check if output ends with .bed

bin/1.2_filter_motifs/compareBed.sh

@@ -10,7 +10,7 @@
 #             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
 
-# Two R scripts are used, compareBed_runinfo.R and abs_max_score.R, stored in the same directory.
+# One R scripts is used, compareBed_runinfo.R, stored in the same directory.
 
 # default parameters
 workdir=$PWD
@@ -173,6 +173,10 @@ then
 	echo "directory $workdir does not exist. Please check parameter -w / --workdir"
 	exit 1
 fi
+if [[ ${output: -4: -1} != '.bed' ]]
+then
+	output=`echo $output | sed "s|$|.bed|g"`
+fi
 
 # remove trailing tabs in footprints
 cat $data | sed 's/[ \t]*$//' > "$workdir"/filtered.bed
@@ -219,14 +223,6 @@ if [ $all_empty == true ]
 		exit 1
 fi
 
-#calculate absolute max_score position
-Rscript $path/abs_max_score.R "$workdir"/filtered.bed
-# check if Rscript executed without errors
-if [ $? -gt 0 ] 
-then
-	exit 1
-fi
-
 # comparing unknown footprints with regions of known motifs
 # comparison is done iteratively
 # remove overlapping regions in unknown footprints
@@ -292,6 +288,7 @@ else
 fi
 
 # add fasta sequences to bed and create fasta file
+out_fasta=`echo $output | sed "s|.bed$|.fasta|g"`
 echo getting sequences from fasta-file
 bedtools getfasta -fi $fasta -bed "$workdir"/filtered_flagged.bed -bedOut >> $output
-bedtools getfasta -name -fi $fasta -bed "$output" -fo "$output".fasta
+bedtools getfasta -name -fi $fasta -bed "$output" -fo "$out_fasta"