Mercurial > repos > fubar > jbrowse2

comparison jbrowse2.py @ 24:fb6cc7bc24df draft

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planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit cde4b8a574ded34a0ff8df3ecafc1a057787dcfb-dirty
author fubar
date Sat, 03 Feb 2024 11:49:56 +0000
parents 39b717d934a8
children 172acf9c7a53
comparison
equal deleted inserted replaced
23:39b717d934a8 24:fb6cc7bc24df
459 genome_name # first one for all tracks - other than paf 459 genome_name # first one for all tracks - other than paf
460 ) 460 )
461 self.genome_firstcontig = None 461 self.genome_firstcontig = None
462 fl = open(fapath, "r").readline().strip().split(">", 1) 462 fl = open(fapath, "r").readline().strip().split(">", 1)
463 if len(fl) > 1: 463 if len(fl) > 1:
464 self.genome_firstcontig = fl[1].strip() 464 self.genome_firstcontig = fl[1].split().strip()
465 if self.config_json.get("assemblies", None): 465 if self.config_json.get("assemblies", None):
466 self.config_json["assemblies"] += assemblies 466 self.config_json["assemblies"] += assemblies
467 else: 467 else:
468 self.config_json["assemblies"] = assemblies 468 self.config_json["assemblies"] = assemblies
469 469
1146 self.add_hic( 1146 self.add_hic(
1147 dataset_path, 1147 dataset_path,
1148 outputTrackConfig, 1148 outputTrackConfig,
1149 ) 1149 )
1150 elif dataset_ext in ("cool", "mcool", "scool"): 1150 elif dataset_ext in ("cool", "mcool", "scool"):
1151 hictempd = tempfile.mkdtemp()
1152 hic_path = os.path.join( 1151 hic_path = os.path.join(
1153 self.outdir, "%s_%d_%s.hic" % (track_human_label, i, dataset_ext) 1152 self.outdir, "%s_%d_%s.hic" % (track_human_label, i, dataset_ext)
1154 ) 1153 )
1155 self.subprocess_check_call( 1154 self.subprocess_check_call(
1156 [ 1155 [
1157 "hictk", 1156 "hictk",
1158 "convert", 1157 "convert",
1159 "-f", 1158 "-f",
1160 "--output-fmt", 1159 "--output-fmt",
1161 "hic", 1160 "hic",
1162 "--tmpdir",
1163 hictempd,
1164 dataset_path, 1161 dataset_path,
1165 hic_path, 1162 hic_path,
1166 ] 1163 ]
1167 ) 1164 )
1168 self.add_hic( 1165 self.add_hic(
1169 hic_path, 1166 hic_path,
1170 outputTrackConfig, 1167 outputTrackConfig,
1171 ) 1168 )
1172 shutil.rmtree(hictempd)
1173 elif dataset_ext in ("bed",): 1169 elif dataset_ext in ("bed",):
1174 self.add_bed( 1170 self.add_bed(
1175 dataset_path, 1171 dataset_path,
1176 dataset_ext, 1172 dataset_ext,
1177 outputTrackConfig, 1173 outputTrackConfig,
1281 loc_match = re.search(r"^([^:]+):([\d,]*)\.*([\d,]*)$", ddl) 1277 loc_match = re.search(r"^([^:]+):([\d,]*)\.*([\d,]*)$", ddl)
1282 if loc_match: 1278 if loc_match:
1283 refName = loc_match.group(1) 1279 refName = loc_match.group(1)
1284 drdict["refName"] = refName 1280 drdict["refName"] = refName
1285 if loc_match.group(2) > "": 1281 if loc_match.group(2) > "":
1286 drdict["start"] = int(loc_match.group(2)) 1282 drdict["start"] = int(loc_match.group(2).replace(',',''))
1287 if loc_match.group(3) > "": 1283 if loc_match.group(3) > "":
1288 drdict["end"] = int(loc_match.group(3)) 1284 drdict["end"] = int(loc_match.group(3).replace(',',''))
1289 else: 1285 else:
1290 logging.info( 1286 logging.info(
1291 "@@@ 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"
1292 % ddl 1288 % ddl
1293 ) 1289 )