Mercurial > repos > fubar > jbrowse2
diff jbrowse2.py @ 109:27e9ddaaf325 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 9de1453a009c254ab11b16ae8a56cb5c22b131bf-dirty
| author | fubar |
|---|---|
| date | Sat, 29 Jun 2024 07:22:18 +0000 |
| parents | 5d1259b88c27 |
| children | c017111e976a |
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--- a/jbrowse2.py Sat Jun 29 06:10:22 2024 +0000 +++ b/jbrowse2.py Sat Jun 29 07:22:18 2024 +0000 @@ -674,13 +674,20 @@ "trackId": tId, "name": trackData["name"], "assemblyNames": [trackData["assemblyNames"]], + "displays": [ + { + "type": "LinearHicDisplay", + "displayId": "%s-LinearHicDisplay" % tId, + } + ], "category": [ categ, ], "adapter": {"type": "HicAdapter", "hicLocation": {"uri": uri}}, + } self.tracksToAdd[trackData["assemblyNames"]].append(copy.copy(trackDict)) - self.trackIdlist.append(copy.copy(tId)) + self.trackIdlist.append(tId) def add_maf(self, data, trackData): """ @@ -754,7 +761,7 @@ style_json = self._prepare_track_style(trackDict) trackDict["style"] = style_json self.tracksToAdd[gname].append(copy.copy(trackDict)) - self.trackIdlist.append(copy.copy(tId)) + self.trackIdlist.append(tId) if self.config_json.get("plugins", None): self.config_json["plugins"].append(mafPlugin["plugins"][0]) else: @@ -828,7 +835,7 @@ style_json = self._prepare_track_style(trackDict) trackDict["style"] = style_json self.tracksToAdd[trackData["assemblyNames"]].append(copy.copy(trackDict)) - self.trackIdlist.append(copy.copy(tId)) + self.trackIdlist.append(tId) def add_bam(self, data, trackData, bam_indexes=None, **kwargs): tId = trackData["label"] @@ -885,7 +892,7 @@ style_json = self._prepare_track_style(trackDict) trackDict["style"] = style_json self.tracksToAdd[trackData["assemblyNames"]].append(copy.copy(trackDict)) - self.trackIdlist.append(copy.copy(tId)) + self.trackIdlist.append(tId) def add_cram(self, data, trackData, cram_indexes=None, **kwargs): tId = trackData["label"] @@ -951,7 +958,7 @@ style_json = self._prepare_track_style(trackDict) trackDict["style"] = style_json self.tracksToAdd[trackData["assemblyNames"]].append(copy.copy(trackDict)) - self.trackIdlist.append(copy.copy(tId)) + self.trackIdlist.append(tId) def add_vcf(self, data, trackData): tId = trackData["label"] @@ -1001,7 +1008,7 @@ style_json = self._prepare_track_style(trackDict) trackDict["style"] = style_json self.tracksToAdd[trackData["assemblyNames"]].append(copy.copy(trackDict)) - self.trackIdlist.append(copy.copy(tId)) + self.trackIdlist.append(tId) def _sort_gff(self, data, dest): # Only index if not already done @@ -1064,7 +1071,7 @@ style_json = self._prepare_track_style(trackDict) trackDict["style"] = style_json self.tracksToAdd[trackData["assemblyNames"]].append(copy.copy(trackDict)) - self.trackIdlist.append(copy.copy(tId)) + self.trackIdlist.append(tId) def add_bed(self, data, ext, trackData): bedPlugin = {"name": "BedScorePlugin", "umdLoc": { "uri": "bedscoreplugin.js" } } @@ -1130,7 +1137,7 @@ else: self.config_json["plugins"] = [bedPlugin,] self.tracksToAdd[trackData["assemblyNames"]].append(copy.copy(trackDict)) - self.trackIdlist.append(copy.copy(tId)) + self.trackIdlist.append(tId) def add_paf(self, data, trackData, pafOpts, **kwargs): tname = trackData["name"] @@ -1212,7 +1219,7 @@ } trackDict["style"] = style_json self.tracksToAdd[trackData["assemblyNames"]].append(copy.copy(trackDict)) - self.trackIdlist.append(copy.copy(tId)) + self.trackIdlist.append(tId) def process_annotations(self, track): category = track["category"].replace("__pd__date__pd__", TODAY) @@ -1357,9 +1364,11 @@ if tId in default_data[gnome]["visibility"]["default_on"]: track_types[tId] = track_conf["type"] display = {"type": "linearBasicDisplay"} - if "displays" in track_conf: + if track_conf.get("displays", None): display["type"] = track_conf["displays"][0]["type"] - display["configuration"] = track_conf["displays"][0]["displayId"] + display["configuration"] = track_conf["displays"][0]["displayId"] + else: + logging.debug("no display in track_conf for %s" % tId) 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?