Mercurial > repos > fubar > jbrowse2
diff jbrowse2.py @ 85:3b2ff9864995 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 264a3d6c7a29f396d359f33164ddf2cb1d9903f8-dirty
| author | fubar |
|---|---|
| date | Tue, 09 Apr 2024 00:26:49 +0000 |
| parents | 746eae952c18 |
| children | 408781c080fc |
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--- a/jbrowse2.py Wed Apr 03 02:56:39 2024 +0000 +++ b/jbrowse2.py Tue Apr 09 00:26:49 2024 +0000 @@ -475,12 +475,7 @@ 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"] - wstyle = { - "displays": [ - style_data, - ] - } - return wstyle + return style_data def getNrow(self, url): useuri = url.startswith("https://") or url.startswith("http://") @@ -681,18 +676,23 @@ """ tId = trackData["label"] + wasCool = trackData["wasCool"] # can be served - if public. # dsId = trackData["metadata"]["dataset_id"] # url = "%s/api/datasets/%s/display?to_ext=hic " % (self.giURL, dsId) useuri = trackData["useuri"].lower() == "yes" + logging.debug("wasCool=%s, data=%s, tId=%s" % (wasCool, data, tId)) if useuri: uri = data else: - uri = tId - # slashes in names cause path trouble - dest = os.path.join(self.outdir, uri) - cmd = ["cp", data, dest] - self.subprocess_check_call(cmd) + uri = tId + ".hic" + if not wasCool: + dest = os.path.join(self.outdir, uri) + if not os.path.exists(dest): + cmd = ["cp", data, dest] + self.subprocess_check_call(cmd) + else: + logging.error("not wasCool but %s exists" % dest) categ = trackData["category"] trackDict = { "type": "HicTrack", @@ -854,10 +854,10 @@ self.tracksToAdd[trackData["assemblyNames"]].append(trackDict) self.trackIdlist.append(tId) - def add_bam(self, data, trackData, bam_index=None, **kwargs): + def add_bam(self, data, trackData, bam_indexes=None, **kwargs): tId = trackData["label"] + realFName = trackData["key"] useuri = trackData["useuri"].lower() == "yes" - bindex = bam_index categ = trackData["category"] if useuri: url = data @@ -867,6 +867,20 @@ url = fname bindex = fname + ".bai" self.subprocess_check_call(["cp", data, dest]) + bi = bam_indexes.split() + bam_index = [ + x.split(",")[1].strip() + for x in bi + if "," in x and x.split(",")[0].strip() == realFName + ] + if len(bam_index) > 0: + bam_index = bam_index[0] + else: + bam_index = None + logging.debug( + "===realFName=%s got %s as bi, %s for bam_index" + % (realFName, bi, bam_index) + ) if bam_index is not None and os.path.exists(bam_index): if not os.path.exists(bindex): # bai most probably made by galaxy and stored in galaxy dirs, need to copy it to dest @@ -909,8 +923,9 @@ self.tracksToAdd[trackData["assemblyNames"]].append(trackDict) self.trackIdlist.append(tId) - def add_cram(self, data, trackData, cram_index=None, **kwargs): + def add_cram(self, data, trackData, cram_indexes=None, **kwargs): tId = trackData["label"] + realFName = trackData["key"] categ = trackData["category"] useuri = trackData["useuri"].lower() == "yes" gsa = self.assmeta.get(trackData["assemblyNames"], None) @@ -926,7 +941,21 @@ dest = os.path.join(self.outdir, fname) url = fname self.subprocess_check_call(["cp", data, dest]) - if cram_index is not None and os.path.exists(cram_index): + ci = cram_indexes.split() + cram_index = [ + x.split(",")[1].strip() + for x in ci + if "," in x and x.split(",")[0] == realFName + ] + if len(cram_index) > 0: + cram_index = cram_index[0] + else: + cram_index = None + logging.debug( + "=== for %s got %s as cram_indexes, %s for cram_index" + % (realFName, cram_indexes, cram_index) + ) + if cram_index and os.path.exists(cram_index): if not os.path.exists(dest + ".crai"): # most probably made by galaxy and stored in galaxy dirs, need to copy it to dest self.subprocess_check_call( @@ -1088,7 +1117,7 @@ if useuri: url = data else: - url = tId + '.gz' + url = tId + ".gz" dest = "%s/%s" % (self.outdir, url) self._sort_bed(data, dest) trackDict = { @@ -1203,25 +1232,16 @@ }, ], } - if nrow > 20000: + if nrow > 10000: style_json = { - "displays": [ - { - "type": "LGVSyntenyDisplay", - "displayId": "%s-LGVSyntenyDisplay" % tId, - } - ] + "type": "LGVSyntenyDisplay", + "displayId": "%s-LGVSyntenyDisplay" % tId, } else: style_json = { - "displays": [ - { - "type": "LinearBasicDisplay", - "displayId": "%s-LinearBasicDisplay" % tId, - } - ] + "type": "LinearBasicDisplay", + "displayId": "%s-LinearBasicDisplay" % tId, } - trackDict["style"] = style_json self.tracksToAdd[trackData["assemblyNames"]].append(trackDict) self.trackIdlist.append(tId) @@ -1266,13 +1286,15 @@ outputTrackConfig, ) elif dataset_ext in ("hic", "juicebox_hic"): + outputTrackConfig["wasCool"] = False self.add_hic( dataset_path, outputTrackConfig, ) elif dataset_ext in ("cool", "mcool", "scool"): hic_url = outputTrackConfig["label"] - hic_path = os.path.join(self.outdir, hic_url) + hic_path = os.path.join(self.outdir, hic_url) + ".hic" + outputTrackConfig["wasCool"] = True self.subprocess_check_call( [ "hictk", @@ -1284,8 +1306,12 @@ hic_path, ] ) + logging.debug( + "### ext=cool: wasCool=%s, hic_path=%s" + % (outputTrackConfig["wasCool"], hic_path) + ) self.add_hic( - hic_url, + hic_path, outputTrackConfig, ) elif dataset_ext in ("bed",): @@ -1306,17 +1332,19 @@ ) elif dataset_ext == "bam": real_indexes = track["conf"]["options"]["bam"]["bam_index"] + logging.debug("**** add bam got %s for indexes" % real_indexes) self.add_bam( dataset_path, outputTrackConfig, - bam_index=real_indexes, + bam_indexes=real_indexes, ) elif dataset_ext == "cram": real_indexes = track["conf"]["options"]["cram"]["cram_index"] + logging.debug("**** add cram got %s for indexes" % real_indexes) self.add_cram( dataset_path, outputTrackConfig, - cram_index=real_indexes, + cram_indexes=real_indexes, ) elif dataset_ext == "blastxml": self.add_blastxml( @@ -1355,85 +1383,82 @@ else: session_json = {} session_views = [] - for gnome in self.genome_names: + for gnome in self.assmeta.keys(): # assemblies have their own tracks tracks_data = [] for track_conf in self.tracksToAdd[gnome]: tId = track_conf["trackId"] - track_types[tId] = track_conf["type"] - style_data = default_data[gnome]["style"].get(tId, None) - if not style_data: - logging.debug( - "### No style data in default data %s for %s" - % (default_data, tId) + if tId in default_data[gnome]["visibility"]["default_on"]: + track_types[tId] = track_conf["type"] + style_data = default_data[gnome]["style"].get(tId, None) + if not style_data: + logging.debug( + "### No style data for %s in available default data %s" + % (tId, default_data) + ) + style_data = {"type": "LinearBasicDisplay"} + if "displays" in track_conf: + disp = track_conf["displays"][0]["type"] + style_data["type"] = 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], + } ) - style_data = {"type": "LinearBasicDisplay"} - if "displays" in track_conf: - disp = track_conf["displays"][0]["type"] - style_data["type"] = 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], - } - ) - # paf genomes have no tracks associated so nothing for the view - if len(tracks_data) > 0: - view_json = { - "type": "LinearGenomeView", - "offsetPx": 0, - "minimized": False, - "tracks": tracks_data, + view_json = { + "type": "LinearGenomeView", + "offsetPx": 0, + "minimized": False, + "tracks": tracks_data, + } + logging.debug( + "Looking for %s in self.ass_ %s" % (gnome, self.ass_first_contigs) + ) + first = [x for x in self.ass_first_contigs if x[0] == gnome] + if len(first) > 0: + [gnome, refName, end] = first[0] + start = 0 + end = int(end) + drdict = { + "refName": refName, + "start": start, + "end": end, + "reversed": False, + "assemblyName": gnome, } - logging.debug( - "Looking for %s in self.ass_ %s" % (gnome, self.ass_first_contigs) + else: + ddl = default_data.get("defaultLocation", None) + if ddl: + loc_match = re.search(r"^([^:]+):([\d,]*)\.*([\d,]*)$", ddl) + # allow commas like 100,000 but ignore as integer + if loc_match: + refName = loc_match.group(1) + drdict["refName"] = refName + if loc_match.group(2) > "": + drdict["start"] = int(loc_match.group(2).replace(",", "")) + if loc_match.group(3) > "": + drdict["end"] = int(loc_match.group(3).replace(",", "")) + else: + logging.info( + "@@@ regexp could not match contig:start..end in the supplied location %s - please fix" + % ddl + ) + if drdict.get("refName", None): + # TODO displayedRegions is not just zooming to the region, it hides the rest of the chromosome + view_json["displayedRegions"] = [ + drdict, + ] + logging.info("@@@ defaultlocation %s for default session" % drdict) + else: + logging.info( + "@@@ no track location for default session - please add one!" ) - first = [x for x in self.ass_first_contigs if x[0] == gnome] - if len(first) > 0: - [gnome, refName, end] = first[0] - start = 0 - end = int(end) - drdict = { - "refName": refName, - "start": start, - "end": end, - "reversed": False, - "assemblyName": gnome, - } - else: - ddl = default_data.get("defaultLocation", None) - if ddl: - loc_match = re.search(r"^([^:]+):([\d,]*)\.*([\d,]*)$", ddl) - # allow commas like 100,000 but ignore as integer - if loc_match: - refName = loc_match.group(1) - drdict["refName"] = refName - if loc_match.group(2) > "": - drdict["start"] = int( - loc_match.group(2).replace(",", "") - ) - if loc_match.group(3) > "": - drdict["end"] = int(loc_match.group(3).replace(",", "")) - else: - logging.info( - "@@@ regexp could not match contig:start..end in the supplied location %s - please fix" - % ddl - ) - 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, - ] - logging.info("@@@ defaultlocation %s for default session" % drdict) - else: - logging.info( - "@@@ no track location for default session - please add one!" - ) - session_views.append(view_json) + session_views.append(view_json) session_name = default_data.get("session_name", "New session") for key, value in mapped_chars.items(): session_name = session_name.replace(value, key) @@ -1455,17 +1480,7 @@ Included on request of the new codeowner, from Anthony's IUC PR. Had to be fixed to keep each assembly with the associated tracks for a default view. Originally used only the first assembly, putting all tracks there and so breaking some - when tested with 2 or more. Seems ironic that this vital feature could not have ever been tested - given that my declining to add it was the basis for a reviewer's rejection of my original IUC PR. - A simple 2 line diff apparently. - - The technical problem is that this index.html hack breaks the promise of all the form fields - for track controls such as visibility default that were working mostly. They need to be removed from the form by whoever - thought this method was a good solution to the JB2 bug breaking config.json style default - view coordinates. - - And no, dear reviewer of this code, please leave this piece of history. - It is true and I prefer that it remain here to document my considerable discomfort at this unfair treatment. + when tested with 2 or more. ---------------------------------------------------------- Add some default session settings: set some assemblies/tracks on/off @@ -1648,7 +1663,7 @@ trackfiles = track.findall("files/trackFile") if trackfiles: - for x in track.findall("files/trackFile"): + for x in trackfiles: track_conf["label"] = x.attrib["label"] track_conf["useuri"] = x.attrib["useuri"] if is_multi_bigwig: @@ -1698,8 +1713,6 @@ track_conf["category"] = track.attrib["cat"] track_conf["format"] = track.attrib["format"] track_conf["conf"] = etree_to_dict(track.find("options")) - track_conf["category"] = track.attrib["cat"] - track_conf["format"] = track.attrib["format"] keys = jc.process_annotations(track_conf) if keys: @@ -1708,20 +1721,24 @@ if not vis: vis = "default_off" default_session_data[assref_name]["visibility"][vis].append(key) - if track.find("options/style"): - default_session_data[assref_name]["style"][key] = { - item.tag: parse_style_conf(item) - for item in track.find("options/style") - } - else: - default_session_data[assref_name]["style"][key] = {} - logging.debug("no options/style found for %s" % (key)) - - if track.find("options/style_labels"): - default_session_data[assref_name]["style_labels"][key] = { - item.tag: parse_style_conf(item) - for item in track.find("options/style_labels") - } + trakdat = jc.tracksToAdd[assref_name] + stile = {} + for trak in trakdat: + if trak["trackId"] == key: + stile = trak.get("style", {}) + if track.find("options/style"): + supdate = { + item.tag: parse_style_conf(item) + for item in track.find("options/style") + } + stile.update(supdate) + default_session_data[assref_name]["style"][key] = stile + logging.debug("@@@ for %s got style=%s" % (key, stile)) + if track.find("options/style_labels"): + default_session_data[assref_name]["style_labels"][key] = { + item.tag: parse_style_conf(item) + for item in track.find("options/style_labels") + } default_session_data[assref_name]["tracks"].append(key) default_session_data["defaultLocation"] = root.find( "metadata/general/defaultLocation"