Mercurial > repos > fubar > jbrowse2

comparison jbrowse2.py @ 29:f728cf0df71d draft

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planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit fe89199bded3f50aefb6958f0c4e85eede77ad81-dirty
author fubar
date Fri, 16 Feb 2024 00:04:37 +0000
parents 9a5c409f33f4
children 8f02a84ee278
comparison
equal deleted inserted replaced
28:9a5c409f33f4 29:f728cf0df71d
562 """ 562 """
563 tId = trackData["label"] 563 tId = trackData["label"]
564 # can be served - if public. 564 # can be served - if public.
565 # dsId = trackData["metadata"]["dataset_id"] 565 # dsId = trackData["metadata"]["dataset_id"]
566 # url = "%s/api/datasets/%s/display?to_ext=hic " % (self.giURL, dsId) 566 # url = "%s/api/datasets/%s/display?to_ext=hic " % (self.giURL, dsId)
567 hname = trackData["name"] 567 hname = trackData["hic_url"]
568 dest = os.path.join(self.outdir, hname)
569 cmd = ["cp", data, dest]
570 # these can be very big.
571 self.subprocess_check_call(cmd)
572 floc = { 568 floc = {
573 "uri": hname, 569 "uri": hname,
574 } 570 }
575 trackDict = { 571 trackDict = {
576 "type": "HicTrack", 572 "type": "HicTrack",
772 } 768 }
773 style_json = self._prepare_track_style(trackDict) 769 style_json = self._prepare_track_style(trackDict)
774 trackDict["style"] = style_json 770 trackDict["style"] = style_json
775 self.tracksToAdd.append(trackDict) 771 self.tracksToAdd.append(trackDict)
776 self.trackIdlist.append(tId) 772 self.trackIdlist.append(tId)
777 logging.info("#### wig trackData=%s" % str(trackData))
778 773
779 def add_bam(self, data, trackData, bamOpts, bam_index=None, **kwargs): 774 def add_bam(self, data, trackData, bamOpts, bam_index=None, **kwargs):
780 tId = trackData["label"] 775 tId = trackData["label"]
781 fname = "%s.bam" % trackData["label"] 776 fname = "%s.bam" % trackData["label"]
782 dest = "%s/%s" % (self.outdir, fname) 777 dest = "%s/%s" % (self.outdir, fname)
1150 self.add_hic( 1145 self.add_hic(
1151 dataset_path, 1146 dataset_path,
1152 outputTrackConfig, 1147 outputTrackConfig,
1153 ) 1148 )
1154 elif dataset_ext in ("cool", "mcool", "scool"): 1149 elif dataset_ext in ("cool", "mcool", "scool"):
1155 hic_path = os.path.join( 1150 hic_url = "%s_%d.hic" % (track_human_label, i)
1156 self.outdir, "%s_%d_%s.hic" % (track_human_label, i, dataset_ext) 1151 hic_path = os.path.join(self.outdir, hic_url)
1157 )
1158 self.subprocess_check_call( 1152 self.subprocess_check_call(
1159 [ 1153 [
1160 "hictk", 1154 "hictk",
1161 "convert", 1155 "convert",
1162 "-f", 1156 "-f",
1164 "hic", 1158 "hic",
1165 dataset_path, 1159 dataset_path,
1166 hic_path, 1160 hic_path,
1167 ] 1161 ]
1168 ) 1162 )
1163 outputTrackConfig["hic_url"] = hic_url
1169 self.add_hic( 1164 self.add_hic(
1170 hic_path, 1165 hic_path,
1171 outputTrackConfig, 1166 outputTrackConfig,
1172 ) 1167 )
1173 elif dataset_ext in ("bed",): 1168 elif dataset_ext in ("bed",):
1225 dataset_path, 1220 dataset_path,
1226 outputTrackConfig, 1221 outputTrackConfig,
1227 track["conf"]["options"]["paf"], 1222 track["conf"]["options"]["paf"],
1228 ) 1223 )
1229 else: 1224 else:
1230 log.warn("Do not know how to handle %s", dataset_ext) 1225 logging.warn("Do not know how to handle %s", dataset_ext)
1231 # Return non-human label for use in other fields 1226 # Return non-human label for use in other fields
1232 yield outputTrackConfig["label"] 1227 yield outputTrackConfig["label"]
1233 1228
1234 def add_default_session(self, data): 1229 def add_default_session(self, data):
1235 """ 1230 """
1290 else: 1285 else:
1291 logging.info( 1286 logging.info(
1292 "@@@ regexp could not match contig:start..end in the supplied location %s - please fix" 1287 "@@@ regexp could not match contig:start..end in the supplied location %s - please fix"
1293 % ddl 1288 % ddl
1294 ) 1289 )
1295 1290 else:
1291 drdict["refName"] = self.genome_firstcontig
1296 if drdict.get("refName", None): 1292 if drdict.get("refName", None):
1297 # TODO displayedRegions is not just zooming to the region, it hides the rest of the chromosome 1293 # TODO displayedRegions is not just zooming to the region, it hides the rest of the chromosome
1298 view_json["displayedRegions"] = [ 1294 view_json["displayedRegions"] = [
1299 drdict, 1295 drdict,
1300 ] 1296 ]