--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/autogenJB2.py	Tue Jan 30 06:05:03 2024 +0000
@@ -0,0 +1,88 @@
+import argparse
+import os
+
+from jbrowse2 import jbrowseConnector as jbC
+
+
+
+
+if __name__ == "__main__":
+    parser = argparse.ArgumentParser(description="", epilog="")
+    parser.add_argument("--yaml", help="Track Configuration")
+    parser.add_argument("--outdir", help="Output directory", default="out")
+    parser.add_argument("--version", "-V", action="version", version="%(prog)s 0.0.1")
+    args = parser.parse_args()
+    if os.path.exists(args.outdir):
+        root = args.outdir
+        dirList =  os.scandir(root)
+        subdirs = [f.path for f in dirList if f.is_dir()]
+        genome_paths = [f.path for f in dirList if f.name.startswith('genome') and f.is_file()]
+        if len(genome_paths) > 0:
+            genome_fnames = [os.path.basename(x).split('_')[2:] for x in genome_paths]  # expect genome_1_genomename.fasta etc
+            jc = jbC(
+                outdir=args.outdir,
+                genomes=[
+                    {
+                        "path":  x,
+                        "meta": {"name" : genome_fnames[i], },
+                    }
+                    for i,x in enumerate(genome_paths)
+                ],
+            )
+            jc.process_genomes()
+            # .add_default_view() replace from https://github.com/abretaud/tools-iuc/blob/jbrowse2/tools/jbrowse2/jbrowse2.py
+            default_session_data = {
+                "visibility": {
+                    "default_on": [],
+                    "default_off": [],
+                },
+                "style": {},
+                "style_labels": {},
+            }
+
+            track_paths = [x for x in genome_paths if not x.startswith('genome') and  x.is_file()]
+            for i, track in enumerate(track_paths):
+                track_conf = {}
+                track_conf['format']= os.path.basename(track).split('_')[0]
+                track_conf["name"] = os.path.basename(track).split('_')[2:]   # expect genome_1_genomename.fasta etc
+                fext = os.path.splitext(os.path.basename(track)).replace('.','')
+                track_conf["label"] = "%s_%i" % (os.path.basename(track), i)
+                track_conf["trackfiles"] = []
+                keys = jc.process_annotations(track_conf)
+
+                if keys:
+                    for key in keys:
+                        default_session_data["visibility"][
+                            track.attrib.get("visibility", "default_off")
+                        ].append(key)
+                        if track_conf.get("style", None):
+                            default_session_data["style"][key] = track_conf[
+                                "style"
+                            ]  # TODO do we need this anymore?
+                        if track_conf.get("style_lables", None):
+                            default_session_data["style_labels"][key] = track_conf.get(
+                                "style_labels", None
+                            )
+            # default_session_data["defaultLocation"] = root.find(
+                # "metadata/general/defaultLocation"
+            # ).text
+            # default_session_data["session_name"] = root.find(
+                # "metadata/general/session_name"
+            # ).text
+            # general_data = {
+                # "analytics": root.find("metadata/general/analytics").text,
+                # "primary_color": root.find("metadata/general/primary_color").text,
+                # "secondary_color": root.find("metadata/general/secondary_color").text,
+                # "tertiary_color": root.find("metadata/general/tertiary_color").text,
+                # "quaternary_color": root.find("metadata/general/quaternary_color").text,
+                # "font_size": root.find("metadata/general/font_size").text,
+            # }
+            # jc.add_general_configuration(general_data)
+            trackconf = jc.config_json.get("tracks", None)
+            if trackconf:
+                jc.config_json["tracks"].update(jc.tracksToAdd)
+            else:
+                jc.config_json["tracks"] = jc.tracksToAdd
+            jc.write_config()
+            jc.add_default_session(default_session_data)
+            # jc.text_index() not sure what broke here.