Mercurial > repos > fubar > jbrowse2

comparison jbrowse2.py @ 6:79f7265f90bd draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 79e81bef99f582680d9aa4eec88980c675f3fae9-dirty
author fubar
date Tue, 09 Jan 2024 06:55:34 +0000
parents efc64d8f4b72
children b04fd993b31e
comparison
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5:efc64d8f4b72 6:79f7265f90bd
1161 # We need to know the track type from the config.json generated just before 1161 # We need to know the track type from the config.json generated just before
1162 track_types = {} 1162 track_types = {}
1163 with open(self.config_json_file, "r") as config_file: 1163 with open(self.config_json_file, "r") as config_file:
1164 config_json = json.load(config_file) 1164 config_json = json.load(config_file)
1165 1165
1166 for track_conf in self.tracksToAdd: # config_json["tracks"]: 1166 for track_conf in self.tracksToAdd:
1167 track_types[track_conf["trackId"]] = track_conf["type"] 1167 track_types[track_conf["trackId"]] = track_conf["type"]
1168 1168
1169 for on_track in data["visibility"]["default_on"]: 1169 for on_track in data["visibility"]["default_on"]:
1170 style_data = {"type": "LinearBasicDisplay", "height": 100} 1170 style_data = {"type": "LinearBasicDisplay", "height": 100}
1171 if on_track in data["style"]: 1171 if on_track in data["style"]:
1197 start = int(loc_match.group(2)) 1197 start = int(loc_match.group(2))
1198 end = int(loc_match.group(3)) 1198 end = int(loc_match.group(3))
1199 elif self.genome_name is not None: 1199 elif self.genome_name is not None:
1200 refName = self.genome_name 1200 refName = self.genome_name
1201 start = 0 1201 start = 0
1202 end = 1000 # Booh, hard coded! waiting for https://github.com/GMOD/jbrowse-components/issues/2708 1202 end = 100000 # Booh, hard coded! waiting for https://github.com/GMOD/jbrowse-components/issues/2708
1203 1203
1204 if refName is not None: 1204 if refName is not None:
1205 # TODO displayedRegions is not just zooming to the region, it hides the rest of the chromosome 1205 # TODO displayedRegions is not just zooming to the region, it hides the rest of the chromosome
1206 view_json["displayedRegions"] = [ 1206 view_json["displayedRegions"] = [
1207 { 1207 {