor,Condition,Treatment,Replicate,bamReads,ControlID,bamControl,Peaks,PeakCaller)" >> $SCRIPT
echo "mydata = dba(sampleSheet=myinputdata)" >> $SCRIPT
echo "mydata = dba.count(mydata, minOverlap=1)" >> $SCRIPT
echo "mydata = dba.contrast(mydata, categories=DBA_CONDITION,minMembers=2)" >> $SCRIPT
echo "mydata = dba.analyze(mydata,method=$DBMETHOD,bFullLibrarySize=T,bSubControl=T)" >> $SCRIPT
#save as csv..
echo "options(scipen = 999)" >> $SCRIPT
echo "rep = dba.report(mydata, bCounts=T, bCalled=T, bCalledDetail=T, th=1, method=$DBMETHOD, file=\"diff_peaks\")" >> $SCRIPT
STARTTIME=`date +%s.%N`
#run it...
/usr/bin/time -o mem.txt -f "%K %M" R CMD BATCH --vanilla $SCRIPT
#save result
PSHORT=$(basename $PCALLER)
MSHORT=$(basename $PMODE)
OUT_NAME=$(basename $NAME _sample1-rep1_mm)"_"$PSHORT"_"$MSHORT"_"$DBMETHOD"_4.bed"
ENDTIME=`date +%s.%N`
TIMEDIFF=`echo "$ENDTIME - $STARTTIME" | bc | awk -F"." '{print}'`
echo $PSHORT"_"$MSHORT"_"$DBMETHOD"_4 $TIMEDIFF" >> time.txt
MEMUSAGE=$(sed '/non-zero status/d' mem.txt )
echo $PSHORT"_"$MSHORT"_"$DBMETHOD"_4 $MEMUSAGE" >> memory.txt
if [ -e DBA_diff_peaks.csv ]; then
#reformat for eval
cut -f1,2,3,7,9 -d, DBA_diff_peaks.csv | grep -v "^\"Chr\",\"Start\"" | sed "s/\"//g" | sed "s/,/\t/g" | awk '{print $1"\t"$2"\t"$3"\t"$5"\t"$4}' | sort -k1,1 -k2,2n > $OUT_NAME
else
#create empty file
touch $OUT_NAME
fi
#save log
cat script.Rout >> $LOG
#clean up
rm -f $SCRIPT script.Rout .RData DBA_diff_peaks.csv
done
#clean up
rm -rf s11_peaks.bed s12_peaks.bed s21_peaks.bed s22_peaks.bed mem.txt
done
done
else
echo "results/$TOOL/$SET/bed already exists exiting..."
fi