Mercurial > repos > fubar > jbrowse2
changeset 76:9e3eb6b26f85 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit d03454f949af9f3fff638f6a3e52fe42bc96be3b-dirty
| author | fubar |
|---|---|
| date | Mon, 01 Apr 2024 04:15:03 +0000 |
| parents | 9c8459ce7d88 |
| children | 3dcda36b97b4 |
| files | jbrowse2.py |
| diffstat | 1 files changed, 18 insertions(+), 19 deletions(-) [+] |
line wrap: on
line diff
--- a/jbrowse2.py Mon Apr 01 04:03:16 2024 +0000 +++ b/jbrowse2.py Mon Apr 01 04:15:03 2024 +0000 @@ -1490,24 +1490,23 @@ logging.debug("first contig=%s" % self.ass_first_contigs) [gnome, refName, end] = first_contig start = 0 - if False or data.get("defaultLocation", ""): - loc_match = re.search( - r"^([^:]+):([\d,]*)\.*([\d,]*)$", data["defaultLocation"] - ) - # loc_match = re.search(r"^(\w+):(\d+)\.+(\d+)$", data["defaultLocation"]) - if loc_match: - refName = loc_match.group(1) - start = int(loc_match.group(2)) - end = int(loc_match.group(3)) - else: - if refName: - view = { - "assembly": gnome, - "loc": "{}:{}-{}".format(refName, start, end), - "type": "LinearGenomeView", - "tracks": data[gnome]["tracks"], - } - session_spec["views"].append(view) + # if False or data.get("defaultLocation", ""): + # loc_match = re.search( + # r"^([^:]+):([\d,]*)\.*([\d,]*)$", data["defaultLocation"] + # ) + # # loc_match = re.search(r"^(\w+):(\d+)\.+(\d+)$", data["defaultLocation"]) + # if loc_match: + # refName = loc_match.group(1) + # start = int(loc_match.group(2)) + # end = int(loc_match.group(3)) + # else: + aview = { + "assembly": gnome, + "loc": "{}:{}..{}".format(refName, start, end), + "type": "LinearGenomeView", + "tracks": data[gnome]["tracks"], + } + session_spec["views"].append(aview) sess = json.dumps(session_spec, sort_keys=True, indent=2) new_index = INDEX_TEMPLATE.replace( "__SESSION_SPEC__", "&session=spec-{}".format(sess) @@ -1753,6 +1752,6 @@ jc.config_json["assemblies"] = assconf logging.debug("assemblies=%s, gnames=%s" % (assconf, jc.genome_names)) jc.write_config() - jc.add_default_session(default_session_data) + # jc.add_default_session(default_session_data) jc.add_defsess_to_index(default_session_data) # jc.text_index() not sure what broke here.