add convertion script

convertPhyloTo.sh

+#!/bin/bash
+
+
+#
+# To convert a phylo DOT file into a phylo JSON / SVG file
+#
+
+
+exitWithError()
+{
+    echo "$1" 1>&2
+    exit 1
+}
+
+
+exitWithUsage()
+{
+    echo "$1" 1>&2
+    usage
+    exit 1
+}
+
+
+usage()
+{
+    cat << EOF
+USAGE: ./`basename $0` options
+OPTIONS: 
+   --from (required) [path to the original phylo dot file]
+   --to   (required) [format of the output file - json / svg]
+   --help (optional) [displays this message]
+ 
+EOF
+}
+
+
+init()
+{ 
+    FROM=""
+    TO=""    
+
+    while getopts ":-:" OPTION
+    do
+        LONG_OPTION="${OPTARG%%=*}"
+        OPTARG="${OPTARG#*=}"
+
+        case ${LONG_OPTION} in
+            from)
+                FROM=${OPTARG}
+                ;;
+
+            to)
+                TO=${OPTARG}
+                ;;                                         
+
+            help) 
+                usage ; 
+                exit 0
+                ;;
+
+            *) 
+                echo "Unknown option ${LONG_OPTION}" ; 
+                usage ; 
+                exit 1 
+                ;;
+        esac
+    done
+
+    if [ "${FROM}" == "" ] || [ "${TO}" == "" ]; then 
+        exitWithUsage $'\nAt least one required option is missing.\n'
+    fi
+
+    if [ "${TO}" != "json" ] && [ "${TO}" != "svg" ]; then
+        exitWithUsage $'\nOutput format has to be json or svg.\n'
+    fi
+
+    if [ ! -f "${FROM}" ]; then 
+        exitWithError $'\nOriginal phylo DOT file does not exist.\n'
+    fi 
+
+    NAME=$(basename ${FROM} .dot)
+
+    FILEPATH=$(dirname "${FROM}")
+}
+
+convert()
+{
+    if [ "${TO}" == "svg" ]; then
+        `dot ${FROM} -Tsvg > "${FILEPATH}/${NAME}.svg"`
+    fi
+
+    if [ "${TO}" == "json" ]; then
+        `dot -Tdot -o "tmp.dot" ${FROM}`
+        `dot -Txdot_json -o "${FILEPATH}/${NAME}.json" "tmp.dot"`
+    fi    
+}
+
+
+init "$@"
+
+convert
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