add gene of interest extraction

tobias/utils/TFs2genesOfInterest.sh

@@ -0,0 +1,60 @@
+#!/bin/bash
+
+# author afust
+
+# capability: 
+# extracts all TF information for a target gene list
+
+# parameters:
+# target gene list: file with Ensembl gene ids in first column
+# directory: directory containing files of interest (TFBS)
+# pattern: file pattern ("*_overview.txt")
+# output: output file
+
+
+# help message
+usage() {
+	echo -e "Usage: $0 [options]"
+	echo -e ""
+	echo -e "	-g <string> []			file with Ensembl gene ids in first column"
+	echo -e "	-d <string> []			directory containing files of interest (TFBS)"
+	echo -e "	-p <string> []			file pattern ('*_overview.txt')"
+	echo -e "   -o <string> []			output file"
+	echo -e ""
+	exit 1
+}
+export LC_ALL=C
+
+genes=""
+TFBS_dir=""
+TFBS_pattern=""
+output=""
+
+while getopts ":g:d:p:o:" op; do
+	case $op in
+		g) genes=${OPTARG} ;;
+		d) TFBS_dir=${OPTARG} ;;
+		p) TFBS_pattern=${OPTARG} ;;
+		o) output=${OPTARG} ;;
+		*) usage ;;
+	esac
+done
+shift $((OPTIND-1))
+
+# check parameters
+if [[ -z $genes ]] || [[ -z $TFBS_dir ]] || [[ -z $TFBS_pattern ]] || [[ -z $output ]] ; then
+	echo -e "input missing, please specify"
+	usage
+	exit -1
+fi
+
+# format gene list to expression used for grep (should not end with "|")
+gene_list=$(awk 'BEGIN { ORS = "|" } { print }' ${genes})
+if [ "${gene_list: -1}" == "|" ]; then
+	gene_list=${gene_list::-1}
+fi
+# create header
+f=$(find ${TFBS_dir} -name ${TFBS_pattern} | head -1)
+head -1 ${f} > ${output}
+# append all entries for all target genes to output
+grep -h -E -r --include "${TFBS_pattern}" ${gene_list} ${TFBS_dir} >> ${output}