Mercurial > repos > fubar > jbrowse2
changeset 12:247e17ce504b draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4baeb144cafbb61ae0587cce731066129097c168-dirty
| author | fubar |
|---|---|
| date | Sat, 20 Jan 2024 10:04:08 +0000 |
| parents | f5ce31c2f47d |
| children | 1d86925dbb4c |
| files | jbrowse2.py |
| diffstat | 1 files changed, 18 insertions(+), 1 deletions(-) [+] |
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--- a/jbrowse2.py Sat Jan 20 09:33:22 2024 +0000 +++ b/jbrowse2.py Sat Jan 20 10:04:08 2024 +0000 @@ -1174,15 +1174,24 @@ refName = None if data.get("defaultLocation", ""): - loc_match = re.search(r"^(\w.+):(\d+)\.+(\d+)$", data["defaultLocation"]) + ddl = data["defaultLocation"] + loc_match = re.search(r"^(\w.+):(\d+)\.+(\d+)$", ddl) if loc_match: refName = loc_match.group(1) start = int(loc_match.group(2)) end = int(loc_match.group(3)) + else: + logging.info( + "@@@ regexp could not match contig:start..end in the supplied location %s - please fix" + % ddl + ) elif self.genome_name is not None: refName = self.genome_name 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!" + ) if refName is not None: # TODO displayedRegions is not just zooming to the region, it hides the rest of the chromosome @@ -1196,6 +1205,14 @@ } ] + logging.info( + "@@@ defaultlocation %s for default session" + % view_json["displayedRegions"] + ) + else: + logging.info( + "@@@ no assembly name found default session - suggest adding one!" + ) session_name = data.get("session_name", "New session") for key, value in mapped_chars.items(): session_name = session_name.replace(value, key)