Mercurial > repos > fubar > jbrowse2
diff jbrowse2.py @ 15:cce8dacb240f draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 1a20cf06627d429a211427753f223467188dbe7f-dirty
| author | fubar |
|---|---|
| date | Thu, 25 Jan 2024 07:39:41 +0000 |
| parents | 7c2e28e144f3 |
| children | 4c201a3d4755 |
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--- a/jbrowse2.py Mon Jan 22 12:05:09 2024 +0000 +++ b/jbrowse2.py Thu Jan 25 07:39:41 2024 +0000 @@ -18,7 +18,7 @@ logging.basicConfig(level=logging.INFO) log = logging.getLogger("jbrowse") -JB2VER = "v2.10.0" +JB2VER = "v2.10.1" # version pinned for cloning TODAY = datetime.datetime.now().strftime("%Y-%m-%d") @@ -458,10 +458,10 @@ self.genome_name = ( genome_name # first one for all tracks - other than paf ) - if self.config_json.get("assemblies", None): - self.config_json["assemblies"] += assemblies - else: - self.config_json["assemblies"] = assemblies + if self.config_json.get("assemblies", None): + self.config_json["assemblies"] += assemblies + else: + self.config_json["assemblies"] = assemblies def make_assembly(self, fapath, gname): hashData = [ @@ -727,6 +727,14 @@ os.unlink(gff3) def add_bigwig(self, data, trackData): + """ "type": "LinearWiggleDisplay", + "configuration": {}, + "selectedRendering": "", + "resolution": 1, + "posColor": "rgb(228, 26, 28)", + "negColor": "rgb(255, 255, 51)", + "constraints": {} + """ url = "%s.bigwig" % trackData["label"] # slashes in names cause path trouble dest = os.path.join(self.outdir, url) @@ -756,7 +764,7 @@ trackDict["style"] = style_json self.tracksToAdd.append(trackDict) self.trackIdlist.append(tId) - logging.debug("#### wig trackData=%s" % str(trackData)) + logging.info("#### wig trackData=%s" % str(trackData)) def add_bam(self, data, trackData, bamOpts, bam_index=None, **kwargs): tId = trackData["label"] @@ -949,11 +957,11 @@ tname = trackData["name"] tId = trackData["label"] pgname = pafOpts["genome_label"] - if len(pgname.split() > 1): + if len(pgname.split()) > 1: pgname = pgname.split()[ 0 ] # trouble from spacey names in command lines avoidance - asstrack, gname = self.make_assembly(pafOpts["genome"], pgname) + asstrack = self.make_assembly(pafOpts["genome"], pgname) self.genome_names.append(pgname) if self.config_json.get("assemblies", None): self.config_json["assemblies"].append(asstrack) @@ -961,7 +969,6 @@ 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) @@ -975,6 +982,16 @@ "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 @@ -1130,6 +1147,10 @@ ) elif dataset_ext == "vcf": self.add_vcf(dataset_path, outputTrackConfig) + elif dataset_ext == "paf": + self.add_paf( + 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 @@ -1177,7 +1198,7 @@ ddl = data["defaultLocation"] loc_match = re.search( r"^([^:]+):(\d+)\.+(\d+)$", ddl - ) # was re.search(r"^(\w.+):(\d+)\.+(\d+)$" + ) if loc_match: refName = loc_match.group(1) start = int(loc_match.group(2)) @@ -1407,6 +1428,15 @@ } track_conf["conf"] = etree_to_dict(track.find("options")) + track_conf["category"] = track.attrib["cat"] + track_conf["format"] = track.attrib["format"] + try: + # Only pertains to gff3 + blastxml. TODO? + track_conf["style"] = {t.tag: t.text for t in track.find("options/style")} + except TypeError: + track_conf["style"] = {} + pass + track_conf["conf"] = etree_to_dict(track.find("options")) keys = jc.process_annotations(track_conf) if keys: @@ -1422,34 +1452,26 @@ default_session_data["style_labels"][key] = track_conf.get( "style_labels", None ) - - default_session_data["defaultLocation"] = root.find( - "metadata/general/defaultLocation" - ).text - default_session_data["session_name"] = root.find( - "metadata/general/session_name" - ).text - - 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, - "tertiary_color": root.find("metadata/general/tertiary_color").text, - "quaternary_color": root.find("metadata/general/quaternary_color").text, - "font_size": root.find("metadata/general/font_size").text, - } - track_conf["category"] = track.attrib["cat"] - track_conf["format"] = track.attrib["format"] - try: - # Only pertains to gff3 + blastxml. TODO? - track_conf["style"] = {t.tag: t.text for t in track.find("options/style")} - except TypeError: - track_conf["style"] = {} - pass - track_conf["conf"] = etree_to_dict(track.find("options")) - jc.add_general_configuration(general_data) - jc.config_json["tracks"] = jc.tracksToAdd + default_session_data["defaultLocation"] = root.find( + "metadata/general/defaultLocation" + ).text + default_session_data["session_name"] = root.find( + "metadata/general/session_name" + ).text + 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, + "tertiary_color": root.find("metadata/general/tertiary_color").text, + "quaternary_color": root.find("metadata/general/quaternary_color").text, + "font_size": root.find("metadata/general/font_size").text, + } + jc.add_general_configuration(general_data) + trackconf = jc.config_json.get("tracks", None) + if trackconf: + jc.config_json["tracks"].update(jc.tracksToAdd) + else: + jc.config_json["tracks"] = jc.tracksToAdd jc.write_config() jc.add_default_session(default_session_data) - # jc.text_index() not sure what broke here.