diff jbrowse2.py @ 13:1d86925dbb4c draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 873a12803692b0a84814a6dc08331d772d0e5492-dirty

--- a/jbrowse2.py	Sat Jan 20 10:04:08 2024 +0000
+++ b/jbrowse2.py	Mon Jan 22 11:52:19 2024 +0000
@@ -1175,7 +1175,9 @@
         refName = None
         if data.get("defaultLocation", ""):
             ddl = data["defaultLocation"]
-            loc_match = re.search(r"^(\w.+):(\d+)\.+(\d+)$", ddl)
+            loc_match = re.search(
+                r"^([^:]+):(\d+)\.+(\d+)$", ddl
+            )  # was re.search(r"^(\w.+):(\d+)\.+(\d+)$"
             if loc_match:
                 refName = loc_match.group(1)
                 start = int(loc_match.group(2))
@@ -1190,7 +1192,7 @@
             start = 0
             end = 10000  # Booh, hard coded! waiting for https://github.com/GMOD/jbrowse-components/issues/2708
             logging.info(
-                "@@@ no defaultlocation found for default session - suggest adding one!"
+                "@@@ no defaultlocation found for default session - please add one"
             )
 
         if refName is not None:
@@ -1211,7 +1213,7 @@
             )
         else:
             logging.info(
-                "@@@ no assembly name found default session - suggest adding one!"
+                "@@@ no contig name found for default session - please add one!"
             )
         session_name = data.get("session_name", "New session")
         for key, value in mapped_chars.items():