docs: json2svg utils

README.md

@@ -137,13 +137,15 @@ The file needs to contain three lines: moelcule description line (starts with th
 	other lines are filled with LABELS and BRACKETS in dot-bracket notation of secondary structure pairing
 	match-tree must contain both LABELS and BRACKETS, templated-tree need only BRACKETS
 
-### Example 1a: Visualize mouse 18S rRNA using human 18S rRNA as template using CRW ps image as the template layout.
+### Example 1a: Visualize mouse 18S rRNA using human 18S rRNA as template using CRW ps image as the template layout
 	$ mkdir test
 	$ bin/traveler \
 		--target-structure data/metazoa/mouse.fasta \
 		--template-structure data/metazoa/human.ps data/metazoa/human.fasta \
 		--all test/mouse_from_human
 
+Outputs a SVG and JSON file (see Example3 below for details)
+
 ### Example 1b: Visualize mouse 18S rRNA using human 18S rRNA as template using Traveler's XML input format as the template layout.
 	$ mkdir test
 	$ bin/traveler \
@@ -164,9 +166,18 @@ The file needs to contain three lines: moelcule description line (starts with th
 		--target-structure data/metazoa/mouse.fasta \
 		--template-structure data/metazoa/human.ps data/metazoa/human.fasta \
 		--draw --overlaps test/mouse_from_human.map test/mouse_from_human
+    # checks also if output molecule has overlaps and draws them in output image, but this information is not available in the json file (see below)
+
+
+The above example enerates 2 files - 1 .svg file (see COLOR CODING section) and 1 .json file in the
+[RNA2D data schema format](https://github.com/LDWLab/RNA2D-data-schema/). The json file can then be
+converted into a SVG format using the `json2svg` utility (see the utils directory):
 
-	$ # generates 3 files - 2 .svg files (with/without colored bases (see COLOR CODING section)) and 1 .xml file with the basic layout information
-	$ # checks also if output molecule has overlaps and draws them in output image
+```shell
+python3 utils/json2svg.py -i test/mouse_from_human.json -o test/mouse_from_human.json.svg
+```
+
+
 
 
 #### Note:

utils/README.md

@@ -13,3 +13,12 @@ To specify residue font size, label font size or thickness of lines of labels, r
 ```
 traveler2xrna -i test_data/mouse_from_human.colored.xml -o test_data/mouse_from_human.colored.xrna -rfs 21 -lfs 5 -ll 0.1
 ```
+
+## json2svg
+
+Converts the Travaler's JSON output (in the [RNA2D data schema format](https://github.com/LDWLab/RNA2D-data-schema/))
+to SVG.
+
+``
+python3 json2svg.py -i test_data/mouse_from_human.json -o test_data/mouse_from_human.json.svg
+``