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comparison jbrowse2.py @ 89:408781c080fc draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 03400b3f71140ce62dba0db266a1f7b94b6c1a11
author fubar
date Wed, 17 Apr 2024 22:18:47 +0000
parents 3b2ff9864995
children 3c4db8203fad
comparison
equal deleted inserted replaced
88:efd1d41f11b4 89:408781c080fc
19 logging.basicConfig(level=logging.DEBUG) 19 logging.basicConfig(level=logging.DEBUG)
20 log = logging.getLogger("jbrowse") 20 log = logging.getLogger("jbrowse")
21 21
22 JB2VER = "v2.10.3" 22 JB2VER = "v2.10.3"
23 # version pinned if cloning - but not cloning now 23 # version pinned if cloning - but not cloning now
24 24 logCommands = True
25 # useful for seeing what's being written but not for production setups
25 TODAY = datetime.datetime.now().strftime("%Y-%m-%d") 26 TODAY = datetime.datetime.now().strftime("%Y-%m-%d")
26 SELF_LOCATION = os.path.dirname(os.path.realpath(__file__)) 27 SELF_LOCATION = os.path.dirname(os.path.realpath(__file__))
27 GALAXY_INFRASTRUCTURE_URL = None 28 GALAXY_INFRASTRUCTURE_URL = None
28 mapped_chars = { 29 mapped_chars = {
29 ">": "__gt__", 30 ">": "__gt__",
425 return subprocess.check_output(["pwd"]).decode("utf-8").strip() 426 return subprocess.check_output(["pwd"]).decode("utf-8").strip()
426 # return None 427 # return None
427 428
428 def subprocess_check_call(self, command, output=None, cwd=True): 429 def subprocess_check_call(self, command, output=None, cwd=True):
429 if output: 430 if output:
430 log.debug("cd %s && %s > %s", self.get_cwd(cwd), " ".join(command), output) 431 if logCommands:
432 log.debug(
433 "cd %s && %s > %s", self.get_cwd(cwd), " ".join(command), output
434 )
431 subprocess.check_call(command, cwd=self.get_cwd(cwd), stdout=output) 435 subprocess.check_call(command, cwd=self.get_cwd(cwd), stdout=output)
432 else: 436 else:
433 log.debug("cd %s && %s", self.get_cwd(cwd), " ".join(command)) 437 if logCommands:
438 log.debug("cd %s && %s", self.get_cwd(cwd), " ".join(command))
434 subprocess.check_call(command, cwd=self.get_cwd(cwd)) 439 subprocess.check_call(command, cwd=self.get_cwd(cwd))
435 440
436 def subprocess_popen(self, command, cwd=True): 441 def subprocess_popen(self, command, cwd=True):
437 log.debug(command) 442 if logCommands:
443 log.debug(command)
438 p = subprocess.Popen( 444 p = subprocess.Popen(
439 command, 445 command,
440 cwd=self.get_cwd(cwd), 446 cwd=self.get_cwd(cwd),
441 shell=True, 447 shell=True,
442 stdin=subprocess.PIPE, 448 stdin=subprocess.PIPE,
450 log.error(output) 456 log.error(output)
451 log.error(err) 457 log.error(err)
452 raise RuntimeError("Command failed with exit code %s" % (retcode)) 458 raise RuntimeError("Command failed with exit code %s" % (retcode))
453 459
454 def subprocess_check_output(self, command): 460 def subprocess_check_output(self, command):
455 log.debug(" ".join(command)) 461 if logCommands:
462 log.debug(" ".join(command))
456 return subprocess.check_output(command, cwd=self.outdir) 463 return subprocess.check_output(command, cwd=self.outdir)
457 464
458 def symlink_or_copy(self, src, dest): 465 def symlink_or_copy(self, src, dest):
459 if "GALAXY_JBROWSE_SYMLINKS" in os.environ and bool( 466 if "GALAXY_JBROWSE_SYMLINKS" in os.environ and bool(
460 os.environ["GALAXY_JBROWSE_SYMLINKS"] 467 os.environ["GALAXY_JBROWSE_SYMLINKS"]
489 with urllib.request.urlopen(url, context=scontext) as f: 496 with urllib.request.urlopen(url, context=scontext) as f:
490 fl = f.readlines() 497 fl = f.readlines()
491 nrow = len(fl) 498 nrow = len(fl)
492 except Exception: 499 except Exception:
493 nrow = 0 500 nrow = 0
494 logging.debug("### getNrow returning %d" % nrow) 501 logging.debug("### getNrow %s returning %d" % (url, nrow))
495 return nrow 502 return nrow
496 503
497 def process_genomes(self, genomes): 504 def process_genomes(self, genomes):
498 assembly = [] 505 assembly = []
499 assmeta = [] 506 assmeta = []
500 useuri = False 507 useuri = False
501 genome_names = [] 508 primaryGenome = None
502 for i, genome_node in enumerate(genomes): 509 for i, genome_node in enumerate(genomes):
503 this_genome = {} 510 this_genome = {}
504 if genome_node["useuri"] == "yes": 511 if genome_node["useuri"] == "yes":
505 useuri = True 512 useuri = True
506 genome_name = genome_node["label"].strip() 513 genome_name = genome_node["label"].strip()
507 if len(genome_name) == 0: 514 if len(genome_name) == 0:
508 genome_name = os.path.splitext(os.path.basename(genome_node["path"]))[0] 515 genome_name = os.path.splitext(os.path.basename(genome_node["path"]))[0]
509 if len(genome_name.split()) > 1: 516 if len(genome_name.split()) > 1:
510 genome_name = genome_name.split()[0] 517 genome_name = genome_name.split()[0]
511 # spaces and cruft break scripts when substituted 518 # spaces and cruft break scripts when substituted
512 if genome_name not in genome_names: 519 if not primaryGenome:
513 # pafs with shared references 520 primaryGenome = genome_name
521 if genome_name not in self.genome_names:
522 self.genome_names.append(genome_name)
514 fapath = genome_node["path"] 523 fapath = genome_node["path"]
515 if not useuri: 524 if not useuri:
516 fapath = os.path.realpath(fapath) 525 fapath = os.path.realpath(fapath)
517 assem, first_contig = self.make_assembly(fapath, genome_name, useuri) 526 assem, first_contig = self.make_assembly(fapath, genome_name, useuri)
518 assembly.append(assem) 527 assembly.append(assem)
519 self.ass_first_contigs.append(first_contig) 528 self.ass_first_contigs.append(first_contig)
520 if len(genome_names) == 0: 529 if genome_name == primaryGenome: # first one
521 this_genome["genome_name"] = genome_name # first one for all tracks 530 this_genome["genome_name"] = genome_name # first one for all tracks
522 genome_names.append(genome_name)
523 this_genome["genome_sequence_adapter"] = assem["sequence"][ 531 this_genome["genome_sequence_adapter"] = assem["sequence"][
524 "adapter" 532 "adapter"
525 ] 533 ]
526 this_genome["genome_firstcontig"] = None 534 this_genome["genome_firstcontig"] = None
527 if not useuri: 535 if not useuri:
549 this_genome["genome_firstcontig"] = ( 557 this_genome["genome_firstcontig"] = (
550 fl.decode("utf8").strip().split()[0] 558 fl.decode("utf8").strip().split()[0]
551 ) 559 )
552 assmeta.append(this_genome) 560 assmeta.append(this_genome)
553 self.assemblies += assembly 561 self.assemblies += assembly
554 self.assmeta[genome_names[0]] = assmeta 562 self.assmeta[primaryGenome] = assmeta
555 self.tracksToAdd[genome_names[0]] = [] 563 self.tracksToAdd[primaryGenome] = []
556 self.genome_names += genome_names 564 return primaryGenome
557 return this_genome["genome_name"]
558 565
559 def make_assembly(self, fapath, gname, useuri): 566 def make_assembly(self, fapath, gname, useuri):
560 """added code to grab the first contig name and length for broken default session from Anthony and Helena's code 567 """added code to grab the first contig name and length for broken default session from Anthony and Helena's code
561 that poor Bjoern is trying to figure out. 568 that poor Bjoern is trying to figure out.
562 """ 569 """
741 mafss = [x for x in mafs if (x.startswith("s\t") or x.startswith("s "))] 748 mafss = [x for x in mafs if (x.startswith("s\t") or x.startswith("s "))]
742 samp = [x.split()[1] for x in mafss if len(x.split()) > 0] 749 samp = [x.split()[1] for x in mafss if len(x.split()) > 0]
743 sampu = list(dict.fromkeys(samp)) 750 sampu = list(dict.fromkeys(samp))
744 samples = [x.split(".")[0] for x in sampu] 751 samples = [x.split(".")[0] for x in sampu]
745 samples.sort() 752 samples.sort()
746 logging.debug( 753 if logCommands:
747 "$$$$ cmd=%s, mafss=%s samp=%s samples=%s" 754 logging.debug(
748 % (" ".join(cmd), mafss, samp, samples) 755 "$$$$ cmd=%s, mafss=%s samp=%s samples=%s"
749 ) 756 % (" ".join(cmd), mafss, samp, samples)
757 )
750 trackDict = { 758 trackDict = {
751 "type": "MafTrack", 759 "type": "MafTrack",
752 "trackId": tId, 760 "trackId": tId,
753 "name": trackData["name"], 761 "name": trackData["name"],
754 "category": [ 762 "category": [
1170 nrow = self.getNrow(dest) 1178 nrow = self.getNrow(dest)
1171 else: 1179 else:
1172 url = data 1180 url = data
1173 nrow = self.getNrow(url) 1181 nrow = self.getNrow(url)
1174 categ = trackData["category"] 1182 categ = trackData["category"]
1175 pgnames = [x.strip() for x in pafOpts["genome_label"].split(",")] 1183 pg = pafOpts["genome"].split(",")
1176 pgpaths = [ 1184 pgc = [x.strip() for x in pg if x.strip() > ""]
1177 x.strip() for x in pafOpts["genome"].split(",") if len(x.strip()) > 0 1185 gnomes = [x.split(":") for x in pgc]
1178 ]
1179 passnames = [trackData["assemblyNames"]] # always first 1186 passnames = [trackData["assemblyNames"]] # always first
1180 for i, gp in enumerate(pgpaths): 1187 for i, (gpath, gname) in enumerate(gnomes):
1181 if len(pgnames[i].strip()) == 0: 1188 # may have been forgotten by user for uri
1182 # user may have left it blank - cannot make non-optional if want optional tracks. 1189 if len(gname) == 0:
1183 gn = os.path.basename(gp) 1190 gn = os.path.basename(gpath)
1184 pgnames[i] = os.path.splitext(gn)[0] 1191 gname = os.path.splitext(gn)[0]
1185 logging.debug( 1192 # trouble from spacey names in command lines avoidance
1186 "### add_paf got pafOpts=%s, pgnames=%s, pgpaths=%s for %s"
1187 % (pafOpts, pgnames, pgpaths, tId)
1188 )
1189 for i, gp in enumerate(pgpaths):
1190 gname = pgnames[i]
1191 if len(gname.split()) > 1: 1193 if len(gname.split()) > 1:
1192 gname = gname.split()[0] 1194 gname = gname.split()[0]
1193 passnames.append(gname) 1195 if gname not in passnames:
1194 # trouble from spacey names in command lines avoidance 1196 passnames.append(gname)
1195 useuri = gp.startswith("http://") or gp.startswith("https://") 1197 useuri = gpath.startswith("http://") or gpath.startswith("https://")
1196
1197 if gname not in self.genome_names: 1198 if gname not in self.genome_names:
1198 # ignore if already there - eg for duplicates among pafs. 1199 # ignore if already there - eg for duplicates among pafs.
1199 asstrack, first_contig = self.make_assembly(gp, gname, useuri) 1200 asstrack, first_contig = self.make_assembly(gpath, gname, useuri)
1200 self.genome_names.append(gname) 1201 self.genome_names.append(gname)
1201 self.tracksToAdd[gname] = [] 1202 self.tracksToAdd[gname] = []
1202 self.assemblies.append(asstrack) 1203 self.assemblies.append(asstrack)
1204 self.ass_first_contigs.append(first_contig)
1203 trackDict = { 1205 trackDict = {
1204 "type": "SyntenyTrack", 1206 "type": "SyntenyTrack",
1205 "trackId": tId, 1207 "trackId": tId,
1206 "assemblyNames": passnames, 1208 "assemblyNames": passnames,
1207 "category": [ 1209 "category": [
1269 outputTrackConfig["useuri"] = useuri 1271 outputTrackConfig["useuri"] = useuri
1270 outputTrackConfig["path"] = dataset_path 1272 outputTrackConfig["path"] = dataset_path
1271 outputTrackConfig["ext"] = dataset_ext 1273 outputTrackConfig["ext"] = dataset_ext
1272 1274
1273 outputTrackConfig["trackset"] = track.get("trackset", {}) 1275 outputTrackConfig["trackset"] = track.get("trackset", {})
1274 outputTrackConfig["label"] = "%s_%d.%s" % ( 1276 outputTrackConfig["label"] = track["label"]
1275 track_human_label,
1276 self.trackCounter,
1277 dataset_ext,
1278 )
1279 self.trackCounter += 1
1280 outputTrackConfig["metadata"] = extra_metadata 1277 outputTrackConfig["metadata"] = extra_metadata
1281 outputTrackConfig["name"] = track_human_label 1278 outputTrackConfig["name"] = track_human_label
1282 1279 if track["label"] in self.trackIdlist:
1280 logging.error(
1281 "### not adding %s already in %s"
1282 % (track["label"], self.trackIdlist)
1283 )
1284 yield None
1283 if dataset_ext in ("gff", "gff3"): 1285 if dataset_ext in ("gff", "gff3"):
1284 self.add_gff( 1286 self.add_gff(
1285 dataset_path, 1287 dataset_path,
1286 outputTrackConfig, 1288 outputTrackConfig,
1287 ) 1289 )
1414 "type": "LinearGenomeView", 1416 "type": "LinearGenomeView",
1415 "offsetPx": 0, 1417 "offsetPx": 0,
1416 "minimized": False, 1418 "minimized": False,
1417 "tracks": tracks_data, 1419 "tracks": tracks_data,
1418 } 1420 }
1419 logging.debug(
1420 "Looking for %s in self.ass_ %s" % (gnome, self.ass_first_contigs)
1421 )
1422 first = [x for x in self.ass_first_contigs if x[0] == gnome] 1421 first = [x for x in self.ass_first_contigs if x[0] == gnome]
1423 if len(first) > 0: 1422 if len(first) > 0:
1424 [gnome, refName, end] = first[0] 1423 [gnome, refName, end] = first[0]
1425 start = 0 1424 start = 0
1426 end = int(end) 1425 end = int(end)
1475 with open(self.config_json_file, "w") as config_file: 1474 with open(self.config_json_file, "w") as config_file:
1476 json.dump(self.config_json, config_file, indent=2) 1475 json.dump(self.config_json, config_file, indent=2)
1477 1476
1478 def add_defsess_to_index(self, data): 1477 def add_defsess_to_index(self, data):
1479 """ 1478 """
1479 PROBABLY NOW BROKEN by changes since this was deprecated temporarily as at April 18
1480
1480 Included on request of the new codeowner, from Anthony's IUC PR. 1481 Included on request of the new codeowner, from Anthony's IUC PR.
1481 Had to be fixed to keep each assembly with the associated tracks for a default view. 1482 Had to be fixed to keep each assembly with the associated tracks for a default view.
1482 Originally used only the first assembly, putting all tracks there and so breaking some 1483 Originally used only the first assembly, putting all tracks there and so breaking some
1483 when tested with 2 or more. 1484 when tested with 2 or more.
1484 1485
1624 GALAXY_INFRASTRUCTURE_URL = "http://" + GALAXY_INFRASTRUCTURE_URL 1625 GALAXY_INFRASTRUCTURE_URL = "http://" + GALAXY_INFRASTRUCTURE_URL
1625 1626
1626 jc = JbrowseConnector(outdir=args.outdir, jbrowse2path=args.jbrowse2path) 1627 jc = JbrowseConnector(outdir=args.outdir, jbrowse2path=args.jbrowse2path)
1627 1628
1628 default_session_data = {} 1629 default_session_data = {}
1630 trackI = 0
1629 for ass in root.findall("assembly"): 1631 for ass in root.findall("assembly"):
1630 genomes = [ 1632 genomes = [
1631 { 1633 {
1632 "path": x.attrib["path"], 1634 "path": x.attrib["path"],
1633 "label": x.attrib["label"], 1635 "label": x.attrib["label"],
1634 "useuri": x.attrib["useuri"], 1636 "useuri": x.attrib["useuri"],
1635 "meta": metadata_from_node(x.find("metadata")), 1637 "meta": metadata_from_node(x.find("metadata")),
1636 } 1638 }
1637 for x in ass.findall("metadata/genomes/genome") 1639 for x in ass.findall("metadata/genomes/genome")
1638 ] 1640 ]
1639 assref_name = jc.process_genomes(genomes) 1641 primaryGenome = jc.process_genomes(genomes)
1640 if not default_session_data.get(assref_name, None): 1642 if not default_session_data.get(primaryGenome, None):
1641 default_session_data[assref_name] = { 1643 default_session_data[primaryGenome] = {
1642 "tracks": [], 1644 "tracks": [],
1643 "style": {}, 1645 "style": {},
1644 "style_labels": {}, 1646 "style_labels": {},
1645 "visibility": { 1647 "visibility": {
1646 "default_on": [], 1648 "default_on": [],
1648 }, 1650 },
1649 } 1651 }
1650 for track in ass.find("tracks"): 1652 for track in ass.find("tracks"):
1651 track_conf = {} 1653 track_conf = {}
1652 track_conf["trackfiles"] = [] 1654 track_conf["trackfiles"] = []
1653 track_conf["assemblyNames"] = assref_name 1655 track_conf["assemblyNames"] = primaryGenome
1654 is_multi_bigwig = False 1656 is_multi_bigwig = False
1655 try: 1657 try:
1656 if track.find("options/wiggle/multibigwig") and ( 1658 if track.find("options/wiggle/multibigwig") and (
1657 track.find("options/wiggle/multibigwig").text == "True" 1659 track.find("options/wiggle/multibigwig").text == "True"
1658 ): 1660 ):
1662 pass 1664 pass
1663 1665
1664 trackfiles = track.findall("files/trackFile") 1666 trackfiles = track.findall("files/trackFile")
1665 if trackfiles: 1667 if trackfiles:
1666 for x in trackfiles: 1668 for x in trackfiles:
1667 track_conf["label"] = x.attrib["label"] 1669 track_conf["label"] = "%s_%d" % (x.attrib["label"], trackI)
1670 trackI += 1
1668 track_conf["useuri"] = x.attrib["useuri"] 1671 track_conf["useuri"] = x.attrib["useuri"]
1669 if is_multi_bigwig: 1672 if is_multi_bigwig:
1670 multi_bigwig_paths.append( 1673 multi_bigwig_paths.append(
1671 ( 1674 (
1672 x.attrib["label"], 1675 track_conf["label"],
1673 x.attrib["useuri"], 1676 track_conf["useuri"],
1674 os.path.realpath(x.attrib["path"]), 1677 os.path.realpath(x.attrib["path"]),
1675 ) 1678 )
1676 ) 1679 )
1677 else: 1680 else:
1678 if trackfiles: 1681 if trackfiles:
1683 if x.attrib["useuri"].lower() == "yes": 1686 if x.attrib["useuri"].lower() == "yes":
1684 tfa = ( 1687 tfa = (
1685 x.attrib["path"], 1688 x.attrib["path"],
1686 x.attrib["ext"], 1689 x.attrib["ext"],
1687 x.attrib["useuri"], 1690 x.attrib["useuri"],
1688 x.attrib["label"], 1691 track_conf["label"],
1689 metadata, 1692 metadata,
1690 ) 1693 )
1691 else: 1694 else:
1692 tfa = ( 1695 tfa = (
1693 os.path.realpath(x.attrib["path"]), 1696 os.path.realpath(x.attrib["path"]),
1694 x.attrib["ext"], 1697 x.attrib["ext"],
1695 x.attrib["useuri"], 1698 x.attrib["useuri"],
1696 x.attrib["label"], 1699 track_conf["label"],
1697 metadata, 1700 metadata,
1698 ) 1701 )
1699 track_conf["trackfiles"].append(tfa) 1702 track_conf["trackfiles"].append(tfa)
1700 1703
1701 if is_multi_bigwig: 1704 if is_multi_bigwig:
1712 1715
1713 track_conf["category"] = track.attrib["cat"] 1716 track_conf["category"] = track.attrib["cat"]
1714 track_conf["format"] = track.attrib["format"] 1717 track_conf["format"] = track.attrib["format"]
1715 track_conf["conf"] = etree_to_dict(track.find("options")) 1718 track_conf["conf"] = etree_to_dict(track.find("options"))
1716 keys = jc.process_annotations(track_conf) 1719 keys = jc.process_annotations(track_conf)
1717
1718 if keys: 1720 if keys:
1719 for key in keys: 1721 for key in keys:
1720 vis = track.attrib.get("visibility", "default_off") 1722 vis = track.attrib.get("visibility", "default_off")
1721 if not vis: 1723 if not vis:
1722 vis = "default_off" 1724 vis = "default_off"
1723 default_session_data[assref_name]["visibility"][vis].append(key) 1725 default_session_data[primaryGenome]["visibility"][vis].append(key)
1724 trakdat = jc.tracksToAdd[assref_name] 1726 trakdat = jc.tracksToAdd[primaryGenome]
1725 stile = {} 1727 stile = {}
1726 for trak in trakdat: 1728 for trak in trakdat:
1727 if trak["trackId"] == key: 1729 if trak["trackId"] == key:
1728 stile = trak.get("style", {}) 1730 stile = trak.get("style", {})
1729 if track.find("options/style"): 1731 if track.find("options/style"):
1730 supdate = { 1732 supdate = {
1731 item.tag: parse_style_conf(item) 1733 item.tag: parse_style_conf(item)
1732 for item in track.find("options/style") 1734 for item in track.find("options/style")
1733 } 1735 }
1734 stile.update(supdate) 1736 stile.update(supdate)
1735 default_session_data[assref_name]["style"][key] = stile 1737 default_session_data[primaryGenome]["style"][key] = stile
1736 logging.debug("@@@ for %s got style=%s" % (key, stile))
1737 if track.find("options/style_labels"): 1738 if track.find("options/style_labels"):
1738 default_session_data[assref_name]["style_labels"][key] = { 1739 default_session_data[primaryGenome]["style_labels"][key] = {
1739 item.tag: parse_style_conf(item) 1740 item.tag: parse_style_conf(item)
1740 for item in track.find("options/style_labels") 1741 for item in track.find("options/style_labels")
1741 } 1742 }
1742 default_session_data[assref_name]["tracks"].append(key) 1743 default_session_data[primaryGenome]["tracks"].append(key)
1743 default_session_data["defaultLocation"] = root.find( 1744 default_session_data["defaultLocation"] = root.find(
1744 "metadata/general/defaultLocation" 1745 "metadata/general/defaultLocation"
1745 ).text 1746 ).text
1746 default_session_data["session_name"] = root.find( 1747 default_session_data["session_name"] = root.find(
1747 "metadata/general/session_name" 1748 "metadata/general/session_name"
1748 ).text 1749 ).text
1749 logging.debug("default_session=%s" % (default_session_data)) 1750 logging.debug("default_session=%s" % (json.dumps(default_session_data, indent=2)))
1750 jc.zipOut = root.find("metadata/general/zipOut").text == "true" 1751 jc.zipOut = root.find("metadata/general/zipOut").text == "true"
1751 general_data = { 1752 general_data = {
1752 "analytics": root.find("metadata/general/analytics").text, 1753 "analytics": root.find("metadata/general/analytics").text,
1753 "primary_color": root.find("metadata/general/primary_color").text, 1754 "primary_color": root.find("metadata/general/primary_color").text,
1754 "secondary_color": root.find("metadata/general/secondary_color").text, 1755 "secondary_color": root.find("metadata/general/secondary_color").text,
1757 "font_size": root.find("metadata/general/font_size").text, 1758 "font_size": root.find("metadata/general/font_size").text,
1758 } 1759 }
1759 jc.add_general_configuration(general_data) 1760 jc.add_general_configuration(general_data)
1760 trackconf = jc.config_json.get("tracks", []) 1761 trackconf = jc.config_json.get("tracks", [])
1761 for gnome in jc.genome_names: 1762 for gnome in jc.genome_names:
1762 trackconf += jc.tracksToAdd[gnome] 1763 gtracks = jc.tracksToAdd[gnome]
1764 if len(gtracks) > 0:
1765 logging.debug(
1766 "for genome %s adding gtracks %s"
1767 % (gnome, json.dumps(gtracks, indent=2))
1768 )
1769 trackconf += gtracks
1763 jc.config_json["tracks"] = trackconf 1770 jc.config_json["tracks"] = trackconf
1764 assconf = jc.config_json.get("assemblies", []) 1771 assconf = jc.config_json.get("assemblies", [])
1765 assconf += jc.assemblies 1772 assconf += jc.assemblies
1766 jc.config_json["assemblies"] = assconf 1773 jc.config_json["assemblies"] = assconf
1767 logging.debug("assemblies=%s, gnames=%s" % (assconf, jc.genome_names)) 1774 logging.debug(
1775 "assmeta=%s, first_contigs=%s, assemblies=%s, gnames=%s, trackidlist=%s, tracks=%s"
1776 % (
1777 jc.assmeta,
1778 jc.ass_first_contigs,
1779 json.dumps(assconf, indent=2),
1780 jc.genome_names,
1781 jc.trackIdlist,
1782 json.dumps(trackconf, indent=2),
1783 )
1784 )
1768 jc.write_config() 1785 jc.write_config()
1769 jc.add_default_session(default_session_data) 1786 jc.add_default_session(default_session_data)
1770 # note that this can be left in the config.json but has NO EFFECT if add_defsess_to_index is called. 1787 # note that this can be left in the config.json but has NO EFFECT if add_defsess_to_index is called.
1771 # jc.add_defsess_to_index(default_session_data) 1788 # jc.add_defsess_to_index(default_session_data)
1772 # jc.text_index() not sure what broke here. 1789 # jc.text_index() not sure what broke here.