changed stats file name to compareBed.stats

bin/1.2_filter_motifs/compareBed.sh

@@ -8,7 +8,7 @@
 #             BED-format. 
 
 #             For parameter description, run the script without parameters or -h.
-#             The output is a file with the filtered footprints and the log file FilterMotivs.stats
+#             The output is a file with the filtered footprints and the log file compareBed.stats
 
 # One R scripts is used, compareBed_runinfo.R, stored in the same directory.
 
@@ -120,7 +120,7 @@ then
 	echo "                                  default is the current directory"
 	echo "              -min --min          minimum size of footprints; default is 10"
 	echo "              -max --max          maximum size of footprints; default is 80"
-	echo "              -o   --output       output path/file ; default dir current directory and filename is newMotifs.bed and newMotifs.fasta"
+	echo "              -o   --output       output path/file ; default dir current directory and filename is newMotifs.bed and newMotifs.bed.fasta"
 	echo "              -h --help           shows this help message"
 	exit 0
 fi
@@ -260,7 +260,7 @@ fi
 
 # remove short/long motivs, make unique ids (relevant for some splitted tfbs from subtract) and handle maxScorePosition
 # also creates a small output file with information about the comparison
-Rscript $path/compareBed_runinfo.R $min $max $data "$workdir"/filtered.bed "$workdir"/filtered_flagged.bed "$workdir"/FilterMotifs.stats
+Rscript $path/compareBed_runinfo.R $min $max $data "$workdir"/filtered.bed "$workdir"/filtered_flagged.bed "$workdir"/compareBed.stats
 # check if Rscript executed without errors
 if [ $? -gt 0 ] 
 then
@@ -277,14 +277,14 @@ then
 	fp_initial=`expr $fp_initial - 1`
 	fp_final=`cat "$workdir"/filtered.bed | wc -l`
 	fp_final=`expr $fp_final - 1`
-	echo $fp_initial | sed 's/^/initial number of footprints: /g' >> "$workdir"/FilterMotifs.stats
-	echo $fp_final | sed 's/^/number of footprints after subtract: /g' >> "$workdir"/FilterMotifs.stats
+	echo $fp_initial | sed 's/^/initial number of footprints: /g' >> "$workdir"/compareBed.stats
+	echo $fp_final | sed 's/^/number of footprints after subtract: /g' >> "$workdir"/compareBed.stats
 else
 	# output will be overwritten if it exists
 	rm -f $output
 	# add some final values to the log file
-	cat $data | wc -l | sed 's/^/initial number of footprints: /g' >> "$workdir"/FilterMotifs.stats
-	cat "$workdir"/filtered.bed | wc -l | sed 's/^/number of footprints after subtract: /g' >> "$workdir"/FilterMotifs.stats
+	cat $data | wc -l | sed 's/^/initial number of footprints: /g' >> "$workdir"/compareBed.stats
+	cat "$workdir"/filtered.bed | wc -l | sed 's/^/number of footprints after subtract: /g' >> "$workdir"/compareBed.stats
 fi
 
 # add fasta sequences to bed and create fasta file