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comparison jbrowse2.py @ 59:f807e219cec3 draft

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planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit faada92caf5aaabe58e52b161687a30d542a07b9
author fubar
date Fri, 22 Mar 2024 22:04:08 +0000
parents 94264fe60478
children 81d535970196
comparison
equal deleted inserted replaced
58:0e592dcaeb7f 59:f807e219cec3
437 } 437 }
438 438
439 if trackDict.get("displays", None): # use first if multiple like bed 439 if trackDict.get("displays", None): # use first if multiple like bed
440 style_data["type"] = trackDict["displays"][0]["type"] 440 style_data["type"] = trackDict["displays"][0]["type"]
441 style_data["displayId"] = trackDict["displays"][0]["displayId"] 441 style_data["displayId"] = trackDict["displays"][0]["displayId"]
442 return { 442 wstyle = {
443 "displays": [ 443 "displays": [
444 style_data, 444 style_data,
445 ] 445 ]
446 } 446 }
447 logging.warn("style=%s" % (wstyle))
448 return wstyle
447 449
448 def process_genomes(self): 450 def process_genomes(self):
449 assemblies = [] 451 assemblies = []
450 useuri = False 452 useuri = False
451 for i, genome_node in enumerate(self.genome_paths): 453 for i, genome_node in enumerate(self.genome_paths):
494 faname = fapath 496 faname = fapath
495 adapter = { 497 adapter = {
496 "type": "BgzipFastaAdapter", 498 "type": "BgzipFastaAdapter",
497 "fastaLocation": { 499 "fastaLocation": {
498 "uri": faname, 500 "uri": faname,
499 "locationType": "UriLocation", 501 "locationType": "UriLocation"
500 }, 502 },
501 "faiLocation": { 503 "faiLocation": {
502 "uri": faname + ".fai", 504 "uri": faname + ".fai",
503 "locationType": "UriLocation", 505 "locationType": "UriLocation"
504 }, 506 },
505 "gziLocation": { 507 "gziLocation": {
506 "uri": faname + ".gzi", 508 "uri": faname + ".gzi",
507 "locationType": "UriLocation", 509 "locationType": "UriLocation"
508 }, 510 }
509 } 511 }
510 else: 512 else:
511 faname = gname + ".fa.gz" 513 faname = gname + ".fa.gz"
512 fadest = os.path.realpath(os.path.join(self.outdir, faname)) 514 fadest = os.path.realpath(os.path.join(self.outdir, faname))
513 cmd = "bgzip -i -c %s -I %s.gzi > %s && samtools faidx %s" % ( 515 cmd = "bgzip -i -c %s -I %s.gzi > %s && samtools faidx %s" % (
526 "faiLocation": { 528 "faiLocation": {
527 "uri": faname + ".fai", 529 "uri": faname + ".fai",
528 }, 530 },
529 "gziLocation": { 531 "gziLocation": {
530 "uri": faname + ".gzi", 532 "uri": faname + ".gzi",
531 }, 533 }
532 } 534 }
533 535
534 trackDict = { 536 trackDict = {
535 "name": gname, 537 "name": gname,
536 "sequence": { 538 "sequence": {
537 "type": "ReferenceSequenceTrack", 539 "type": "ReferenceSequenceTrack",
538 "trackId": gname, 540 "trackId": gname,
539 "adapter": adapter, 541 "adapter": adapter,
540 }, 542 },
541 "rendering": {"type": "DivSequenceRenderer"},
542 "displays": [ 543 "displays": [
543 { 544 {
544 "type": "LinearReferenceSequenceDisplay", 545 "type": "LinearReferenceSequenceDisplay",
545 "displayId": "%s-LinearReferenceSequenceDisplay" % gname, 546 "displayId": "%s-LinearReferenceSequenceDisplay" % gname,
546 }, 547 },
547 { 548 {
548 "type": "LinearGCContentDisplay", 549 "type": "LinearGCContentDisplay",
549 "displayId": "%s-LinearGCContentDisplay" % gname, 550 "displayId": "%s-LinearGCContentDisplay" % gname,
550 }, 551 },
551 ], 552 ]
552 } 553 }
553 return trackDict 554 return trackDict
554 555
555 def add_default_view(self): 556 def add_default_view(self):
556 cmd = [ 557 cmd = [
633 "type": "LinearHicDisplay", 634 "type": "LinearHicDisplay",
634 "displayId": "%s-LinearHicDisplay" % tId, 635 "displayId": "%s-LinearHicDisplay" % tId,
635 }, 636 },
636 ], 637 ],
637 } 638 }
639 style_json = self._prepare_track_style(trackDict)
640 trackDict["style"] = style_json
638 self.tracksToAdd.append(trackDict) 641 self.tracksToAdd.append(trackDict)
639 self.trackIdlist.append(tId) 642 self.trackIdlist.append(tId)
640 643
641 def add_maf(self, data, trackData): 644 def add_maf(self, data, trackData):
642 """ 645 """
706 "type": "LinearArcDisplay", 709 "type": "LinearArcDisplay",
707 "displayId": "%s-LinearArcDisplay" % tId, 710 "displayId": "%s-LinearArcDisplay" % tId,
708 }, 711 },
709 ], 712 ],
710 } 713 }
714 style_json = self._prepare_track_style(trackDict)
715 trackDict["style"] = style_json
711 self.tracksToAdd.append(trackDict) 716 self.tracksToAdd.append(trackDict)
712 self.trackIdlist.append(tId) 717 self.trackIdlist.append(tId)
713 if self.config_json.get("plugins", None): 718 if self.config_json.get("plugins", None):
714 self.config_json["plugins"].append(mafPlugin[0]) 719 self.config_json["plugins"].append(mafPlugin[0])
715 else: 720 else:
779 "type": "LinearArcDisplay", 784 "type": "LinearArcDisplay",
780 "displayId": "%s-LinearArcDisplay" % tId, 785 "displayId": "%s-LinearArcDisplay" % tId,
781 }, 786 },
782 ], 787 ],
783 } 788 }
789 style_json = self._prepare_track_style(trackDict)
790 trackDict["style"] = style_json
784 self.tracksToAdd.append(trackDict) 791 self.tracksToAdd.append(trackDict)
785 self.trackIdlist.append(tId) 792 self.trackIdlist.append(tId)
786 os.unlink(gff3) 793 os.unlink(gff3)
787 794
788 def add_bigwig(self, data, trackData): 795 def add_bigwig(self, data, trackData):
825 "type": "LinearWiggleDisplay", 832 "type": "LinearWiggleDisplay",
826 "displayId": "%s-LinearWiggleDisplay" % tId, 833 "displayId": "%s-LinearWiggleDisplay" % tId,
827 } 834 }
828 ], 835 ],
829 } 836 }
837 style_json = self._prepare_track_style(trackDict)
838 trackDict["style"] = style_json
830 self.tracksToAdd.append(trackDict) 839 self.tracksToAdd.append(trackDict)
831 self.trackIdlist.append(tId) 840 self.trackIdlist.append(tId)
832 841
833 def add_bam(self, data, trackData, bam_index=None, **kwargs): 842 def add_bam(self, data, trackData, bam_index=None, **kwargs):
834 tId = trackData["label"] 843 tId = trackData["label"]
878 "type": "LinearAlignmentsDisplay", 887 "type": "LinearAlignmentsDisplay",
879 "displayId": "%s-LinearAlignmentsDisplay" % tId, 888 "displayId": "%s-LinearAlignmentsDisplay" % tId,
880 }, 889 },
881 ], 890 ],
882 } 891 }
892 style_json = self._prepare_track_style(trackDict)
893 trackDict["style"] = style_json
883 self.tracksToAdd.append(trackDict) 894 self.tracksToAdd.append(trackDict)
884 self.trackIdlist.append(tId) 895 self.trackIdlist.append(tId)
885 896
886 def add_cram(self, data, trackData, cram_index=None, **kwargs): 897 def add_cram(self, data, trackData, cram_index=None, **kwargs):
887 tId = trackData["label"] 898 tId = trackData["label"]
926 "type": "LinearAlignmentsDisplay", 937 "type": "LinearAlignmentsDisplay",
927 "displayId": "%s-LinearAlignmentsDisplay" % tId, 938 "displayId": "%s-LinearAlignmentsDisplay" % tId,
928 }, 939 },
929 ], 940 ],
930 } 941 }
942 style_json = self._prepare_track_style(trackDict)
943 trackDict["style"] = style_json
931 self.tracksToAdd.append(trackDict) 944 self.tracksToAdd.append(trackDict)
932 self.trackIdlist.append(tId) 945 self.trackIdlist.append(tId)
933 946
934 def add_vcf(self, data, trackData): 947 def add_vcf(self, data, trackData):
935 tId = trackData["label"] 948 tId = trackData["label"]
978 "type": "LinearPairedArcDisplay", 991 "type": "LinearPairedArcDisplay",
979 "displayId": "%s-LinearPairedArcDisplay" % tId, 992 "displayId": "%s-LinearPairedArcDisplay" % tId,
980 }, 993 },
981 ], 994 ],
982 } 995 }
996 style_json = self._prepare_track_style(trackDict)
997 trackDict["style"] = style_json
983 self.tracksToAdd.append(trackDict) 998 self.tracksToAdd.append(trackDict)
984 self.trackIdlist.append(tId) 999 self.trackIdlist.append(tId)
985 1000
986 def _sort_gff(self, data, dest): 1001 def _sort_gff(self, data, dest):
987 # Only index if not already done 1002 # Only index if not already done
1039 "type": "LinearArcDisplay", 1054 "type": "LinearArcDisplay",
1040 "displayId": "%s-LinearArcDisplay" % tId, 1055 "displayId": "%s-LinearArcDisplay" % tId,
1041 }, 1056 },
1042 ], 1057 ],
1043 } 1058 }
1059 style_json = self._prepare_track_style(trackDict)
1060 trackDict["style"] = style_json
1044 self.tracksToAdd.append(trackDict) 1061 self.tracksToAdd.append(trackDict)
1045 self.trackIdlist.append(tId) 1062 self.trackIdlist.append(tId)
1046 1063
1047 def add_bed(self, data, ext, trackData): 1064 def add_bed(self, data, ext, trackData):
1048 tId = trackData["label"] 1065 tId = trackData["label"]
1086 "type": "LinearArcDisplay", 1103 "type": "LinearArcDisplay",
1087 "displayId": "%s-LinearArcDisplay" % tId, 1104 "displayId": "%s-LinearArcDisplay" % tId,
1088 }, 1105 },
1089 ], 1106 ],
1090 } 1107 }
1108 style_json = self._prepare_track_style(trackDict)
1109 trackDict["style"] = style_json
1091 self.tracksToAdd.append(trackDict) 1110 self.tracksToAdd.append(trackDict)
1092 self.trackIdlist.append(tId) 1111 self.trackIdlist.append(tId)
1093 1112
1094 def add_paf(self, data, trackData, pafOpts, **kwargs): 1113 def add_paf(self, data, trackData, pafOpts, **kwargs):
1095 tname = trackData["name"] 1114 tname = trackData["name"]
1096 tId = trackData["label"] 1115 tId = trackData["label"]
1097 categ = trackData["category"] 1116 categ = trackData["category"]
1098 pgnames = [x.strip() for x in pafOpts["genome_label"].split(",")] 1117 pgnames = [x.strip() for x in pafOpts["genome_label"].split(",") if len(x.strip()) > 0]
1099 pgpaths = [x.strip() for x in pafOpts["genome"].split(",")] 1118 pgpaths = [x.strip() for x in pafOpts["genome"].split(",") if len(x.strip()) > 0]
1100 passnames = [self.genome_name] # always first 1119 passnames = [self.genome_name] # always first
1120 logging.warn("### add_paf got pafOpts=%s, pgnames=%s, pgpaths=%s for %s" % (pafOpts, pgnames, pgpaths, tId))
1101 for i, gname in enumerate(pgnames): 1121 for i, gname in enumerate(pgnames):
1102 if len(gname.split()) > 1: 1122 if len(gname.split()) > 1:
1103 gname = gname.split()[0] 1123 gname = gname.split()[0]
1104 passnames.append(gname) 1124 passnames.append(gname)
1105 # trouble from spacey names in command lines avoidance 1125 # trouble from spacey names in command lines avoidance
1106 if gname not in self.genome_names: 1126 if gname not in self.genome_names:
1107 # ignore if already there - eg for duplicates among pafs. 1127 # ignore if already there - eg for duplicates among pafs.
1108 useuri = pgpaths[i].startswith("http://") or pgpaths[i].startswith( 1128 useuri = pgpaths[i].startswith("http://") or pgpaths[i].startswith(
1109 "https://" 1129 "https://"
1110 ) 1130 )
1111 asstrack = self.make_assembly(pgpaths[i], gname, useuri) 1131 asstrack = self.make_assembly(pgpaths[i], gname, useuri)
1112 self.genome_names.append(gname) 1132 self.genome_names.append(gname)
1113 if self.config_json.get("assemblies", None): 1133 if self.config_json.get("assemblies", None):
1114 self.config_json["assemblies"].append(asstrack) 1134 self.config_json["assemblies"].append(asstrack)
1115 else: 1135 else:
1116 self.config_json["assemblies"] = [ 1136 self.config_json["assemblies"] = [
1117 asstrack, 1137 asstrack,
1118 ] 1138 ]
1119 url = "%s.paf" % (trackData["label"]) 1139 url = "%s.paf" % (trackData["label"])
1120 dest = "%s/%s" % (self.outdir, url) 1140 dest = "%s/%s" % (self.outdir, url)
1121 self.symlink_or_copy(os.path.realpath(data), dest) 1141 self.symlink_or_copy(os.path.realpath(data), dest)
1122 trackDict = { 1142 trackDict = {
1123 "type": "SyntenyTrack", 1143 "type": "SyntenyTrack",
1129 "name": tname, 1149 "name": tname,
1130 "adapter": { 1150 "adapter": {
1131 "type": "PAFAdapter", 1151 "type": "PAFAdapter",
1132 "pafLocation": {"uri": url}, 1152 "pafLocation": {"uri": url},
1133 "assemblyNames": passnames, 1153 "assemblyNames": passnames,
1134 }, 1154 }
1135 "displays": [ 1155 }
1136 { 1156 style_json = {
1137 "type": "LinearSyntenyDisplay", 1157 "displays": [
1138 "displayId": "%s-LinearSyntenyDisplay" % tId, 1158 { "type": "LinearBasicDisplay",
1139 }, 1159 "displayId": "%s-LinearBasicyDisplay" % trackDict["trackId"]
1140 { 1160 }
1141 "type": "DotPlotDisplay", 1161 ]
1142 "displayId": "%s-DotPlotDisplay" % tId, 1162 }
1143 }, 1163 trackDict["style"] = style_json
1144 ],
1145 }
1146 self.tracksToAdd.append(trackDict) 1164 self.tracksToAdd.append(trackDict)
1147 self.trackIdlist.append(tId) 1165 self.trackIdlist.append(tId)
1148 1166
1149 def process_annotations(self, track): 1167 def process_annotations(self, track):
1150 category = track["category"].replace("__pd__date__pd__", TODAY) 1168 category = track["category"].replace("__pd__date__pd__", TODAY)
1282 logging.warn("### No style data in default data for %s" % tId) 1300 logging.warn("### No style data in default data for %s" % tId)
1283 style_data = {"type": "LinearBasicDisplay"} 1301 style_data = {"type": "LinearBasicDisplay"}
1284 if "displays" in track_conf: 1302 if "displays" in track_conf:
1285 disp = track_conf["displays"][0]["type"] 1303 disp = track_conf["displays"][0]["type"]
1286 style_data["type"] = disp 1304 style_data["type"] = disp
1287 style_data["configuration"] = "%s-%s" % (tId, disp)
1288 if track_conf.get("style_labels", None): 1305 if track_conf.get("style_labels", None):
1289 # TODO fix this: it should probably go in a renderer block (SvgFeatureRenderer) but still does not work 1306 # TODO fix this: it should probably go in a renderer block (SvgFeatureRenderer) but still does not work
1290 # TODO move this to per track displays? 1307 # TODO move this to per track displays?
1291 style_data["labels"] = track_conf["style_labels"] 1308 style_data["labels"] = track_conf["style_labels"]
1292 tracks_data.append( 1309 tracks_data.append(
1294 "type": track_types[tId], 1311 "type": track_types[tId],
1295 "configuration": tId, 1312 "configuration": tId,
1296 "displays": [style_data], 1313 "displays": [style_data],
1297 } 1314 }
1298 ) 1315 )
1299
1300 # The view for the assembly we're adding 1316 # The view for the assembly we're adding
1301 view_json = {"type": "LinearGenomeView", "tracks": tracks_data} 1317 view_json = {"type": "LinearGenomeView", "tracks": tracks_data}
1302 1318
1303 refName = None 1319 refName = None
1304 drdict = { 1320 drdict = {
1532 track_conf["style"] = { 1548 track_conf["style"] = {
1533 item.tag: parse_style_conf(item) for item in track.find("options/style") 1549 item.tag: parse_style_conf(item) for item in track.find("options/style")
1534 } 1550 }
1535 else: 1551 else:
1536 track_conf["style"] = {} 1552 track_conf["style"] = {}
1537 tst = track_conf["style"].get("type", None)
1538 if tst:
1539 track_conf["style"]["configuration"] = "%s-%s" % (track_conf["label"], tst)
1540 if track.find("options/style_labels"): 1553 if track.find("options/style_labels"):
1541 track_conf["style_labels"] = { 1554 track_conf["style_labels"] = {
1542 item.tag: parse_style_conf(item) 1555 item.tag: parse_style_conf(item)
1543 for item in track.find("options/style_labels") 1556 for item in track.find("options/style_labels")
1544 } 1557 }
1563 "metadata/general/defaultLocation" 1576 "metadata/general/defaultLocation"
1564 ).text 1577 ).text
1565 default_session_data["session_name"] = root.find( 1578 default_session_data["session_name"] = root.find(
1566 "metadata/general/session_name" 1579 "metadata/general/session_name"
1567 ).text 1580 ).text
1581 logging.warn("default_session=%s" % (default_session_data))
1568 jc.zipOut = root.find("metadata/general/zipOut").text == "true" 1582 jc.zipOut = root.find("metadata/general/zipOut").text == "true"
1569 general_data = { 1583 general_data = {
1570 "analytics": root.find("metadata/general/analytics").text, 1584 "analytics": root.find("metadata/general/analytics").text,
1571 "primary_color": root.find("metadata/general/primary_color").text, 1585 "primary_color": root.find("metadata/general/primary_color").text,
1572 "secondary_color": root.find("metadata/general/secondary_color").text, 1586 "secondary_color": root.find("metadata/general/secondary_color").text,