Mercurial > repos > fubar > jbrowse2
diff jbrowse2.py @ 13:1d86925dbb4c draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 873a12803692b0a84814a6dc08331d772d0e5492-dirty
author | fubar |
---|---|
date | Mon, 22 Jan 2024 11:52:19 +0000 |
parents | 247e17ce504b |
children | 7c2e28e144f3 |
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--- 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():