Merge branch 'master' of https://github.com/jhuapl-bio/mytax

Author: Merritt-Brian

README.md

@@ -1,21 +1,38 @@
 # Mytax2 - Realtime reporting
 
+
+## Create Conda Environment
+```
+conda env create -f environment.yml
+```
+
+
 ## Project setup
 ```
 npm install
 ```
 
-### Compiles and hot-reloads for development
+## Starting Development
+
+Run the below 2 commands:
+
+### Compiles and hot-reloads for development on frontent
 ```
 npm run serve
 ```
 
-### Compiles and minifies for production
+### Compiles and hot-reloads for development on server
+```
+npm run server
+```
+
+
+## Building Production package
 ```
 npm run build
 ```
 
-### Lints and fixes files
+### Lints and fixes files (development only)
 ```
 npm run lint
 ```

server/src/create_name_tab.sh

@@ -0,0 +1,102 @@
+# define colors for error messages
+red='\033[0;31m'
+RED='\033[1;31m'
+green='\033[0;32m'
+GREEN='\033[1;32m'
+yellow='\033[0;33m'
+YELLOW='\033[1;33m'
+blue='\033[0;34m'
+BLUE='\033[1;34m'
+purple='\033[0;35m'
+PURPLE='\033[1;35m'
+cyan='\033[0;36m'
+CYAN='\033[1;36m'
+NC='\033[0m'
+
+# usage function
+usage() {
+	echo -e "usage: ${YELLOW}$0${NC} [options]"
+	echo -e "Creating a taxonomy.tab for a buggy krona script, primarily for the custom taxids from this repo"
+	echo -e "OPTIONS:"
+	echo -e "   -h      show this message"
+	echo -e "   -i      names.dmp and nodes.dmp containing directory"
+	echo -e "   -o      output taxonomy.tab file. Default is the same location as the -i parameter "
+	echo -e ""
+}
+
+gawk_install() {
+	echo -e "" >&2 
+	echo -e "       ${RED}Please make sure gawk is installed.${NC}" >&2
+	echo -e "" >&2
+	echo -e "" >&2
+}
+awk_version=$(gawk --version  | head -n1)
+
+
+#---------------------------------------------------------------------------------------------------
+# set default values here
+
+#---------------------------------------------------------------------------------------------------
+# parse input arguments
+while getopts "hi:o:" OPTION
+do
+	case $OPTION in
+		h) usage; exit 1 ;;
+		i) input=$OPTARG ;;
+		o) output=$OPTARG ;;
+		?) usage; exit ;;
+	esac
+done
+# check input arguments
+if [[ -z "$output" ]]; then
+	echo -e "${CYAN}Warning: no output path for tab file specified, putting in -i ${input} ${NC}" >&2
+    output="$input/taxonomy.tab"
+fi
+if [[ -z "$input" ]]; then
+	echo -e "${RED}ERROR: no input path that contains a names and nodes dmp file -i ${input} ${NC}" >&2
+	usage
+	exit 2
+fi
+
+if [[ ! -s "$input/names.dmp" ]] || [[ ! -s "$input/nodes.dmp" ]]; then
+	echo -e "${RED}ERROR: names or nodes.dmp file dont exist in $input -i ${input}, exiting.... ${NC}" >&2
+	usage
+	exit 2
+fi
+echo $input
+echo $output
+
+
+# names.dmp file
+#1 is taxid (current)
+#2 is the text label of taxid
+#3 is category of  (current) e.g. synonym, common name, scientific name, etc
+
+# nodes.dmp file
+# 1 is child taxid (current)
+# 2 is parent taxid 
+# 3 is tax rank of child (current)
+
+gawk -F "\t" '
+    {
+        if ( NR==FNR){
+            mapping[$1] = $5
+        } else {
+            if ($7 != "" ){
+                names[$1][length(names[$1]) + 1] = $3
+            }
+        }
+       
+    } END {
+        i=0
+        print "name\ttaxid\trank"
+        for (name in names){
+            if (name in mapping){
+                for (i=1; i<=length(names[name]); i++){
+                    print names[name][i]"\t"name"\t"mapping[name]
+                }
+            }
+        }
+    }
+
+' $input/nodes.dmp $input/names.dmp    > $output