Mercurial > repos > fubar > jbrowse2

comparison jbrowse2.py @ 109:27e9ddaaf325 draft

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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
comparison
equal deleted inserted replaced
108:5d1259b88c27 109:27e9ddaaf325
672 trackDict = { 672 trackDict = {
673 "type": "HicTrack", 673 "type": "HicTrack",
674 "trackId": tId, 674 "trackId": tId,
675 "name": trackData["name"], 675 "name": trackData["name"],
676 "assemblyNames": [trackData["assemblyNames"]], 676 "assemblyNames": [trackData["assemblyNames"]],
677 "displays": [
678 {
679 "type": "LinearHicDisplay",
680 "displayId": "%s-LinearHicDisplay" % tId,
681 }
682 ],
677 "category": [ 683 "category": [
678 categ, 684 categ,
679 ], 685 ],
680 "adapter": {"type": "HicAdapter", "hicLocation": {"uri": uri}}, 686 "adapter": {"type": "HicAdapter", "hicLocation": {"uri": uri}},
687
681 } 688 }
682 self.tracksToAdd[trackData["assemblyNames"]].append(copy.copy(trackDict)) 689 self.tracksToAdd[trackData["assemblyNames"]].append(copy.copy(trackDict))
683 self.trackIdlist.append(copy.copy(tId)) 690 self.trackIdlist.append(tId)
684 691
685 def add_maf(self, data, trackData): 692 def add_maf(self, data, trackData):
686 """ 693 """
687 from https://github.com/cmdcolin/maf2bed 694 from https://github.com/cmdcolin/maf2bed
688 Note: Both formats start with a MAF as input, and note that your MAF file should contain the species name and chromosome name 695 Note: Both formats start with a MAF as input, and note that your MAF file should contain the species name and chromosome name
752 ], 759 ],
753 } 760 }
754 style_json = self._prepare_track_style(trackDict) 761 style_json = self._prepare_track_style(trackDict)
755 trackDict["style"] = style_json 762 trackDict["style"] = style_json
756 self.tracksToAdd[gname].append(copy.copy(trackDict)) 763 self.tracksToAdd[gname].append(copy.copy(trackDict))
757 self.trackIdlist.append(copy.copy(tId)) 764 self.trackIdlist.append(tId)
758 if self.config_json.get("plugins", None): 765 if self.config_json.get("plugins", None):
759 self.config_json["plugins"].append(mafPlugin["plugins"][0]) 766 self.config_json["plugins"].append(mafPlugin["plugins"][0])
760 else: 767 else:
761 self.config_json.update(mafPlugin) 768 self.config_json.update(mafPlugin)
762 769
826 ], 833 ],
827 } 834 }
828 style_json = self._prepare_track_style(trackDict) 835 style_json = self._prepare_track_style(trackDict)
829 trackDict["style"] = style_json 836 trackDict["style"] = style_json
830 self.tracksToAdd[trackData["assemblyNames"]].append(copy.copy(trackDict)) 837 self.tracksToAdd[trackData["assemblyNames"]].append(copy.copy(trackDict))
831 self.trackIdlist.append(copy.copy(tId)) 838 self.trackIdlist.append(tId)
832 839
833 def add_bam(self, data, trackData, bam_indexes=None, **kwargs): 840 def add_bam(self, data, trackData, bam_indexes=None, **kwargs):
834 tId = trackData["label"] 841 tId = trackData["label"]
835 realFName = trackData["path"] 842 realFName = trackData["path"]
836 useuri = trackData["useuri"].lower() == "yes" 843 useuri = trackData["useuri"].lower() == "yes"
883 ], 890 ],
884 } 891 }
885 style_json = self._prepare_track_style(trackDict) 892 style_json = self._prepare_track_style(trackDict)
886 trackDict["style"] = style_json 893 trackDict["style"] = style_json
887 self.tracksToAdd[trackData["assemblyNames"]].append(copy.copy(trackDict)) 894 self.tracksToAdd[trackData["assemblyNames"]].append(copy.copy(trackDict))
888 self.trackIdlist.append(copy.copy(tId)) 895 self.trackIdlist.append(tId)
889 896
890 def add_cram(self, data, trackData, cram_indexes=None, **kwargs): 897 def add_cram(self, data, trackData, cram_indexes=None, **kwargs):
891 tId = trackData["label"] 898 tId = trackData["label"]
892 realFName = trackData["path"] 899 realFName = trackData["path"]
893 categ = trackData["category"] 900 categ = trackData["category"]
949 ], 956 ],
950 } 957 }
951 style_json = self._prepare_track_style(trackDict) 958 style_json = self._prepare_track_style(trackDict)
952 trackDict["style"] = style_json 959 trackDict["style"] = style_json
953 self.tracksToAdd[trackData["assemblyNames"]].append(copy.copy(trackDict)) 960 self.tracksToAdd[trackData["assemblyNames"]].append(copy.copy(trackDict))
954 self.trackIdlist.append(copy.copy(tId)) 961 self.trackIdlist.append(tId)
955 962
956 def add_vcf(self, data, trackData): 963 def add_vcf(self, data, trackData):
957 tId = trackData["label"] 964 tId = trackData["label"]
958 categ = trackData["category"] 965 categ = trackData["category"]
959 useuri = trackData["useuri"].lower() == "yes" 966 useuri = trackData["useuri"].lower() == "yes"
999 ], 1006 ],
1000 } 1007 }
1001 style_json = self._prepare_track_style(trackDict) 1008 style_json = self._prepare_track_style(trackDict)
1002 trackDict["style"] = style_json 1009 trackDict["style"] = style_json
1003 self.tracksToAdd[trackData["assemblyNames"]].append(copy.copy(trackDict)) 1010 self.tracksToAdd[trackData["assemblyNames"]].append(copy.copy(trackDict))
1004 self.trackIdlist.append(copy.copy(tId)) 1011 self.trackIdlist.append(tId)
1005 1012
1006 def _sort_gff(self, data, dest): 1013 def _sort_gff(self, data, dest):
1007 # Only index if not already done 1014 # Only index if not already done
1008 if not os.path.exists(dest): 1015 if not os.path.exists(dest):
1009 cmd = "jbrowse sort-gff '%s' | bgzip -c > '%s'" % ( 1016 cmd = "jbrowse sort-gff '%s' | bgzip -c > '%s'" % (
1062 ], 1069 ],
1063 } 1070 }
1064 style_json = self._prepare_track_style(trackDict) 1071 style_json = self._prepare_track_style(trackDict)
1065 trackDict["style"] = style_json 1072 trackDict["style"] = style_json
1066 self.tracksToAdd[trackData["assemblyNames"]].append(copy.copy(trackDict)) 1073 self.tracksToAdd[trackData["assemblyNames"]].append(copy.copy(trackDict))
1067 self.trackIdlist.append(copy.copy(tId)) 1074 self.trackIdlist.append(tId)
1068 1075
1069 def add_bed(self, data, ext, trackData): 1076 def add_bed(self, data, ext, trackData):
1070 bedPlugin = {"name": "BedScorePlugin", "umdLoc": { "uri": "bedscoreplugin.js" } } 1077 bedPlugin = {"name": "BedScorePlugin", "umdLoc": { "uri": "bedscoreplugin.js" } }
1071 tId = trackData["label"] 1078 tId = trackData["label"]
1072 categ = trackData["category"] 1079 categ = trackData["category"]
1128 if self.config_json.get("plugins", None): 1135 if self.config_json.get("plugins", None):
1129 self.config_json["plugins"].append(bedPlugin) 1136 self.config_json["plugins"].append(bedPlugin)
1130 else: 1137 else:
1131 self.config_json["plugins"] = [bedPlugin,] 1138 self.config_json["plugins"] = [bedPlugin,]
1132 self.tracksToAdd[trackData["assemblyNames"]].append(copy.copy(trackDict)) 1139 self.tracksToAdd[trackData["assemblyNames"]].append(copy.copy(trackDict))
1133 self.trackIdlist.append(copy.copy(tId)) 1140 self.trackIdlist.append(tId)
1134 1141
1135 def add_paf(self, data, trackData, pafOpts, **kwargs): 1142 def add_paf(self, data, trackData, pafOpts, **kwargs):
1136 tname = trackData["name"] 1143 tname = trackData["name"]
1137 tId = trackData["label"] 1144 tId = trackData["label"]
1138 url = tId 1145 url = tId
1210 "type": "LinearBasicDisplay", 1217 "type": "LinearBasicDisplay",
1211 "displayId": "%s-LinearBasicDisplay" % tId, 1218 "displayId": "%s-LinearBasicDisplay" % tId,
1212 } 1219 }
1213 trackDict["style"] = style_json 1220 trackDict["style"] = style_json
1214 self.tracksToAdd[trackData["assemblyNames"]].append(copy.copy(trackDict)) 1221 self.tracksToAdd[trackData["assemblyNames"]].append(copy.copy(trackDict))
1215 self.trackIdlist.append(copy.copy(tId)) 1222 self.trackIdlist.append(tId)
1216 1223
1217 def process_annotations(self, track): 1224 def process_annotations(self, track):
1218 category = track["category"].replace("__pd__date__pd__", TODAY) 1225 category = track["category"].replace("__pd__date__pd__", TODAY)
1219 tt1 = ",/ :;\\" 1226 tt1 = ",/ :;\\"
1220 tt2 = "______" 1227 tt2 = "______"
1355 for track_conf in self.tracksToAdd[gnome]: 1362 for track_conf in self.tracksToAdd[gnome]:
1356 tId = track_conf["trackId"] 1363 tId = track_conf["trackId"]
1357 if tId in default_data[gnome]["visibility"]["default_on"]: 1364 if tId in default_data[gnome]["visibility"]["default_on"]:
1358 track_types[tId] = track_conf["type"] 1365 track_types[tId] = track_conf["type"]
1359 display = {"type": "linearBasicDisplay"} 1366 display = {"type": "linearBasicDisplay"}
1360 if "displays" in track_conf: 1367 if track_conf.get("displays", None):
1361 display["type"] = track_conf["displays"][0]["type"] 1368 display["type"] = track_conf["displays"][0]["type"]
1362 display["configuration"] = track_conf["displays"][0]["displayId"] 1369 display["configuration"] = track_conf["displays"][0]["displayId"]
1370 else:
1371 logging.debug("no display in track_conf for %s" % tId)
1363 if track_conf.get("style_labels", None): 1372 if track_conf.get("style_labels", None):
1364 # TODO fix this: it should probably go in a renderer block (SvgFeatureRenderer) but still does not work 1373 # TODO fix this: it should probably go in a renderer block (SvgFeatureRenderer) but still does not work
1365 # TODO move this to per track displays? 1374 # TODO move this to per track displays?
1366 style_data["labels"] = track_conf["style_labels"] 1375 style_data["labels"] = track_conf["style_labels"]
1367 tracks_data.append( 1376 tracks_data.append(