jbrowse2: jbrowse2.py comparison

comparison jbrowse2.py @ 60:81d535970196 draft

planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 403a35e1245fa5e62f4be6116a725b9e4d9c353a

author	fubar
date	Mon, 25 Mar 2024 02:10:05 +0000
parents	f807e219cec3
children	e7a6f7a7148d

comparison

equal deleted inserted replaced

-:f807e219cec3
+:81d535970196
 #!/usr/bin/env python
-# change to accumulating all configuration for config.json based on the default from the clone
 import argparse
 import binascii
 import datetime
 import json
 import logging
 JB2VER = "v2.10.3"
 # version pinned for cloning
 TODAY = datetime.datetime.now().strftime("%Y-%m-%d")
 GALAXY_INFRASTRUCTURE_URL = None
-# version pinned for cloning
 mapped_chars = {
 ">": "__gt__",
 "<": "__lt__",
 "'": "__sq__",
 genome_name = genome_node["meta"]["dataset_dname"].strip()
 if len(genome_name.split()) > 1:
 genome_name = genome_name.split()[0]
 # spaces and cruft break scripts when substituted
 if genome_name not in self.genome_names:
-# ignore dupes - can have multiple pafs with same references?
+# pafs with shared references
 fapath = genome_node["path"]
 if not useuri:
 fapath = os.path.realpath(fapath)
 assem = self.make_assembly(fapath, genome_name, useuri)
 assemblies.append(assem)
 self.genome_names.append(genome_name)
 if self.genome_name is None:
 self.genome_name = (
-genome_name  # first one for all tracks - other than paf
+genome_name  # first one for all tracks
 )
 self.genome_sequence_adapter = assem["sequence"]["adapter"]
 self.genome_firstcontig = None
 if not useuri:
 fl = open(fapath, "r").readline()
 if len(fl.split()) > 1:
 self.genome_firstcontig = fl.split()[0].strip()
 else:
 self.genome_firstcontig = fl
 else:
-fl = urllib.request.urlopen(fapath + ".fai").readline()
+try:
+fl = urllib.request.urlopen(fapath + ".fai").readline()
+except:
+fl = None
 if fl:  # is first row of the text fai so the first contig name
 self.genome_firstcontig = (
 fl.decode("utf8").strip().split()[0]
 )
+else:
+self.genome_firstcontig = None
 if self.config_json.get("assemblies", None):
 self.config_json["assemblies"] += assemblies
 else:
 self.config_json["assemblies"] = assemblies
 faiLocation:
 uri: 'https://s3.amazonaws.com/jbrowse.org/genomes/GRCh38/fasta/GRCh38.fa.gz.fai',
 gziLocation:
 uri: 'https://s3.amazonaws.com/jbrowse.org/genomes/GRCh38/fasta/GRCh38.fa.gz.gzi',
 Cool will not be likely to be a good fit - see discussion at https://github.com/GMOD/jbrowse-components/issues/2438
 """
 tId = trackData["label"]
 # can be served - if public.
 # dsId = trackData["metadata"]["dataset_id"]
 # url = "%s/api/datasets/%s/display?to_ext=hic " % (self.giURL, dsId)
 useuri = trackData["useuri"].lower() == "yes"
 if useuri:
 uri = data
 else:
-uri = trackData["hic_url"]
+uri = "%s.hic" % trackData["label"]
+# slashes in names cause path trouble
+dest = os.path.join(self.outdir, uri)
+cmd = ["cp", data, dest]
+self.subprocess_check_call(cmd)
 categ = trackData["category"]
 trackDict = {
 "type": "HicTrack",
 "trackId": tId,
-"name": uri,
+"name":  trackData["name"],
 "assemblyNames": [self.genome_name],
 "category": [
 categ,
 ],
 "adapter": {
 "type": "HicAdapter",
-"hicLocation": uri,
+"hicLocation": { "uri": uri }
-},
+}
-"displays": [
+}
-{
-"type": "LinearHicDisplay",
-"displayId": "%s-LinearHicDisplay" % tId,
-},
-],
-}
-style_json = self._prepare_track_style(trackDict)
-trackDict["style"] = style_json
 self.tracksToAdd.append(trackDict)
 self.trackIdlist.append(tId)
 def add_maf(self, data, trackData):
 """
 self.tracksToAdd.append(trackDict)
 self.trackIdlist.append(tId)
 os.unlink(gff3)
 def add_bigwig(self, data, trackData):
-""" "type": "LinearWiggleDisplay",
-"configuration": {},
-"selectedRendering": "",
-"resolution": 1,
-"posColor": "rgb(228, 26, 28)",
-"negColor": "rgb(255, 255, 51)",
-"constraints": {}
-"""
 useuri = trackData["useuri"].lower() == "yes"
 if useuri:
 url = data
 else:
 url = "%s.bigwig" % trackData["label"]
 # Return non-human label for use in other fields
 yield outputTrackConfig["label"]
 def add_default_session(self, default_data):
 """
-Add some default session settings: set some assemblies/tracks on/off
+default session settings are hard and fragile.
+.add_default_view() and other configuration code adapted from
+https://github.com/abretaud/tools-iuc/blob/jbrowse2/tools/jbrowse2/jbrowse2.py
 """
 tracks_data = []
 # TODO using the default session for now, but check out session specs in the future https://github.com/GMOD/jbrowse-components/issues/2708
-# We need to know the track type from the config.json generated just before
 track_types = {}
 with open(self.config_json_file, "r") as config_file:
 config_json = json.load(config_file)
 if self.config_json:
 config_json.update(self.config_json)
 for track_conf in self.tracksToAdd:
-track_types[track_conf["trackId"]] = track_conf["type"]
 tId = track_conf["trackId"]
-#if tId in data["visibility"]["default_on"]:
+track_types[tId] = track_conf["type"]
 style_data = default_data["style"].get(tId,  None)
 if not style_data:
-logging.warn("### No style data in default data for %s" % tId)
+logging.warn("### No style data in default data %s for %s" % (default_data, tId))
 style_data = {"type": "LinearBasicDisplay"}
 if "displays" in track_conf:
 disp = track_conf["displays"][0]["type"]
 style_data["type"] = disp
 if track_conf.get("style_labels", None):
 "displays": [style_data],
 }
 )
 # The view for the assembly we're adding
 view_json = {"type": "LinearGenomeView", "tracks": tracks_data}
+logging.warn("### view_json=%s" % view_json)
 refName = None
 drdict = {
 "reversed": False,
 "assemblyName": self.genome_name,
 "start": 1,
 config_json["configuration"].update(config_data)
 self.config_json.update(config_json)
 with open(config_path, "w") as config_file:
 json.dump(self.config_json, config_file, indent=2)
-def clone_jbrowse(self, realclone=True):
+def clone_jbrowse(self, realclone=False):
-"""Clone a JBrowse directory into a destination directory. This also works in Biocontainer testing now"""
+"""Clone a JBrowse directory into a destination directory. This also works in Biocontainer testing now
+Leave as True between version updates on temporary tools - requires manual conda trigger :(
+"""
 dest = self.outdir
 if realclone:
 self.subprocess_check_call(
 ["jbrowse", "create", dest, "-f", "--tag", f"{JB2VER}"]
 )
 for x in root.findall("metadata/genomes/genome")
 ],
 )
 jc.process_genomes()
-# .add_default_view() replace from https://github.com/abretaud/tools-iuc/blob/jbrowse2/tools/jbrowse2/jbrowse2.py
 default_session_data = {
 "visibility": {
 "default_on": [],
 "default_off": [],
 },
 trackfiles = track.findall("files/trackFile")
 if trackfiles:
 for x in track.findall("files/trackFile"):
 track_conf["label"] = x.attrib["label"]
+trackkey = track_conf["label"]
 track_conf["useuri"] = x.attrib["useuri"]
 if is_multi_bigwig:
 multi_bigwig_paths.append(
 (
 x.attrib["label"],
 {},  # No metadata for multiple bigwig
 )
 )
 track_conf["category"] = track.attrib["cat"]
 track_conf["format"] = track.attrib["format"]
-if track.find("options/style"):
-track_conf["style"] = {
-item.tag: parse_style_conf(item) for item in track.find("options/style")
-}
-else:
-track_conf["style"] = {}
-if track.find("options/style_labels"):
-track_conf["style_labels"] = {
-item.tag: parse_style_conf(item)
-for item in track.find("options/style_labels")
-}
 track_conf["conf"] = etree_to_dict(track.find("options"))
 track_conf["category"] = track.attrib["cat"]
 track_conf["format"] = track.attrib["format"]
 keys = jc.process_annotations(track_conf)
 if keys:
 for key in keys:
 default_session_data["visibility"][
 track.attrib.get("visibility", "default_off")
 ].append(key)
-if track_conf.get("style", None):
+if track.find("options/style"):
-default_session_data["style"][key] = track_conf["style"]
+default_session_data["style"][key] = {
-if track_conf.get("style_lables", None):
+item.tag: parse_style_conf(item) for item in track.find("options/style")
-default_session_data["style_labels"][key] = track_conf.get(
+}
-"style_labels", None
+logging.warn("### added %s to defsess %s for %s" % (trackkey, default_session_data, key ))
-)
+else:
+default_session_data["style"][key] = {}
+logging.warn("@@@@ no options/style found for %s" % (key))
+if track.find("options/style_labels"):
+default_session_data["style_labels"][key] = {
+item.tag: parse_style_conf(item)
+for item in track.find("options/style_labels")
+}
 default_session_data["defaultLocation"] = root.find(
 "metadata/general/defaultLocation"
 ).text
 default_session_data["session_name"] = root.find(
 "metadata/general/session_name"

Mercurial > repos > fubar > jbrowse2

comparison jbrowse2.py @ 60:81d535970196 draft