add metaSNP_distances.sh

metaSNP_distances.sh

+#! /bin/bash
+############################################
+#  metaSNP Step III:   `Post-Processing    #
+############################################
+#
+# This code is part of the metagenomic SNP calling pipeline (metaSNP)
+# Copyright (c) 2016 Robin Munch
+# Licenced under the GNU General Public License (see LICENSE) 
+#
+# Helper script for metaSNP distance computation
+
+
+display_usage() {
+	echo >&2 ""
+	echo >&2 "  Usage: $0 input_dir/ output/"
+	echo >&2 ""
+	echo >&2 "Parameters:"
+	echo >&2 "	Required:"
+	echo >&2 "	  input_dir/	DIR	directory with the filtered frequency tables (metaSNP_filtering.py)."
+	echo >&2 "	  output_dir/	DIR	write output to DIR."	
+	echo >&2 ""
+	echo >&2 "Note: Expecting 'metaSNP_filtering.py' to be completed."
+	echo >&2 ""
+}
+
+required_parameter() {
+        echo >&2 ""
+        echo >&2 "ERROR: '$1' is a required parameter"
+        display_usage
+        exit 1
+}
+
+dir_missing() {
+        echo >&2 ""
+        echo >&2 "ERROR: '$1' no such file or directory"
+        display_usage
+        exit 1
+}
+
+IN_DIR="$1"
+OUT_DIR="$2"
+
+## Test
+[ -n "$IN_DIR" ] || required_parameter "input_dir/"
+[ -n "$OUT_DIR" ] || required_parameter "output_dir/"
+
+[ -d "$IN_DIR" ] || dir_missing "$IN_DIR"
+[ -d "$OUT_DIR" ] || dir_missing "$OUT_DIR"
+
+## Commandlines:
+for i in $(ls $IN_DIR"/"*.freq); do echo "/g/bork3/home/costea/R-3.0.2/bin/R --no-save --file=src/computeDistances.R --args $i $OUT_DIR"; done
+
+exit