updated readme andrenamed file

mk_drug_dirs.sh

@@ -0,0 +1,39 @@
+#!/bin/bash
+# Create a drug directory structure for processing
+#
+## Structure:
+#
+# $DATA_DIR/$DRUG/input
+#                 |- original
+#                 |- processed
+#                 |- structure
+#                 
+# $DATA_DIR/$DRUG/output
+#                 |- plots
+#                 |- structure
+
+DATA_DIR=~/git/Data
+
+if [[ $1 == '' ]]; then
+    echo "usage: mk-drug-dirs.sh <drug name>";
+    exit;
+else
+    DRUG=$1
+    echo Creating structure for: $DRUG
+
+    if [ -d $DATA_DIR ]
+    then
+        echo Doing creation in $DATA_DIR
+        mkdir -p $DATA_DIR/$DRUG/input/original
+        mkdir -p $DATA_DIR/$DRUG/input/processed
+        mkdir -p $DATA_DIR/$DRUG/input/structure
+        mkdir -p $DATA_DIR/$DRUG/output/plots
+        mkdir -p $DATA_DIR/$DRUG/output/structure
+        
+    else
+        echo "Error: $DATA_DIR does not exist. Did you check it out of git?"
+        exit
+    fi
+
+fi
+