diff chipmunkv6_wrapper.sh @ 0:299bac53243b draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/chipmunkv6_wrapper.sh	Wed Feb 10 11:13:59 2016 -0500
@@ -0,0 +1,172 @@
+#!/bin/bash
+
+: <<'hey'
+
+ check the logs in case of error:
+ 	- go to : /bioinfo/http/prod/hosted/nebula.curie.fr/galaxy-dist/database/files/XXX
+ 	- see log1 (.log) : run stdout
+	- see log2 (tmp.log): echos, montage log..
+	
+PWM from the mono version are reversed in summary file compared to what's in the raw log, this is done for compatibility with AhoPro.
+diPWM are kept as in the raw log
+
+hey
+
+
+while getopts "f:n:s:m:v:o:z:i:x:r:t:" optionName; do
+case "$optionName" in
+
+f) inputfile="$OPTARG";;
+n) NUMBER="$OPTARG";; #nbr of motifs to search
+s) VERSION="$OPTARG";;
+m) minW="$OPTARG";;
+v) maxW="$OPTARG";;
+o) LOG="$OPTARG";; #raw chipmunk output file
+z) MODE="$OPTARG";; #mask or filter
+i) OUTPNG="$OPTARG";;
+x) NAME="$OPTARG";;
+r) summary="$OPTARG";;
+t) seqType="$OPTARG";;
+esac
+done
+
+
+# my tmp log for debug needs
+TMPLOG1=$OUTPNG.log
+TMPLOG2=$OUTPNG.tmp.log
+echo "$@" > $TMPLOG2
+
+
+### Create tmp working dir :
+
+OUTDIR=`mktemp -d`
+local_path=/usr/bin/chipmunk/ChIPMunk_6.0a
+
+echo $OUTDIR > $TMPLOG2
+#chmod 777 $TMPLOG2
+
+if [ -d $OUTDIR ]; then
+	echo "Directory $OUTDIR exists" >> $TMPLOG2
+	chmod 777 $OUTDIR
+else 
+	mkdir $OUTDIR
+	
+fi 
+chmod -R 777 $OUTDIR
+
+#move to tmp dir
+
+cd $OUTDIR
+
+
+#bluid motif length argument
+motifs="$minW:$maxW"
+for (( c=1; c<$NUMBER; c++ ))
+do
+   motifs="$motifs,$minW:$maxW"
+done
+
+
+if [ "$VERSION" == "Mono" ]; then
+##run run_chiphordre
+# optional option after 's:' <try_limit> <step_limit> <iter_limit> <thread_count>, put only defaut value in order to acess <thread_count> which is set to 4
+
+	
+	echo " ruby $local_path/run_chiphorde6.rb $NAME $motifs $MODE yes 1.0 s:$inputfile 100 10 1 4" >>  $TMPLOG2
+	ruby $local_path/run_chiphorde6.rb $NAME $motifs $MODE yes 1.0 $seqType:$inputfile 100 10 1 4 1>> $TMPLOG1 2>&1 
+	
+## 1ST OUTPUT : raw log
+	mv $NAME\_chiphorde.log $LOG 
+	
+			
+else 	
+##run run_chiphordre
+
+
+	echo "ruby $local_path/run_dichiphorde6.rb $NAME $motifs $MODE yes 1.0 s:$inputfile 200 20 1 4" >> $TMPLOG2
+	ruby $local_path/run_dichiphorde6.rb $NAME $motifs $MODE yes 1.0 $seqType:$inputfile 200 20 1 4 1>> $TMPLOG1 2>&1
+	
+## 1ST OUTPUT : raw log
+	mv $NAME\_dichipmunk.log $LOG #raw log
+	
+fi 
+
+	## get info line for summary file: INFO|found X motifs, used Y sequences
+	INFO=$( awk '/^INFO\|/ {$1=""; print $0}' $LOG )
+	
+	
+	## get nbr of motif X
+	N=$( awk '/^INFO\|/ {split($0,tab); print tab[2] }' $LOG )
+	
+	## get threshold of each motif found : stored in variable Tx / x={1,2,....N}
+	cat $LOG |  awk ' /^THRE\|/ { print $0}' | awk -v n=$N 'BEGIN {c=1} { if (NR <=n) print > "threshold_"c++}'
+
+	
+## 2ND OUTPUT : build the motif's png : use montage command
+	
+	#NB: montage -fill_image colxline -mode framing_style input_images.xml.png final_logo.png
+	myPng=$NAME\_0.png
+	us='_'
+	
+	for (( i=1; i< $N; i++ ))
+	do
+   		myPng="$myPng $NAME$us$i.png"
+	done
+	
+	echo " myPng=$myPng" >> $TMPLOG2
+	echo "	montage -tile 1x$N -mode Concatenate $myPng $OUTPNG " >> $TMPLOG2
+	montage -tile 1x$N -mode Concatenate $myPng $OUTPNG  
+	
+
+
+
+## 3RD OUTPUT : build summary file (run infos + results summary)
+
+	cat <<-SUM > $summary
+	*** Run summary information ***
+	
+	ChiPMunk version used : $VERSION.ChIPMunk V6 17052014
+	Number of different motifs to search : $NUMBER
+	Min:Max width used : $minW:$maxW 
+	Mode used : $MODE
+	
+	*** Results summary ***
+	
+	$VERSION.ChIPMunk found $INFO.
+	PWMs of each motif found, with respective threshold :
+	
+	SUM
+	
+	#now, write (d)pcm in summary : motif 1, 2, 3..
+	
+	for (( i=0 ; i< $N ; i++))
+		do	
+			j=$((i+1))
+			echo "#Motif $j:" >> $summary
+			## append pwm to summary . In case of mono, first reverse pwm (hori -> verti) for compatibility with AhoPro	
+			if [ $VERSION == "Mono" ]; then
+				# append  pmw to summary 
+				cat $NAME$us$i.pwm >> $summary
+			else
+				# append dpwm
+				awk -v pwm="$NAME$us$i.dpwm" -f $local_path/addCol.awk $local_path/di_nuc.txt >> $summary
+				#cat "$NAME$us$i.dpcm" >> $summary
+			fi
+			# append threshold to summary
+			cat threshold_$j >> $summary
+			echo -e "\n" >> $summary
+		
+		done
+echo "For detailed results, see ChIPMunk detailed log." >> $summary
+
+rm $NAME*
+rm threshold*
+#if [ -r $TMPLOG1 ]; then
+#  rm $TMPLOG
+#fi
+
+#if [ -r $TMPLOG2 ]; then
+#  rm $TMPLOG
+#fi
+
+