jbrowse2: jbrowse2.py comparison

comparison jbrowse2.py @ 17:4c201a3d4755 draft

planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit a37bfdfc108501b11c7b2aa15efb1bd16f0c4b66

author	fubar
date	Sun, 28 Jan 2024 06:48:52 +0000
parents	cce8dacb240f
children	bde6b1d09f7d

comparison

equal deleted inserted replaced

-:1fe91657bfd6
+:4c201a3d4755
 self.genome_names.append(genome_name)
 if self.genome_name is None:
 self.genome_name = (
 genome_name  # first one for all tracks - other than paf
 )
+self.genome_firstcontig = None
+fl = open(fapath, "r").readline().strip().split(">", 1)
+if len(fl) > 1:
+self.genome_firstcontig = fl[1].strip()
 if self.config_json.get("assemblies", None):
 self.config_json["assemblies"] += assemblies
 else:
 self.config_json["assemblies"] = assemblies
 """
 tId = trackData["label"]
 # can be served - if public.
 # dsId = trackData["metadata"]["dataset_id"]
 # url = "%s/api/datasets/%s/display?to_ext=hic " % (self.giURL, dsId)
-hname = trackData["label"]
+hname = trackData["name"]
 dest = os.path.join(self.outdir, hname)
 cmd = ["cp", data, dest]
 # these can be very big.
 self.subprocess_check_call(cmd)
 floc = {
 "displays": [
 {
 "type": "LinearBasicDisplay",
 "displayId": "%s-LinearBasicDisplay" % tId,
 },
-{"type": "LinearArcDisplay", "displayId": "%s-LinearArcDisplay" % tId},
+{
+"type": "LinearArcDisplay",
+"displayId": "%s-LinearArcDisplay" % tId,
+},
 ],
 }
 style_json = self._prepare_track_style(trackDict)
 trackDict["style"] = style_json
 self.tracksToAdd.append(trackDict)
 "displays": [
 {
 "type": "LinearBasicDisplay",
 "displayId": "%s-LinearBasicDisplay" % tId,
 },
-{"type": "LinearArcDisplay", "displayId": "%s-LinearArcDisplay" % tId},
+{
+"type": "LinearArcDisplay",
+"displayId": "%s-LinearArcDisplay" % tId,
+},
 ],
 }
 style_json = self._prepare_track_style(trackDict)
 trackDict["style"] = style_json
 self.tracksToAdd.append(trackDict)
 "displays": [
 {
 "type": "LinearBasicDisplay",
 "displayId": "%s-LinearBasicDisplay" % tId,
 },
-{"type": "LinearArcDisplay", "displayId": "%s-LinearArcDisplay" % tId},
+{
+"type": "LinearArcDisplay",
+"displayId": "%s-LinearArcDisplay" % tId,
+},
 ],
 }
 style_json = self._prepare_track_style(trackDict)
 trackDict["style"] = style_json
 self.tracksToAdd.append(trackDict)
 },
 {
 "type": "LinearPileupDisplay",
 "displayId": "%s-LinearPileupDisplay" % tId,
 },
-{"type": "LinearArcDisplay", "displayId": "%s-LinearArcDisplay" % tId},
+{
+"type": "LinearArcDisplay",
+"displayId": "%s-LinearArcDisplay" % tId,
+},
 ],
 }
 style_json = self._prepare_track_style(trackDict)
 trackDict["style"] = style_json
 self.tracksToAdd.append(trackDict)
 "type": "PAFAdapter",
 "pafLocation": {"uri": url},
 "assemblyNames": [self.genome_name, pgname],
 },
 # "displays": [
 # {
 # "type": "LinearSyntenyDisplay",
 # "displayId": "%s-LinearSyntenyDisplay" % tId,
 # },
 # {
 # "type": "DotPlotDisplay",
 # "displayId": "%s-DotPlotDisplay" % tId,
 # },
 # ],
 }
 style_json = self._prepare_track_style(trackDict)
 trackDict["style"] = style_json
 self.tracksToAdd.append(trackDict)
 track["conf"]["options"]["pileup"],
 bam_index=real_indexes[i],
 )
 elif dataset_ext == "blastxml":
 self.add_blastxml(
-dataset_path, outputTrackConfig, track["conf"]["options"]["blast"]
+dataset_path,
+outputTrackConfig,
+track["conf"]["options"]["blast"],
 )
 elif dataset_ext == "vcf":
 self.add_vcf(dataset_path, outputTrackConfig)
 elif dataset_ext == "paf":
 self.add_paf(
-dataset_path, outputTrackConfig, track["conf"]["options"]["synteny"]
+dataset_path,
+outputTrackConfig,
+track["conf"]["options"]["synteny"],
 )
 else:
 log.warn("Do not know how to handle %s", dataset_ext)
 # Return non-human label for use in other fields
 yield outputTrackConfig["label"]
 # The view for the assembly we're adding
 view_json = {"type": "LinearGenomeView", "tracks": tracks_data}
 refName = None
+drdict = {
+"reversed": False,
+"assemblyName": self.genome_name,
+"start": 0,
+"end": 100000,
+}
 if data.get("defaultLocation", ""):
 ddl = data["defaultLocation"]
-loc_match = re.search(
+loc_match = re.search(r"^([^:]+):(\d*)\.*(\d*)$", ddl)
-r"^([^:]+):(\d+)\.+(\d+)$", ddl
-)
 if loc_match:
 refName = loc_match.group(1)
-start = int(loc_match.group(2))
+drdict["refName"] = refName
-end = int(loc_match.group(3))
+if loc_match.group(2) > "":
+drdict["start"] = int(loc_match.group(2))
+if loc_match.group(3) > "":
+drdict["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:
+elif self.genome_firstcontig is not None:
-start = 0
+drdict["refName"] = self.genome_firstcontig
-end = 10000  # Booh, hard coded! waiting for https://github.com/GMOD/jbrowse-components/issues/2708
 logging.info(
-"@@@ no defaultlocation found for default session - please add one"
+"@@@ no defaultlocation found for default session - using %s as first contig found"
+% self.genome_firstcontig
 )
-if refName is not None:
+if drdict.get("refName", None):
 # TODO displayedRegions is not just zooming to the region, it hides the rest of the chromosome
 view_json["displayedRegions"] = [
-{
+drdict,
-"refName": refName,
-"start": start,
-"end": end,
-"reversed": False,
-"assemblyName": self.genome_name,
-}
 ]
-logging.info(
+logging.info("@@@ defaultlocation %s for default session" % drdict)
-"@@@ defaultlocation %s for default session"
-% view_json["displayedRegions"]
-)
 else:
 logging.info(
 "@@@ no contig name found for default session - please add one!"
 )
 session_name = data.get("session_name", "New session")
 "version.txt",
 "test_data",
 ]:
 cmd = ["rm", "-rf", os.path.join(self.outdir, fn)]
 self.subprocess_check_call(cmd)
-cmd = ["cp", os.path.join(INSTALLED_TO, "jb2_webserver.py"), self.outdir]
+cmd = [
+"cp",
+os.path.join(INSTALLED_TO, "jb2_webserver.py"),
+self.outdir,
+]
 self.subprocess_check_call(cmd)
 def parse_style_conf(item):
-if "type" in item.attrib and item.attrib["type"] in ["boolean", "integer"]:
+if "type" in item.attrib and item.attrib["type"] in [
+"boolean",
+"integer",
+]:
 if item.attrib["type"] == "boolean":
 return item.text in ("yes", "true", "True")
 elif item.attrib["type"] == "integer":
 return int(item.text)
 else:
 trackfiles = track.findall("files/trackFile")
 if trackfiles:
 for x in track.findall("files/trackFile"):
 if is_multi_bigwig:
 multi_bigwig_paths.append(
-(x.attrib["label"], os.path.realpath(x.attrib["path"]))
+(
+x.attrib["label"],
+os.path.realpath(x.attrib["path"]),
+)
 )
 else:
 if trackfiles:
 metadata = metadata_from_node(x.find("metadata"))
 track_conf["dataset_id"] = metadata["dataset_id"]

Mercurial > repos > fubar > jbrowse2

comparison jbrowse2.py @ 17:4c201a3d4755 draft