Mercurial > repos > fubar > jbrowse2

comparison jbrowse2.py @ 112:56f9a6e0fe80 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 566509061b742b73c8dd1a1db6813fbf6a7a3792
author bgruening
date Thu, 04 Jul 2024 08:40:21 +0000
parents c017111e976a
children 794aecef8327
comparison
equal deleted inserted replaced
111:0a532764dcfa 112:56f9a6e0fe80
705 } 705 }
706 ] 706 ]
707 } 707 }
708 categ = trackData["category"] 708 categ = trackData["category"]
709 fname = tId 709 fname = tId
710 dest = "%s/%s" % (self.outdir, fname) 710 dest = os.path.join(self.outdir, fname)
711 gname = trackData["assemblyNames"] 711 gname = trackData["assemblyNames"]
712 712
713 cmd = [ 713 cmd = [
714 "bash", 714 "bash",
715 os.path.join(INSTALLED_TO, "convertMAF.sh"), 715 os.path.join(INSTALLED_TO, "convertMAF.sh"),
1072 trackDict["style"] = style_json 1072 trackDict["style"] = style_json
1073 self.tracksToAdd[trackData["assemblyNames"]].append(copy.copy(trackDict)) 1073 self.tracksToAdd[trackData["assemblyNames"]].append(copy.copy(trackDict))
1074 self.trackIdlist.append(tId) 1074 self.trackIdlist.append(tId)
1075 1075
1076 def add_bed(self, data, ext, trackData): 1076 def add_bed(self, data, ext, trackData):
1077 bedPlugin = {"name": "BedScorePlugin", "umdLoc": { "uri": "bedscoreplugin.js" } } 1077 bedPlugin = {"name": "BedScorePlugin", "umdLoc": {"uri": "bedscoreplugin.js"}}
1078 tId = trackData["label"] 1078 tId = trackData["label"]
1079 categ = trackData["category"] 1079 categ = trackData["category"]
1080 useuri = trackData["useuri"].lower() == "yes" 1080 useuri = trackData["useuri"].lower() == "yes"
1081 if useuri: 1081 if useuri:
1082 url = data 1082 url = data
1083 else: 1083 else:
1084 url = tId + ".gz" 1084 url = tId + ".gz"
1085 dest = os.path.join(self.outdir, url) 1085 dest = os.path.join(self.outdir, url)
1086 self._sort_bed(data, dest) 1086 self._sort_bed(data, dest)
1087 if True or trackData.get("usebedscore",None): 1087 if True or trackData.get("usebedscore", None):
1088 bedgzlocation = { 1088 bedgzlocation = {
1089 "uri": url, 1089 "uri": url,
1090 "columnNames": ["chr","start","end","name","score"], 1090 "columnNames": ["chr", "start", "end", "name", "score"],
1091 "scoreColumn": "score", 1091 "scoreColumn": "score",
1092 } 1092 }
1093 else: 1093 else:
1094 bedgzlocation = { 1094 bedgzlocation = {
1095 "uri": url, 1095 "uri": url,
1096 } 1096 }
1097 trackDict = { 1097 trackDict = {
1098 "type": "FeatureTrack", 1098 "type": "FeatureTrack",
1099 "trackId": tId, 1099 "trackId": tId,
1100 "name": trackData["name"], 1100 "name": trackData["name"],
1101 "assemblyNames": [trackData["assemblyNames"]], 1101 "assemblyNames": [trackData["assemblyNames"]],
1116 "type": "LinearBasicDisplay", 1116 "type": "LinearBasicDisplay",
1117 "displayId": "%s-LinearBasicDisplay" % tId, 1117 "displayId": "%s-LinearBasicDisplay" % tId,
1118 "renderer": { 1118 "renderer": {
1119 "type": "SvgFeatureRenderer", 1119 "type": "SvgFeatureRenderer",
1120 "color1": "jexl:customColor(feature)", 1120 "color1": "jexl:customColor(feature)",
1121 }, 1121 },
1122 }, 1122 },
1123 { 1123 {
1124 "type": "LinearPileupDisplay", 1124 "type": "LinearPileupDisplay",
1125 "displayId": "%s-LinearPileupDisplay" % tId, 1125 "displayId": "%s-LinearPileupDisplay" % tId,
1126 }, 1126 },
1169 passnames.append(gname) 1169 passnames.append(gname)
1170 useuri = pafOpts["useuri"] == "true" 1170 useuri = pafOpts["useuri"] == "true"
1171 if gname not in self.genome_names: 1171 if gname not in self.genome_names:
1172 # ignore if already there - eg for duplicates among pafs. 1172 # ignore if already there - eg for duplicates among pafs.
1173 asstrack, first_contig = self.make_assembly(gpath, gname, useuri) 1173 asstrack, first_contig = self.make_assembly(gpath, gname, useuri)
1174 self.genome_names.append(copy.copy(gname)) 1174 self.genome_names.append(gname)
1175 self.tracksToAdd[gname] = [] 1175 self.tracksToAdd[gname] = []
1176 self.assemblies.append(copy.copy(asstrack)) 1176 self.assemblies.append(copy.copy(asstrack))
1177 self.ass_first_contigs.append(copy.copy(first_contig)) 1177 self.ass_first_contigs.append(copy.copy(first_contig))
1178 trackDict = { 1178 trackDict = {
1179 "type": "SyntenyTrack", 1179 "type": "SyntenyTrack",
1223 1223
1224 def process_annotations(self, track): 1224 def process_annotations(self, track):
1225 category = track["category"].replace("__pd__date__pd__", TODAY) 1225 category = track["category"].replace("__pd__date__pd__", TODAY)
1226 tt1 = ",/ :;\\" 1226 tt1 = ",/ :;\\"
1227 tt2 = "______" 1227 tt2 = "______"
1228 labttab = str.maketrans(tt1,tt2) 1228 labttab = str.maketrans(tt1, tt2)
1229 for trackIndex, ( 1229 for trackIndex, (
1230 dataset_path, 1230 dataset_path,
1231 dataset_ext, 1231 dataset_ext,
1232 useuri, 1232 useuri,
1233 track_human_label, 1233 track_human_label,
1333 track["conf"]["options"]["paf"], 1333 track["conf"]["options"]["paf"],
1334 ) 1334 )
1335 else: 1335 else:
1336 logging.warning("Do not know how to handle %s", dataset_ext) 1336 logging.warning("Do not know how to handle %s", dataset_ext)
1337 # Return non-human label for use in other fields 1337 # Return non-human label for use in other fields
1338 logging.debug("### processanno ext=%s trackstoadd = %s" % (dataset_ext, self.tracksToAdd))
1339 yield outputTrackConfig["label"] 1338 yield outputTrackConfig["label"]
1340 1339
1341 def add_default_session(self, default_data): 1340 def add_default_session(self, default_data):
1342 """ 1341 """
1343 default session settings are hard and fragile. 1342 default session settings are hard and fragile.
1344 .add_default_view() and other configuration code adapted from 1343 .add_default_view() and other configuration code adapted from
1345 https://github.com/abretaud/tools-iuc/blob/jbrowse2/tools/jbrowse2/jbrowse2.py 1344 https://github.com/abretaud/tools-iuc/blob/jbrowse2/tools/jbrowse2/jbrowse2.py
1346 """ 1345 """
1347 # TODO using the default session for now, but check out session specs in the future https://github.com/GMOD/jbrowse-components/issues/2708 1346 # TODO using the default session for now, but check out session specs in the future https://github.com/GMOD/jbrowse-components/issues/2708
1348 bpPerPx = self.bpPerPx # Browser window width is unknown and default session cannot be used to figure it out in JB2 code so could be 200-2000+ pixels. 1347 bpPerPx = self.bpPerPx # Browser window width is unknown and default session cannot be used to figure it out in JB2 code so could be 200-2000+ pixels.
1349 track_types = {} 1348 track_types = {}
1350 with open(self.config_json_file, "r") as config_file: 1349 with open(self.config_json_file, "r") as config_file:
1351 config_json = json.load(config_file) 1350 config_json = json.load(config_file)
1352 if self.config_json: 1351 if self.config_json:
1353 config_json.update(self.config_json) 1352 config_json.update(self.config_json)
1372 else: 1371 else:
1373 logging.debug( 1372 logging.debug(
1374 "style data for %s = %s" 1373 "style data for %s = %s"
1375 % (tId, style_data) 1374 % (tId, style_data)
1376 ) 1375 )
1377 if style_data.get('type',None) == None: 1376 if style_data.get('type', None) is None:
1378 style_data["type"] = "LinearBasicDisplay" 1377 style_data["type"] = "LinearBasicDisplay"
1379 if "displays" in track_conf: 1378 if "displays" in track_conf:
1380 disp = track_conf["displays"][0]["type"] 1379 disp = track_conf["displays"][0]["type"]
1381 style_data["type"] = disp 1380 style_data["type"] = disp
1382 if track_conf.get("displays", None): 1381 if track_conf.get("displays", None):
1394 "displays": [style_data], 1393 "displays": [style_data],
1395 } 1394 }
1396 ) 1395 )
1397 first = [x for x in self.ass_first_contigs if x[0] == gnome] 1396 first = [x for x in self.ass_first_contigs if x[0] == gnome]
1398 drdict = { 1397 drdict = {
1399 "reversed": False, 1398 "reversed": False,
1400 "assemblyName": gnome, 1399 "assemblyName": gnome,
1401 } 1400 }
1402 if len(first) > 0: 1401 if len(first) > 0:
1403 [gnome, refName, end] = first[0] 1402 [gnome, refName, end] = first[0]
1404 drdict["refName"] = refName 1403 drdict["refName"] = refName
1405 drdict["start"] = 0 1404 drdict["start"] = 0
1406 end = int(end) 1405 end = int(end)
1407 drdict["end"] = end 1406 drdict["end"] = end
1408 else: 1407 else:
1409 ddl = default_data.get("defaultLocation", None) 1408 ddl = default_data.get("defaultLocation", None)
1410 if ddl: 1409 if ddl:
1411 loc_match = re.search(r"^([^:]+):([\d,]*)\.*([\d,]*)$", ddl) 1410 loc_match = re.search(r"^([^:]+):([\d,]*)\.*([\d,]*)$", ddl)
1412 # allow commas like 100,000 but ignore as integer 1411 # allow commas like 100,000 but ignore as integer
1413 if loc_match: 1412 if loc_match:
1414 refName = loc_match.group(1) 1413 refName = loc_match.group(1)
1415 drdict["refName"] = refName 1414 drdict["refName"] = refName
1416 if loc_match.group(2) > "": 1415 if loc_match.group(2) > "":
1417 drdict["start"] = int(loc_match.group(2).replace(",", "")) 1416 drdict["start"] = int(loc_match.group(2).replace(",", ""))
1423 % ddl 1422 % ddl
1424 ) 1423 )
1425 view_json = { 1424 view_json = {
1426 "type": "LinearGenomeView", 1425 "type": "LinearGenomeView",
1427 "offsetPx": 0, 1426 "offsetPx": 0,
1428 "bpPerPx" : bpPerPx, 1427 "bpPerPx": bpPerPx,
1429 "minimized": False, 1428 "minimized": False,
1430 "tracks": tracks_data 1429 "tracks": tracks_data
1431 } 1430 }
1432 if drdict.get("refName", None): 1431 if drdict.get("refName", None):
1433 # TODO displayedRegions is not just zooming to the region, it hides the rest of the chromosome 1432 # TODO displayedRegions is not just zooming to the region, it hides the rest of the chromosome
1654 trackfiles = track.findall("files/trackFile") 1653 trackfiles = track.findall("files/trackFile")
1655 if trackfiles: 1654 if trackfiles:
1656 for x in trackfiles: 1655 for x in trackfiles:
1657 isBed = False 1656 isBed = False
1658 if x.attrib['ext'] == "bed": 1657 if x.attrib['ext'] == "bed":
1659 isBed = True 1658 isBed = True
1660 track_conf["label"] = "%s_%d" % ( 1659 track_conf["label"] = "%s_%d" % (
1661 x.attrib["label"].replace(" ", "_").replace(",", "_").replace("/","_"), 1660 x.attrib["label"].replace(" ", "_").replace(",", "_").replace("/", "_"),
1662 trackI, 1661 trackI,
1663 ) 1662 )
1664 trackI += 1 1663 trackI += 1
1665 track_conf["useuri"] = x.attrib["useuri"] 1664 track_conf["useuri"] = x.attrib["useuri"]
1666 if is_multi_bigwig: 1665 if is_multi_bigwig: