changeset 0:2e121ae0a2eb draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/ahopro_wrapper.sh	Thu Feb 11 08:14:45 2016 -0500
@@ -0,0 +1,211 @@
+#!usr/bin/bash 
+
+
+:<<'hey'
+Command line looks like this :
+ahopro_wrapper.sh ${ahopro_config} ${motif_file} ${function.function_selector} $outfile $function['seq_name'] $function['nbr_motif'] $actualN
+# if function = p-value :, commad line will looks like this : 
+ahopro_wrapper.sh ${ahopro_config} ${motif_file} ${function.function_selector} $outfile $function['seq_name'] $function['nbr_motif'] $actualN ${letter_freq_file}
+
+
+hey
+
+#sort out arguments
+
+configfile=$1
+motif_file=$2
+function=$3
+#if function is "p-value", get the freqFile pramater
+if [ "$function" == "p-value" ] ; then 
+	letterFreqFile=$8
+fi
+output=$4
+SEQ_NAME=$5
+NBR_MOTIFS=$6
+actual_NBR=$7
+
+
+
+PATH_AHOPRO="/usr/bin/ahopro/AhoPro.1.3/"
+
+
+# create tmp workindg dir and cd
+
+OUTDIR=`mktemp -d`
+
+#hard code the creation of OUTDIR
+if [ -d $OUTDIR ]; then
+	chmod -R 777 $OUTDIR
+else 
+	mkdir $OUTDIR
+fi 
+
+chmod -R 777 $OUTDIR
+
+cd $OUTDIR
+
+
+
+#echo "######configfile out of XML form :" > $output
+#cat $configfile >> $output
+#echo "motifFile :" >> $output
+#cat $motif_file > $output
+
+
+
+
+## ************ First, check if the number of actual motif is met in the entries. If not, warn, and quit ******************************************************
+
+if [[ $NBR_MOTIFS != $actual_NBR ]]; then 
+	
+cat <<doc >$output
+AhoPro error :
+
+The number of motifs set in  "Number of motifs" does not match the the actual number of motif entry in "Motifs" section. They should be the same. 
+
+Number of motifs : $NBR_MOTIFS
+Number of actual motif entered : $actual_NBR
+
+Please recheck these parameters.	
+
+doc
+
+exit 0
+
+fi
+
+## ************ END check ******************************************************
+
+
+
+### **************** Deal with motif entery ****************************************************************************************************
+
+
+if [[ $NBR_MOTIFS = 1 ]]; then
+	
+	#NO PARSING REQUIRED
+	
+	#remove blank lines, tabs, spaces..
+	cat $motif_file | awk '/^[0-9\-ACTGatgc]/ {print}' > motif_tmp_0.txt
+	# reverse if the motif is a pmw, reverse it if necessary
+	type=`cat motif_tmp_0.txt | awk ' END { if ($1 ~ /[acATGC]/) {print "words"} else {print "pmw"} }'`
+	
+	if [[ "$type" == "pmw" ]]; then
+
+		NF=`cat motif_tmp_0.txt | awk ' END {print NF}'`
+	
+		if [[ $NF != 4 ]]; then 	#if it's not vertical, reverse it 
+	
+			for ((c=1 ; c <= $NF; c++)) 
+				do 
+					cat motif_tmp_0.txt | awk -v c=$c '{ printf $c" " } END {printf"\n"}' >> motif_0.txt			
+				done 
+					
+			rm motif_tmp_0.txt
+			
+		
+		elif [[ $NF == 0 ]]; then 
+			echo "Please check the motif entries.Try removing tabulations, spaces." > $output
+			exit 0
+			
+		else #if vertical 
+			mv motif_tmp_0.txt motif_0.txt
+		fi
+	
+	else #if words
+			mv motif_tmp_0.txt motif_0.txt
+
+	fi
+
+
+else # IF there is more than one motif 
+	
+	#check if it's true + parse motifs + warn
+	N=`cat $motif_file | awk '/^[0-9\-ACTGatgc*]/ {print}' | awk ' BEGIN{RS="*"; n=0} {printf $0 > "motif_tmp_"n++} END {print n}'`
+
+	# reverse pmw (or not if it's vertical)
+
+	for ((i=0 ; i< $N ; i++)) 
+		do 
+			# remove empty lines + check if it's a pmw, motif words.
+			cat motif_tmp_$i | awk '/^[0-9\-ACTGatgc]/ {print}' > motif_tmp_tmp_$i
+			type=`cat motif_tmp_tmp_$i | awk ' END { if ($1 ~ /[acATGC]/) {print "words"} else {print "pmw"} }'` 
+	
+			rm motif_tmp_$i
+			# if pmw : check if it is horizontal, if so, reverse it (ahopro takes only vertical pmws !)
+	
+			if [[ "$type" == "pmw" ]]; then
+
+				NF=`cat motif_tmp_tmp_$i | awk ' END {print NF}'`
+	
+				if [[ $NF != 4 ]]; then 	#if it's not vertical, reverse it 
+	
+					for ((c=1 ; c <= $NF; c++)) 
+						do 
+							cat motif_tmp_tmp_$i | awk -v c=$c '{ printf $c" " } END {printf"\n"}' >> motif_$i.txt			
+						done 
+					rm motif_tmp_tmp_$i
+			
+		
+				elif [[ $NF == 0 ]]; then 
+					echo "Please check the motif entries, try removing tabulations, spaces." > $ouput
+					exit 0
+			
+				else #if vertical 
+					mv motif_tmp_tmp_$i motif_$i.txt
+				fi
+	
+			else #if words
+					mv motif_tmp_tmp_$i motif_$i.txt
+	
+			fi
+
+		#cat motif_$i.txt 
+	done
+fi
+
+## ****************************************** END motif entery treatment *********************************************************************************************************************
+
+###motif_0
+# next could be improved in bash (sed..)
+
+#Add motif filenames to the configfile byt writing a new_config.txt (in CWD)
+##but first, check what kind of correction ? basic : motifnames only ? or LetterFreqFile also ?
+
+if [ "$function" == "p-value" ] ; then 
+
+python $PATH_AHOPRO/replaceLine.py $configfile "name_freq" $letterFreqFile
+
+else
+
+python $PATH_AHOPRO/replaceLine.py $configfile "name" 
+
+fi
+
+## get the new config file
+#new_config="$OUTDIR/new_config.txt"
+new_config="new_config.txt"
+
+#echo "******** AhoPro Parameters ******** " >> $output
+#cat $new_config >> $output
+#call ahopro with config file
+
+
+#echo "******** AhoPro Results ******** " >> $output
+
+$PATH_AHOPRO/ahokocc $new_config >> $output 2>&1
+
+# improve line "Search in sequence .." with user entered sequence name (for more clarity). Do only if seq_name != 'X' 
+
+if [ "$SEQ_NAME" != "X" ] ; then 
+
+	#remove sequence (if it exists)
+sed -i '/^Search/d' $output
+	# add new line
+line="\nSearch in sequence : $SEQ_NAME\n"
+sed -i "1s/^/$line/" $output
+
+fi
+
+rm $new_config
+