Mercurial > repos > fubar > jbrowse2

comparison jbrowse2.py @ 31:cb4b32ca9968 draft

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planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 48bc917d34af182e9158915862c8a35723660919-dirty
author fubar
date Fri, 23 Feb 2024 07:15:42 +0000
parents 8f02a84ee278
children fe48ed5810bd
comparison
equal deleted inserted replaced
30:8f02a84ee278 31:cb4b32ca9968
448 for i, genome_node in enumerate(self.genome_paths): 448 for i, genome_node in enumerate(self.genome_paths):
449 genome_name = genome_node["meta"]["dataset_dname"].strip() 449 genome_name = genome_node["meta"]["dataset_dname"].strip()
450 if len(genome_name.split()) > 1: 450 if len(genome_name.split()) > 1:
451 genome_name = genome_name.split()[0] 451 genome_name = genome_name.split()[0]
452 # spaces and cruft break scripts when substituted 452 # spaces and cruft break scripts when substituted
453 fapath = genome_node["path"] 453 if genome_name not in self.genome_names:
454 assem = self.make_assembly(fapath, genome_name) 454 # ignore dupes - can have multiple pafs with same references?
455 assemblies.append(assem) 455 fapath = genome_node["path"]
456 self.genome_names.append(genome_name) 456 assem = self.make_assembly(fapath, genome_name)
457 if self.genome_name is None: 457 assemblies.append(assem)
458 self.genome_name = ( 458 self.genome_names.append(genome_name)
459 genome_name # first one for all tracks - other than paf 459 if self.genome_name is None:
460 ) 460 self.genome_name = (
461 self.genome_firstcontig = None 461 genome_name # first one for all tracks - other than paf
462 fl = open(fapath, "r").readline().strip().split(">") 462 )
463 if len(fl) > 1: 463 self.genome_firstcontig = None
464 fl = fl[1] 464 fl = open(fapath, "r").readline().strip().split(">")
465 if len(fl.split()) > 1: 465 if len(fl) > 1:
466 self.genome_firstcontig = fl.split()[0].strip() 466 fl = fl[1]
467 else: 467 if len(fl.split()) > 1:
468 self.genome_firstcontig = fl 468 self.genome_firstcontig = fl.split()[0].strip()
469 else:
470 self.genome_firstcontig = fl
469 if self.config_json.get("assemblies", None): 471 if self.config_json.get("assemblies", None):
470 self.config_json["assemblies"] += assemblies 472 self.config_json["assemblies"] += assemblies
471 else: 473 else:
472 self.config_json["assemblies"] = assemblies 474 self.config_json["assemblies"] = assemblies
473 475
1011 self.trackIdlist.append(tId) 1013 self.trackIdlist.append(tId)
1012 1014
1013 def add_paf(self, data, trackData, pafOpts, **kwargs): 1015 def add_paf(self, data, trackData, pafOpts, **kwargs):
1014 tname = trackData["name"] 1016 tname = trackData["name"]
1015 tId = trackData["label"] 1017 tId = trackData["label"]
1016 pgname = pafOpts["genome_label"] 1018 pgnames = [x.strip() for x in pafOpts["genome_label"].split(',')]
1017 if len(pgname.split()) > 1: 1019 pgpaths = [x.strip() for x in pafOpts["genome"].split(',')]
1018 pgname = pgname.split()[ 1020 passnames = [self.genome_name] # always first
1019 0 1021 for i, gname in enumerate(pgnames):
1020 ] # trouble from spacey names in command lines avoidance 1022 if len(gname.split()) > 1:
1021 asstrack = self.make_assembly(pafOpts["genome"], pgname) 1023 gname = gname.split()[0]
1022 self.genome_names.append(pgname) 1024 # trouble from spacey names in command lines avoidance
1023 if self.config_json.get("assemblies", None): 1025 if gname not in self.genome_names:
1024 self.config_json["assemblies"].append(asstrack) 1026 passnames.append(gname)
1025 else: 1027 # ignore if already there - eg for duplicates among pafs.
1026 self.config_json["assemblies"] = [ 1028 asstrack = self.make_assembly(pgpaths[i], gname)
1027 asstrack, 1029 self.genome_names.append(gname)
1028 ] 1030 if self.config_json.get("assemblies", None):
1031 self.config_json["assemblies"].append(asstrack)
1032 else:
1033 self.config_json["assemblies"] = [
1034 asstrack,
1035 ]
1029 url = "%s.paf" % (trackData["label"]) 1036 url = "%s.paf" % (trackData["label"])
1030 dest = "%s/%s" % (self.outdir, url) 1037 dest = "%s/%s" % (self.outdir, url)
1031 self.symlink_or_copy(os.path.realpath(data), dest) 1038 self.symlink_or_copy(os.path.realpath(data), dest)
1032 trackDict = { 1039 trackDict = {
1033 "type": "SyntenyTrack", 1040 "type": "SyntenyTrack",
1034 "trackId": tId, 1041 "trackId": tId,
1035 "assemblyNames": [self.genome_name, pgname], 1042 "assemblyNames": passnames,
1036 "name": tname, 1043 "name": tname,
1037 "adapter": { 1044 "adapter": {
1038 "type": "PAFAdapter", 1045 "type": "PAFAdapter",
1039 "pafLocation": {"uri": url}, 1046 "pafLocation": {"uri": url},
1040 "assemblyNames": [self.genome_name, pgname], 1047 "assemblyNames": [self.genome_name, pgname],
1531 "metadata/general/defaultLocation" 1538 "metadata/general/defaultLocation"
1532 ).text 1539 ).text
1533 default_session_data["session_name"] = root.find( 1540 default_session_data["session_name"] = root.find(
1534 "metadata/general/session_name" 1541 "metadata/general/session_name"
1535 ).text 1542 ).text
1543 jc.zipOut = root.find(
1544 "metadata/general/zipOut"
1545 ).text == "true"
1536 general_data = { 1546 general_data = {
1537 "analytics": root.find("metadata/general/analytics").text, 1547 "analytics": root.find("metadata/general/analytics").text,
1538 "primary_color": root.find("metadata/general/primary_color").text, 1548 "primary_color": root.find("metadata/general/primary_color").text,
1539 "secondary_color": root.find("metadata/general/secondary_color").text, 1549 "secondary_color": root.find("metadata/general/secondary_color").text,
1540 "tertiary_color": root.find("metadata/general/tertiary_color").text, 1550 "tertiary_color": root.find("metadata/general/tertiary_color").text,