jbrowse2: jbrowse2.py comparison

comparison jbrowse2.py @ 59:f807e219cec3 draft

planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit faada92caf5aaabe58e52b161687a30d542a07b9

author	fubar
date	Fri, 22 Mar 2024 22:04:08 +0000
parents	94264fe60478
children	81d535970196

comparison

equal deleted inserted replaced

-:0e592dcaeb7f
+:f807e219cec3
 }
 if trackDict.get("displays", None):  # use first if multiple like bed
 style_data["type"] = trackDict["displays"][0]["type"]
 style_data["displayId"] = trackDict["displays"][0]["displayId"]
-return {
+wstyle = {
 "displays": [
 style_data,
 ]
 }
+logging.warn("style=%s" % (wstyle))
+return wstyle
 def process_genomes(self):
 assemblies = []
 useuri = False
 for i, genome_node in enumerate(self.genome_paths):
 faname = fapath
 adapter = {
 "type": "BgzipFastaAdapter",
 "fastaLocation": {
 "uri": faname,
-"locationType": "UriLocation",
+"locationType": "UriLocation"
 },
 "faiLocation": {
 "uri": faname + ".fai",
-"locationType": "UriLocation",
+"locationType": "UriLocation"
 },
 "gziLocation": {
 "uri": faname + ".gzi",
-"locationType": "UriLocation",
+"locationType": "UriLocation"
-},
+}
 }
 else:
 faname = gname + ".fa.gz"
 fadest = os.path.realpath(os.path.join(self.outdir, faname))
 cmd = "bgzip -i -c %s -I %s.gzi > %s && samtools faidx %s" % (
 "faiLocation": {
 "uri": faname + ".fai",
 },
 "gziLocation": {
 "uri": faname + ".gzi",
-},
+}
 }
 trackDict = {
 "name": gname,
 "sequence": {
 "type": "ReferenceSequenceTrack",
 "trackId": gname,
 "adapter": adapter,
 },
-"rendering": {"type": "DivSequenceRenderer"},
 "displays": [
 {
 "type": "LinearReferenceSequenceDisplay",
 "displayId": "%s-LinearReferenceSequenceDisplay" % gname,
 },
 {
 "type": "LinearGCContentDisplay",
 "displayId": "%s-LinearGCContentDisplay" % gname,
 },
-],
+]
 }
 return trackDict
 def add_default_view(self):
 cmd = [
 "type": "LinearHicDisplay",
 "displayId": "%s-LinearHicDisplay" % tId,
 },
 ],
 }
+style_json = self._prepare_track_style(trackDict)
+trackDict["style"] = style_json
 self.tracksToAdd.append(trackDict)
 self.trackIdlist.append(tId)
 def add_maf(self, data, trackData):
 """
 "type": "LinearArcDisplay",
 "displayId": "%s-LinearArcDisplay" % tId,
 },
 ],
 }
+style_json = self._prepare_track_style(trackDict)
+trackDict["style"] = style_json
 self.tracksToAdd.append(trackDict)
 self.trackIdlist.append(tId)
 if self.config_json.get("plugins", None):
 self.config_json["plugins"].append(mafPlugin[0])
 else:
 "type": "LinearArcDisplay",
 "displayId": "%s-LinearArcDisplay" % tId,
 },
 ],
 }
+style_json = self._prepare_track_style(trackDict)
+trackDict["style"] = style_json
 self.tracksToAdd.append(trackDict)
 self.trackIdlist.append(tId)
 os.unlink(gff3)
 def add_bigwig(self, data, trackData):
 "type": "LinearWiggleDisplay",
 "displayId": "%s-LinearWiggleDisplay" % tId,
 }
 ],
 }
+style_json = self._prepare_track_style(trackDict)
+trackDict["style"] = style_json
 self.tracksToAdd.append(trackDict)
 self.trackIdlist.append(tId)
 def add_bam(self, data, trackData, bam_index=None, **kwargs):
 tId = trackData["label"]
 "type": "LinearAlignmentsDisplay",
 "displayId": "%s-LinearAlignmentsDisplay" % tId,
 },
 ],
 }
+style_json = self._prepare_track_style(trackDict)
+trackDict["style"] = style_json
 self.tracksToAdd.append(trackDict)
 self.trackIdlist.append(tId)
 def add_cram(self, data, trackData, cram_index=None, **kwargs):
 tId = trackData["label"]
 "type": "LinearAlignmentsDisplay",
 "displayId": "%s-LinearAlignmentsDisplay" % tId,
 },
 ],
 }
+style_json = self._prepare_track_style(trackDict)
+trackDict["style"] = style_json
 self.tracksToAdd.append(trackDict)
 self.trackIdlist.append(tId)
 def add_vcf(self, data, trackData):
 tId = trackData["label"]
 "type": "LinearPairedArcDisplay",
 "displayId": "%s-LinearPairedArcDisplay" % tId,
 },
 ],
 }
+style_json = self._prepare_track_style(trackDict)
+trackDict["style"] = style_json
 self.tracksToAdd.append(trackDict)
 self.trackIdlist.append(tId)
 def _sort_gff(self, data, dest):
 # Only index if not already done
 "type": "LinearArcDisplay",
 "displayId": "%s-LinearArcDisplay" % tId,
 },
 ],
 }
+style_json = self._prepare_track_style(trackDict)
+trackDict["style"] = style_json
 self.tracksToAdd.append(trackDict)
 self.trackIdlist.append(tId)
 def add_bed(self, data, ext, trackData):
 tId = trackData["label"]
 "type": "LinearArcDisplay",
 "displayId": "%s-LinearArcDisplay" % tId,
 },
 ],
 }
+style_json = self._prepare_track_style(trackDict)
+trackDict["style"] = style_json
 self.tracksToAdd.append(trackDict)
 self.trackIdlist.append(tId)
 def add_paf(self, data, trackData, pafOpts, **kwargs):
 tname = trackData["name"]
 tId = trackData["label"]
 categ = trackData["category"]
-pgnames = [x.strip() for x in pafOpts["genome_label"].split(",")]
+pgnames = [x.strip() for x in pafOpts["genome_label"].split(",") if len(x.strip()) > 0]
-pgpaths = [x.strip() for x in pafOpts["genome"].split(",")]
+pgpaths = [x.strip() for x in pafOpts["genome"].split(",") if len(x.strip()) > 0]
 passnames = [self.genome_name]  # always first
+logging.warn("### add_paf got pafOpts=%s, pgnames=%s, pgpaths=%s for %s" % (pafOpts, pgnames, pgpaths, tId))
 for i, gname in enumerate(pgnames):
 if len(gname.split()) > 1:
 gname = gname.split()[0]
 passnames.append(gname)
 # trouble from spacey names in command lines avoidance
 if gname not in self.genome_names:
 # ignore if already there - eg for duplicates among pafs.
 useuri = pgpaths[i].startswith("http://") or pgpaths[i].startswith(
 "https://"
 )
 asstrack = self.make_assembly(pgpaths[i], gname, useuri)
 self.genome_names.append(gname)
 if self.config_json.get("assemblies", None):
 self.config_json["assemblies"].append(asstrack)
 else:
 self.config_json["assemblies"] = [
 asstrack,
 ]
 url = "%s.paf" % (trackData["label"])
 dest = "%s/%s" % (self.outdir, url)
 self.symlink_or_copy(os.path.realpath(data), dest)
 trackDict = {
 "type": "SyntenyTrack",
 "name": tname,
 "adapter": {
 "type": "PAFAdapter",
 "pafLocation": {"uri": url},
 "assemblyNames": passnames,
-},
+}
-"displays": [
+}
-{
+style_json = {
-"type": "LinearSyntenyDisplay",
+"displays": [
-"displayId": "%s-LinearSyntenyDisplay" % tId,
+{ "type": "LinearBasicDisplay",
-},
+"displayId": "%s-LinearBasicyDisplay" % trackDict["trackId"]
-{
+}
-"type": "DotPlotDisplay",
+]
-"displayId": "%s-DotPlotDisplay" % tId,
+}
-},
+trackDict["style"] = style_json
-],
-}
 self.tracksToAdd.append(trackDict)
 self.trackIdlist.append(tId)
 def process_annotations(self, track):
 category = track["category"].replace("__pd__date__pd__", TODAY)
 logging.warn("### No style data in default data for %s" % tId)
 style_data = {"type": "LinearBasicDisplay"}
 if "displays" in track_conf:
 disp = track_conf["displays"][0]["type"]
 style_data["type"] = disp
-style_data["configuration"] = "%s-%s" % (tId, disp)
 if track_conf.get("style_labels", None):
 # TODO fix this: it should probably go in a renderer block (SvgFeatureRenderer) but still does not work
 # TODO move this to per track displays?
 style_data["labels"] = track_conf["style_labels"]
 tracks_data.append(
 "type": track_types[tId],
 "configuration": tId,
 "displays": [style_data],
 }
 )
 # The view for the assembly we're adding
 view_json = {"type": "LinearGenomeView", "tracks": tracks_data}
 refName = None
 drdict = {
 track_conf["style"] = {
 item.tag: parse_style_conf(item) for item in track.find("options/style")
 }
 else:
 track_conf["style"] = {}
-tst = track_conf["style"].get("type", None)
-if tst:
-track_conf["style"]["configuration"] = "%s-%s" % (track_conf["label"], tst)
 if track.find("options/style_labels"):
 track_conf["style_labels"] = {
 item.tag: parse_style_conf(item)
 for item in track.find("options/style_labels")
 }
 "metadata/general/defaultLocation"
 ).text
 default_session_data["session_name"] = root.find(
 "metadata/general/session_name"
 ).text
+logging.warn("default_session=%s" % (default_session_data))
 jc.zipOut = root.find("metadata/general/zipOut").text == "true"
 general_data = {
 "analytics": root.find("metadata/general/analytics").text,
 "primary_color": root.find("metadata/general/primary_color").text,
 "secondary_color": root.find("metadata/general/secondary_color").text,

Mercurial > repos > fubar > jbrowse2

comparison jbrowse2.py @ 59:f807e219cec3 draft