Mercurial > repos > fubar > jbrowse2

comparison jbrowse2.py @ 35:15da358c3108 draft

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planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 80b849766a962bac4bd0bb8cb69c118cc42699cd-dirty
author fubar
date Wed, 28 Feb 2024 10:08:57 +0000
parents 2893ef33fba9
children 7adde511daa1
comparison
equal deleted inserted replaced
34:2893ef33fba9 35:15da358c3108
1060 style_json = self._prepare_track_style(trackDict) 1060 style_json = self._prepare_track_style(trackDict)
1061 trackDict["style"] = style_json 1061 trackDict["style"] = style_json
1062 self.tracksToAdd.append(trackDict) 1062 self.tracksToAdd.append(trackDict)
1063 self.trackIdlist.append(tId) 1063 self.trackIdlist.append(tId)
1064 1064
1065 def add_hicab(self, data, trackData, hicOpts, **kwargs):
1066 rel_dest = os.path.join("data", trackData["label"] + ".hic")
1067 dest = os.path.join(self.outdir, rel_dest)
1068
1069 self.symlink_or_copy(os.path.realpath(data), dest)
1070
1071 self._add_track(
1072 trackData["label"],
1073 trackData["key"],
1074 trackData["category"],
1075 rel_dest,
1076 config={},
1077 )
1078
1079 def add_sparql(self, url, query, query_refnames, trackData):
1080
1081 json_track_data = {
1082 "type": "FeatureTrack",
1083 "trackId": id,
1084 "name": trackData["label"],
1085 "adapter": {
1086 "type": "SPARQLAdapter",
1087 "endpoint": {"uri": url, "locationType": "UriLocation"},
1088 "queryTemplate": query,
1089 },
1090 "category": [trackData["category"]],
1091 "assemblyNames": [self.genome_name],
1092 }
1093
1094 if query_refnames:
1095 json_track_data["adapter"]["refNamesQueryTemplate"]: query_refnames
1096
1097 self.subprocess_check_call(
1098 [
1099 "jbrowse",
1100 "add-track-json",
1101 "--target",
1102 os.path.join(self.outdir, "data"),
1103 json_track_data,
1104 ]
1105 )
1106
1107 # Doesn't work as of 1.6.4, might work in the future
1108 # self.subprocess_check_call([
1109 # 'jbrowse', 'add-track',
1110 # '--trackType', 'sparql',
1111 # '--name', trackData['label'],
1112 # '--category', trackData['category'],
1113 # '--target', os.path.join(self.outdir, 'data'),
1114 # '--trackId', id,
1115 # '--config', '{"queryTemplate": "%s"}' % query,
1116 # url])
1117
1118 def process_annotations(self, track): 1065 def process_annotations(self, track):
1119 category = track["category"].replace("__pd__date__pd__", TODAY) 1066 category = track["category"].replace("__pd__date__pd__", TODAY)
1120 for i, ( 1067 for i, (
1121 dataset_path, 1068 dataset_path,
1122 dataset_ext, 1069 dataset_ext,
1188 self.add_bigwig( 1135 self.add_bigwig(
1189 dataset_path, 1136 dataset_path,
1190 outputTrackConfig, 1137 outputTrackConfig,
1191 ) 1138 )
1192 elif dataset_ext == "bam": 1139 elif dataset_ext == "bam":
1193 real_indexes = track["conf"]["options"]["pileup"]["bam_indices"][ 1140 real_indexes = track["conf"]["options"]["bam"]["bam_indices"][
1194 "bam_index" 1141 "bam_index"
1195 ] 1142 ]
1196 if not isinstance(real_indexes, list): 1143 if not isinstance(real_indexes, list):
1197 real_indexes = [real_indexes] 1144 real_indexes = [real_indexes]
1198 1145
1199 self.add_bam( 1146 self.add_bam(
1200 dataset_path, 1147 dataset_path,
1201 outputTrackConfig, 1148 outputTrackConfig,
1202 track["conf"]["options"]["pileup"], 1149 track["conf"]["options"]["bam"],
1203 bam_index=real_indexes[i], 1150 bam_index=real_indexes[i],
1204 ) 1151 )
1205 elif dataset_ext == "cram": 1152 elif dataset_ext == "cram":
1206 real_indexes = track["conf"]["options"]["cram"]["cram_indices"][ 1153 real_indexes = track["conf"]["options"]["cram"]["cram_indices"][
1207 "cram_index" 1154 "cram_index"
1473 x.attrib["ext"], 1420 x.attrib["ext"],
1474 x.attrib["label"], 1421 x.attrib["label"],
1475 metadata, 1422 metadata,
1476 ) 1423 )
1477 ) 1424 )
1478 else:
1479 # For tracks without files (rest, sparql)
1480 track_conf["trackfiles"].append(
1481 (
1482 "", # N/A, no path for rest or sparql
1483 track.attrib["format"],
1484 track.find("options/label").text,
1485 {},
1486 )
1487 )
1488 1425
1489 if is_multi_bigwig: 1426 if is_multi_bigwig:
1490 metadata = metadata_from_node(x.find("metadata")) 1427 metadata = metadata_from_node(x.find("metadata"))
1491 1428
1492 track_conf["trackfiles"].append( 1429 track_conf["trackfiles"].append(