Mercurial > repos > fubar > jbrowse2
comparison jbrowse2.py @ 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 | 7bb6259ea52f |
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| 75:9c8459ce7d88 | 76:9e3eb6b26f85 |
|---|---|
| 1488 logging.debug("def ass_first=%s\ndata=%s" % (self.ass_first_contigs, data)) | 1488 logging.debug("def ass_first=%s\ndata=%s" % (self.ass_first_contigs, data)) |
| 1489 for first_contig in self.ass_first_contigs: | 1489 for first_contig in self.ass_first_contigs: |
| 1490 logging.debug("first contig=%s" % self.ass_first_contigs) | 1490 logging.debug("first contig=%s" % self.ass_first_contigs) |
| 1491 [gnome, refName, end] = first_contig | 1491 [gnome, refName, end] = first_contig |
| 1492 start = 0 | 1492 start = 0 |
| 1493 if False or data.get("defaultLocation", ""): | 1493 # if False or data.get("defaultLocation", ""): |
| 1494 loc_match = re.search( | 1494 # loc_match = re.search( |
| 1495 r"^([^:]+):([\d,]*)\.*([\d,]*)$", data["defaultLocation"] | 1495 # r"^([^:]+):([\d,]*)\.*([\d,]*)$", data["defaultLocation"] |
| 1496 ) | 1496 # ) |
| 1497 # loc_match = re.search(r"^(\w+):(\d+)\.+(\d+)$", data["defaultLocation"]) | 1497 # # loc_match = re.search(r"^(\w+):(\d+)\.+(\d+)$", data["defaultLocation"]) |
| 1498 if loc_match: | 1498 # if loc_match: |
| 1499 refName = loc_match.group(1) | 1499 # refName = loc_match.group(1) |
| 1500 start = int(loc_match.group(2)) | 1500 # start = int(loc_match.group(2)) |
| 1501 end = int(loc_match.group(3)) | 1501 # end = int(loc_match.group(3)) |
| 1502 else: | 1502 # else: |
| 1503 if refName: | 1503 aview = { |
| 1504 view = { | 1504 "assembly": gnome, |
| 1505 "assembly": gnome, | 1505 "loc": "{}:{}..{}".format(refName, start, end), |
| 1506 "loc": "{}:{}-{}".format(refName, start, end), | 1506 "type": "LinearGenomeView", |
| 1507 "type": "LinearGenomeView", | 1507 "tracks": data[gnome]["tracks"], |
| 1508 "tracks": data[gnome]["tracks"], | 1508 } |
| 1509 } | 1509 session_spec["views"].append(aview) |
| 1510 session_spec["views"].append(view) | |
| 1511 sess = json.dumps(session_spec, sort_keys=True, indent=2) | 1510 sess = json.dumps(session_spec, sort_keys=True, indent=2) |
| 1512 new_index = INDEX_TEMPLATE.replace( | 1511 new_index = INDEX_TEMPLATE.replace( |
| 1513 "__SESSION_SPEC__", "&session=spec-{}".format(sess) | 1512 "__SESSION_SPEC__", "&session=spec-{}".format(sess) |
| 1514 ) | 1513 ) |
| 1515 | 1514 |
| 1751 assconf = jc.config_json.get("assemblies", []) | 1750 assconf = jc.config_json.get("assemblies", []) |
| 1752 assconf += jc.assemblies | 1751 assconf += jc.assemblies |
| 1753 jc.config_json["assemblies"] = assconf | 1752 jc.config_json["assemblies"] = assconf |
| 1754 logging.debug("assemblies=%s, gnames=%s" % (assconf, jc.genome_names)) | 1753 logging.debug("assemblies=%s, gnames=%s" % (assconf, jc.genome_names)) |
| 1755 jc.write_config() | 1754 jc.write_config() |
| 1756 jc.add_default_session(default_session_data) | 1755 # jc.add_default_session(default_session_data) |
| 1757 jc.add_defsess_to_index(default_session_data) | 1756 jc.add_defsess_to_index(default_session_data) |
| 1758 # jc.text_index() not sure what broke here. | 1757 # jc.text_index() not sure what broke here. |