Mercurial > repos > fubar > jbrowse2
changeset 14:7c2e28e144f3 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 5d84967148d45684d585d4e12b210dc5e12e4776
| author | fubar |
|---|---|
| date | Mon, 22 Jan 2024 12:05:09 +0000 |
| parents | 1d86925dbb4c |
| children | cce8dacb240f |
| files | abjbrowse2.py jbrowse2.py |
| diffstat | 2 files changed, 584 insertions(+), 410 deletions(-) [+] |
line wrap: on
line diff
--- a/abjbrowse2.py Mon Jan 22 11:52:19 2024 +0000 +++ b/abjbrowse2.py Mon Jan 22 12:05:09 2024 +0000 @@ -15,7 +15,7 @@ from collections import defaultdict logging.basicConfig(level=logging.INFO) -log = logging.getLogger('jbrowse') +log = logging.getLogger("jbrowse") TODAY = datetime.datetime.now().strftime("%Y-%m-%d") GALAXY_INFRASTRUCTURE_URL = None @@ -75,20 +75,20 @@ """ OPACITY_MATH = { - 'linear': """ + "linear": """ var opacity = (score - ({min})) / (({max}) - ({min})); """, - 'logarithmic': """ + "logarithmic": """ var opacity = Math.log10(score - ({min})) / Math.log10(({max}) - ({min})); """, - 'blast': """ + "blast": """ var opacity = 0; if(score == 0.0) {{ opacity = 1; }} else {{ opacity = (20 - Math.log10(score)) / 180; }} - """ + """, } BREWER_COLOUR_IDX = 0 @@ -113,15 +113,15 @@ ] BREWER_DIVERGING_PALLETES = { - 'BrBg': ("#543005", "#003c30"), - 'PiYg': ("#8e0152", "#276419"), - 'PRGn': ("#40004b", "#00441b"), - 'PuOr': ("#7f3b08", "#2d004b"), - 'RdBu': ("#67001f", "#053061"), - 'RdGy': ("#67001f", "#1a1a1a"), - 'RdYlBu': ("#a50026", "#313695"), - 'RdYlGn': ("#a50026", "#006837"), - 'Spectral': ("#9e0142", "#5e4fa2"), + "BrBg": ("#543005", "#003c30"), + "PiYg": ("#8e0152", "#276419"), + "PRGn": ("#40004b", "#00441b"), + "PuOr": ("#7f3b08", "#2d004b"), + "RdBu": ("#67001f", "#053061"), + "RdGy": ("#67001f", "#1a1a1a"), + "RdYlBu": ("#a50026", "#313695"), + "RdYlGn": ("#a50026", "#006837"), + "Spectral": ("#9e0142", "#5e4fa2"), } def __init__(self): @@ -129,15 +129,15 @@ def rgb_from_hex(self, hexstr): # http://stackoverflow.com/questions/4296249/how-do-i-convert-a-hex-triplet-to-an-rgb-tuple-and-back - return struct.unpack('BBB', binascii.unhexlify(hexstr)) + return struct.unpack("BBB", binascii.unhexlify(hexstr)) def min_max_gff(self, gff_file): min_val = None max_val = None - with open(gff_file, 'r') as handle: + with open(gff_file, "r") as handle: for line in handle: try: - value = float(line.split('\t')[5]) + value = float(line.split("\t")[5]) min_val = min(value, (min_val or value)) max_val = max(value, (max_val or value)) @@ -151,112 +151,128 @@ return min_val, max_val def hex_from_rgb(self, r, g, b): - return '#%02x%02x%02x' % (r, g, b) + return "#%02x%02x%02x" % (r, g, b) def _get_colours(self): - r, g, b = self.BREWER_COLOUR_SCHEMES[self.brewer_colour_idx % len(self.BREWER_COLOUR_SCHEMES)] + r, g, b = self.BREWER_COLOUR_SCHEMES[ + self.brewer_colour_idx % len(self.BREWER_COLOUR_SCHEMES) + ] self.brewer_colour_idx += 1 return r, g, b def parse_menus(self, track): - trackConfig = {'menuTemplate': [{}, {}, {}, {}]} + trackConfig = {"menuTemplate": [{}, {}, {}, {}]} - if 'menu' in track['menus']: - menu_list = [track['menus']['menu']] - if isinstance(track['menus']['menu'], list): - menu_list = track['menus']['menu'] + if "menu" in track["menus"]: + menu_list = [track["menus"]["menu"]] + if isinstance(track["menus"]["menu"], list): + menu_list = track["menus"]["menu"] for m in menu_list: tpl = { - 'action': m['action'], - 'label': m.get('label', '{name}'), - 'iconClass': m.get('iconClass', 'dijitIconBookmark'), + "action": m["action"], + "label": m.get("label", "{name}"), + "iconClass": m.get("iconClass", "dijitIconBookmark"), } - if 'url' in m: - tpl['url'] = m['url'] - if 'content' in m: - tpl['content'] = m['content'] - if 'title' in m: - tpl['title'] = m['title'] + if "url" in m: + tpl["url"] = m["url"] + if "content" in m: + tpl["content"] = m["content"] + if "title" in m: + tpl["title"] = m["title"] - trackConfig['menuTemplate'].append(tpl) + trackConfig["menuTemplate"].append(tpl) return trackConfig def parse_colours(self, track, trackFormat, gff3=None): # Wiggle tracks have a bicolor pallete - trackConfig = {'style': {}} - if trackFormat == 'wiggle': + trackConfig = {"style": {}} + if trackFormat == "wiggle": + + trackConfig["style"]["pos_color"] = track["wiggle"]["color_pos"] + trackConfig["style"]["neg_color"] = track["wiggle"]["color_neg"] - trackConfig['style']['pos_color'] = track['wiggle']['color_pos'] - trackConfig['style']['neg_color'] = track['wiggle']['color_neg'] - - if trackConfig['style']['pos_color'] == '__auto__': - trackConfig['style']['neg_color'] = self.hex_from_rgb(*self._get_colours()) - trackConfig['style']['pos_color'] = self.hex_from_rgb(*self._get_colours()) + if trackConfig["style"]["pos_color"] == "__auto__": + trackConfig["style"]["neg_color"] = self.hex_from_rgb( + *self._get_colours() + ) + trackConfig["style"]["pos_color"] = self.hex_from_rgb( + *self._get_colours() + ) # Wiggle tracks can change colour at a specified place - bc_pivot = track['wiggle']['bicolor_pivot'] - if bc_pivot not in ('mean', 'zero'): + bc_pivot = track["wiggle"]["bicolor_pivot"] + if bc_pivot not in ("mean", "zero"): # The values are either one of those two strings # or a number bc_pivot = float(bc_pivot) - trackConfig['bicolor_pivot'] = bc_pivot - elif 'scaling' in track: - if track['scaling']['method'] == 'ignore': - if track['scaling']['scheme']['color'] != '__auto__': - trackConfig['style']['color'] = track['scaling']['scheme']['color'] + trackConfig["bicolor_pivot"] = bc_pivot + elif "scaling" in track: + if track["scaling"]["method"] == "ignore": + if track["scaling"]["scheme"]["color"] != "__auto__": + trackConfig["style"]["color"] = track["scaling"]["scheme"]["color"] else: - trackConfig['style']['color'] = self.hex_from_rgb(*self._get_colours()) + trackConfig["style"]["color"] = self.hex_from_rgb( + *self._get_colours() + ) else: # Scored method - algo = track['scaling']['algo'] + algo = track["scaling"]["algo"] # linear, logarithmic, blast - scales = track['scaling']['scales'] + scales = track["scaling"]["scales"] # type __auto__, manual (min, max) - scheme = track['scaling']['scheme'] + scheme = track["scaling"]["scheme"] # scheme -> (type (opacity), color) # ================================== # GENE CALLS OR BLAST # ================================== - if trackFormat == 'blast': + if trackFormat == "blast": red, green, blue = self._get_colours() - color_function = self.COLOR_FUNCTION_TEMPLATE.format(**{ - 'score': "feature._parent.get('score')", - 'opacity': self.OPACITY_MATH['blast'], - 'red': red, - 'green': green, - 'blue': blue, - }) - trackConfig['style']['color'] = color_function.replace('\n', '') - elif trackFormat == 'gene_calls': + color_function = self.COLOR_FUNCTION_TEMPLATE.format( + **{ + "score": "feature._parent.get('score')", + "opacity": self.OPACITY_MATH["blast"], + "red": red, + "green": green, + "blue": blue, + } + ) + trackConfig["style"]["color"] = color_function.replace("\n", "") + elif trackFormat == "gene_calls": # Default values, based on GFF3 spec min_val = 0 max_val = 1000 # Get min/max and build a scoring function since JBrowse doesn't - if scales['type'] == 'automatic' or scales['type'] == '__auto__': + if scales["type"] == "automatic" or scales["type"] == "__auto__": min_val, max_val = self.min_max_gff(gff3) else: - min_val = scales.get('min', 0) - max_val = scales.get('max', 1000) + min_val = scales.get("min", 0) + max_val = scales.get("max", 1000) - if scheme['color'] == '__auto__': - user_color = 'undefined' + if scheme["color"] == "__auto__": + user_color = "undefined" auto_color = "'%s'" % self.hex_from_rgb(*self._get_colours()) - elif scheme['color'].startswith('#'): - user_color = "'%s'" % self.hex_from_rgb(*self.rgb_from_hex(scheme['color'][1:])) - auto_color = 'undefined' + elif scheme["color"].startswith("#"): + user_color = "'%s'" % self.hex_from_rgb( + *self.rgb_from_hex(scheme["color"][1:]) + ) + auto_color = "undefined" else: - user_color = 'undefined' + user_color = "undefined" auto_color = "'%s'" % self.hex_from_rgb(*self._get_colours()) - color_function = self.COLOR_FUNCTION_TEMPLATE_QUAL.format(**{ - 'opacity': self.OPACITY_MATH[algo].format(**{'max': max_val, 'min': min_val}), - 'user_spec_color': user_color, - 'auto_gen_color': auto_color, - }) + color_function = self.COLOR_FUNCTION_TEMPLATE_QUAL.format( + **{ + "opacity": self.OPACITY_MATH[algo].format( + **{"max": max_val, "min": min_val} + ), + "user_spec_color": user_color, + "auto_gen_color": auto_color, + } + ) - trackConfig['style']['color'] = color_function.replace('\n', '') + trackConfig["style"]["color"] = color_function.replace("\n", "") return trackConfig @@ -273,12 +289,12 @@ dd[k].append(v) d = {t.tag: {k: v[0] if len(v) == 1 else v for k, v in dd.items()}} if t.attrib: - d[t.tag].update(('@' + k, v) for k, v in t.attrib.items()) + d[t.tag].update(("@" + k, v) for k, v in t.attrib.items()) if t.text: text = t.text.strip() if children or t.attrib: if text: - d[t.tag]['#text'] = text + d[t.tag]["#text"] = text else: d[t.tag] = text return d @@ -292,43 +308,52 @@ def metadata_from_node(node): metadata = {} try: - if len(node.findall('dataset')) != 1: + if len(node.findall("dataset")) != 1: # exit early return metadata except Exception: return {} - for (key, value) in node.findall('dataset')[0].attrib.items(): - metadata['dataset_%s' % key] = value + for (key, value) in node.findall("dataset")[0].attrib.items(): + metadata["dataset_%s" % key] = value - for (key, value) in node.findall('history')[0].attrib.items(): - metadata['history_%s' % key] = value + for (key, value) in node.findall("history")[0].attrib.items(): + metadata["history_%s" % key] = value - for (key, value) in node.findall('metadata')[0].attrib.items(): - metadata['metadata_%s' % key] = value + for (key, value) in node.findall("metadata")[0].attrib.items(): + metadata["metadata_%s" % key] = value - for (key, value) in node.findall('tool')[0].attrib.items(): - metadata['tool_%s' % key] = value + for (key, value) in node.findall("tool")[0].attrib.items(): + metadata["tool_%s" % key] = value # Additional Mappings applied: - metadata['dataset_edam_format'] = '<a target="_blank" href="http://edamontology.org/{0}">{1}</a>'.format(metadata['dataset_edam_format'], metadata['dataset_file_ext']) - metadata['history_user_email'] = '<a href="mailto:{0}">{0}</a>'.format(metadata['history_user_email']) - metadata['history_display_name'] = '<a target="_blank" href="{galaxy}/history/view/{encoded_hist_id}">{hist_name}</a>'.format( + metadata[ + "dataset_edam_format" + ] = '<a target="_blank" href="http://edamontology.org/{0}">{1}</a>'.format( + metadata["dataset_edam_format"], metadata["dataset_file_ext"] + ) + metadata["history_user_email"] = '<a href="mailto:{0}">{0}</a>'.format( + metadata["history_user_email"] + ) + metadata[ + "history_display_name" + ] = '<a target="_blank" href="{galaxy}/history/view/{encoded_hist_id}">{hist_name}</a>'.format( galaxy=GALAXY_INFRASTRUCTURE_URL, - encoded_hist_id=metadata['history_id'], - hist_name=metadata['history_display_name'] + encoded_hist_id=metadata["history_id"], + hist_name=metadata["history_display_name"], ) - metadata['tool_tool'] = '<a target="_blank" href="{galaxy}/datasets/{encoded_id}/show_params">{tool_id}</a>'.format( + metadata[ + "tool_tool" + ] = '<a target="_blank" href="{galaxy}/datasets/{encoded_id}/show_params">{tool_id}</a>'.format( galaxy=GALAXY_INFRASTRUCTURE_URL, - encoded_id=metadata['dataset_id'], - tool_id=metadata['tool_tool_id'], + encoded_id=metadata["dataset_id"], + tool_id=metadata["tool_tool_id"], # tool_version=metadata['tool_tool_version'], ) return metadata class JbrowseConnector(object): - def __init__(self, jbrowse, outdir, genomes): self.cs = ColorScaling() self.jbrowse = jbrowse @@ -349,67 +374,81 @@ def subprocess_check_call(self, command, output=None): if output: - log.debug('cd %s && %s > %s', self.outdir, ' '.join(command), output) + log.debug("cd %s && %s > %s", self.outdir, " ".join(command), output) subprocess.check_call(command, cwd=self.outdir, stdout=output) else: - log.debug('cd %s && %s', self.outdir, ' '.join(command)) + log.debug("cd %s && %s", self.outdir, " ".join(command)) subprocess.check_call(command, cwd=self.outdir) def subprocess_popen(self, command): - log.debug('cd %s && %s', self.outdir, command) - p = subprocess.Popen(command, shell=True, stdin=subprocess.PIPE, stdout=subprocess.PIPE, stderr=subprocess.PIPE) + log.debug("cd %s && %s", self.outdir, command) + p = subprocess.Popen( + command, + shell=True, + stdin=subprocess.PIPE, + stdout=subprocess.PIPE, + stderr=subprocess.PIPE, + ) output, err = p.communicate() retcode = p.returncode if retcode != 0: - log.error('cd %s && %s', self.outdir, command) + log.error("cd %s && %s", self.outdir, command) log.error(output) log.error(err) raise RuntimeError("Command failed with exit code %s" % (retcode)) def subprocess_check_output(self, command): - log.debug('cd %s && %s', self.outdir, ' '.join(command)) + log.debug("cd %s && %s", self.outdir, " ".join(command)) return subprocess.check_output(command, cwd=self.outdir) def symlink_or_copy(self, src, dest): - if 'GALAXY_JBROWSE_SYMLINKS' in os.environ and bool(os.environ['GALAXY_JBROWSE_SYMLINKS']): - cmd = ['ln', '-s', src, dest] + if "GALAXY_JBROWSE_SYMLINKS" in os.environ and bool( + os.environ["GALAXY_JBROWSE_SYMLINKS"] + ): + cmd = ["ln", "-s", src, dest] else: - cmd = ['cp', src, dest] + cmd = ["cp", src, dest] return self.subprocess_check_call(cmd) def symlink_or_copy_load_action(self): - if 'GALAXY_JBROWSE_SYMLINKS' in os.environ and bool(os.environ['GALAXY_JBROWSE_SYMLINKS']): - return 'symlink' + if "GALAXY_JBROWSE_SYMLINKS" in os.environ and bool( + os.environ["GALAXY_JBROWSE_SYMLINKS"] + ): + return "symlink" else: - return 'copy' + return "copy" def check_existing(self, destination): - existing = os.path.join(destination, 'data', "config.json") + existing = os.path.join(destination, "data", "config.json") if os.path.exists(existing): - with open(existing, 'r') as existing_conf: + with open(existing, "r") as existing_conf: conf = json.load(existing_conf) - if 'assemblies' in conf: - for assembly in conf['assemblies']: - if 'name' in assembly: - self.assembly_ids[assembly['name']] = None + if "assemblies" in conf: + for assembly in conf["assemblies"]: + if "name" in assembly: + self.assembly_ids[assembly["name"]] = None def process_genomes(self): for genome_node in self.genome_paths: # We only expect one input genome per run. This for loop is just # easier to write than the alternative / catches any possible # issues. - self.add_assembly(genome_node['path'], genome_node['label']) + self.add_assembly(genome_node["path"], genome_node["label"]) def add_assembly(self, path, label, default=True): # Find a non-existing filename for the new genome # (to avoid colision when upgrading an existing instance) - rel_seq_path = os.path.join('data', 'assembly') + rel_seq_path = os.path.join("data", "assembly") seq_path = os.path.join(self.outdir, rel_seq_path) fn_try = 1 - while (os.path.exists(seq_path + '.fasta') or os.path.exists(seq_path + '.fasta.gz') - or os.path.exists(seq_path + '.fasta.gz.fai') or os.path.exists(seq_path + '.fasta.gz.gzi')): - rel_seq_path = os.path.join('data', 'assembly%s' % fn_try) + while ( + os.path.exists(seq_path + ".fasta") + or os.path.exists(seq_path + ".fasta.gz") + or os.path.exists(seq_path + ".fasta.gz.fai") + or os.path.exists(seq_path + ".fasta.gz.gzi") + ): + rel_seq_path = os.path.join("data", "assembly%s" % fn_try) seq_path = os.path.join(self.outdir, rel_seq_path) fn_try += 1 @@ -423,84 +462,101 @@ # Find a default scaffold to display # TODO this may not be necessary in the future, see https://github.com/GMOD/jbrowse-components/issues/2708 - with open(path, 'r') as fa_handle: - fa_header = fa_handle.readline()[1:].strip().split(' ')[0] + with open(path, "r") as fa_handle: + fa_header = fa_handle.readline()[1:].strip().split(" ")[0] self.assembly_ids[uniq_label] = fa_header if default: self.current_assembly_id = uniq_label - copied_genome = seq_path + '.fasta' + copied_genome = seq_path + ".fasta" shutil.copy(path, copied_genome) # Compress with bgzip - cmd = ['bgzip', copied_genome] + cmd = ["bgzip", copied_genome] self.subprocess_check_call(cmd) # FAI Index - cmd = ['samtools', 'faidx', copied_genome + '.gz'] + cmd = ["samtools", "faidx", copied_genome + ".gz"] self.subprocess_check_call(cmd) - self.subprocess_check_call([ - 'jbrowse', 'add-assembly', - '--load', 'inPlace', - '--name', uniq_label, - '--type', 'bgzipFasta', - '--target', os.path.join(self.outdir, 'data'), - '--skipCheck', - rel_seq_path + '.fasta.gz']) + self.subprocess_check_call( + [ + "jbrowse", + "add-assembly", + "--load", + "inPlace", + "--name", + uniq_label, + "--type", + "bgzipFasta", + "--target", + os.path.join(self.outdir, "data"), + "--skipCheck", + rel_seq_path + ".fasta.gz", + ] + ) return uniq_label def text_index(self): # Index tracks args = [ - 'jbrowse', 'text-index', - '--target', os.path.join(self.outdir, 'data'), - '--assemblies', self.current_assembly_id, + "jbrowse", + "text-index", + "--target", + os.path.join(self.outdir, "data"), + "--assemblies", + self.current_assembly_id, ] - tracks = ','.join(self.tracksToIndex) + tracks = ",".join(self.tracksToIndex) if tracks: - args += ['--tracks', tracks] + args += ["--tracks", tracks] self.subprocess_check_call(args) def _blastxml_to_gff3(self, xml, min_gap=10): gff3_unrebased = tempfile.NamedTemporaryFile(delete=False) - cmd = ['python', os.path.join(INSTALLED_TO, 'blastxml_to_gapped_gff3.py'), - '--trim', '--trim_end', '--include_seq', '--min_gap', str(min_gap), xml] - log.debug('cd %s && %s > %s', self.outdir, ' '.join(cmd), gff3_unrebased.name) + cmd = [ + "python", + os.path.join(INSTALLED_TO, "blastxml_to_gapped_gff3.py"), + "--trim", + "--trim_end", + "--include_seq", + "--min_gap", + str(min_gap), + xml, + ] + log.debug("cd %s && %s > %s", self.outdir, " ".join(cmd), gff3_unrebased.name) subprocess.check_call(cmd, cwd=self.outdir, stdout=gff3_unrebased) gff3_unrebased.close() return gff3_unrebased.name def _prepare_track_style(self, xml_conf): - style_data = { - "type": "LinearBasicDisplay" - } + style_data = {"type": "LinearBasicDisplay"} + + if "display" in xml_conf["style"]: + style_data["type"] = xml_conf["style"]["display"] + del xml_conf["style"]["display"] - if 'display' in xml_conf['style']: - style_data['type'] = xml_conf['style']['display'] - del xml_conf['style']['display'] + style_data["displayId"] = "%s_%s" % (xml_conf["label"], style_data["type"]) - style_data['displayId'] = "%s_%s" % (xml_conf['label'], style_data['type']) + style_data.update(xml_conf["style"]) - style_data.update(xml_conf['style']) - - return {'displays': [style_data]} + return {"displays": [style_data]} def add_blastxml(self, data, trackData, blastOpts, **kwargs): - gff3 = self._blastxml_to_gff3(data, min_gap=blastOpts['min_gap']) + gff3 = self._blastxml_to_gff3(data, min_gap=blastOpts["min_gap"]) - if 'parent' in blastOpts and blastOpts['parent'] != 'None': + if "parent" in blastOpts and blastOpts["parent"] != "None": gff3_rebased = tempfile.NamedTemporaryFile(delete=False) - cmd = ['python', os.path.join(INSTALLED_TO, 'gff3_rebase.py')] - if blastOpts.get('protein', 'false') == 'true': - cmd.append('--protein2dna') - cmd.extend([os.path.realpath(blastOpts['parent']), gff3]) - log.debug('cd %s && %s > %s', self.outdir, ' '.join(cmd), gff3_rebased.name) + cmd = ["python", os.path.join(INSTALLED_TO, "gff3_rebase.py")] + if blastOpts.get("protein", "false") == "true": + cmd.append("--protein2dna") + cmd.extend([os.path.realpath(blastOpts["parent"]), gff3]) + log.debug("cd %s && %s > %s", self.outdir, " ".join(cmd), gff3_rebased.name) subprocess.check_call(cmd, cwd=self.outdir, stdout=gff3_rebased) gff3_rebased.close() @@ -508,7 +564,7 @@ shutil.copy(gff3_rebased.name, gff3) os.unlink(gff3_rebased.name) - rel_dest = os.path.join('data', trackData['label'] + '.gff') + rel_dest = os.path.join("data", trackData["label"] + ".gff") dest = os.path.join(self.outdir, rel_dest) self._sort_gff(gff3, dest) @@ -516,17 +572,29 @@ style_json = self._prepare_track_style(trackData) - self._add_track(trackData['label'], trackData['key'], trackData['category'], rel_dest + '.gz', config=style_json) + self._add_track( + trackData["label"], + trackData["key"], + trackData["category"], + rel_dest + ".gz", + config=style_json, + ) def add_bigwig(self, data, trackData, wiggleOpts, **kwargs): - rel_dest = os.path.join('data', trackData['label'] + '.bw') + rel_dest = os.path.join("data", trackData["label"] + ".bw") dest = os.path.join(self.outdir, rel_dest) self.symlink_or_copy(os.path.realpath(data), dest) style_json = self._prepare_track_style(trackData) - self._add_track(trackData['label'], trackData['key'], trackData['category'], rel_dest, config=style_json) + self._add_track( + trackData["label"], + trackData["key"], + trackData["category"], + rel_dest, + config=style_json, + ) # Anything ending in "am" (Bam or Cram) def add_xam(self, data, trackData, xamOpts, index=None, ext="bam", **kwargs): @@ -535,121 +603,164 @@ if ext == "cram": index_ext = "crai" - rel_dest = os.path.join('data', trackData['label'] + '.%s' % ext) + rel_dest = os.path.join("data", trackData["label"] + ".%s" % ext) dest = os.path.join(self.outdir, rel_dest) self.symlink_or_copy(os.path.realpath(data), dest) if index is not None and os.path.exists(os.path.realpath(index)): # xai most probably made by galaxy and stored in galaxy dirs, need to copy it to dest - self.subprocess_check_call(['cp', os.path.realpath(index), dest + '.%s' % index_ext]) + self.subprocess_check_call( + ["cp", os.path.realpath(index), dest + ".%s" % index_ext] + ) else: # Can happen in exotic condition # e.g. if bam imported as symlink with datatype=unsorted.bam, then datatype changed to bam # => no index generated by galaxy, but there might be one next to the symlink target # this trick allows to skip the bam sorting made by galaxy if already done outside - if os.path.exists(os.path.realpath(data) + '.%s' % index_ext): - self.symlink_or_copy(os.path.realpath(data) + '.%s' % index_ext, dest + '.%s' % index_ext) + if os.path.exists(os.path.realpath(data) + ".%s" % index_ext): + self.symlink_or_copy( + os.path.realpath(data) + ".%s" % index_ext, dest + ".%s" % index_ext + ) else: - log.warn('Could not find a bam index (.%s file) for %s', (index_ext, data)) + log.warn( + "Could not find a bam index (.%s file) for %s", (index_ext, data) + ) style_json = self._prepare_track_style(trackData) - self._add_track(trackData['label'], trackData['key'], trackData['category'], rel_dest, config=style_json) + self._add_track( + trackData["label"], + trackData["key"], + trackData["category"], + rel_dest, + config=style_json, + ) def add_vcf(self, data, trackData, vcfOpts={}, zipped=False, **kwargs): if zipped: - rel_dest = os.path.join('data', trackData['label'] + '.vcf.gz') + rel_dest = os.path.join("data", trackData["label"] + ".vcf.gz") dest = os.path.join(self.outdir, rel_dest) shutil.copy(os.path.realpath(data), dest) else: - rel_dest = os.path.join('data', trackData['label'] + '.vcf') + rel_dest = os.path.join("data", trackData["label"] + ".vcf") dest = os.path.join(self.outdir, rel_dest) shutil.copy(os.path.realpath(data), dest) - cmd = ['bgzip', dest] + cmd = ["bgzip", dest] self.subprocess_check_call(cmd) - cmd = ['tabix', dest + '.gz'] + cmd = ["tabix", dest + ".gz"] self.subprocess_check_call(cmd) - rel_dest = os.path.join('data', trackData['label'] + '.vcf.gz') + rel_dest = os.path.join("data", trackData["label"] + ".vcf.gz") style_json = self._prepare_track_style(trackData) - self._add_track(trackData['label'], trackData['key'], trackData['category'], rel_dest, config=style_json) + self._add_track( + trackData["label"], + trackData["key"], + trackData["category"], + rel_dest, + config=style_json, + ) def add_gff(self, data, format, trackData, gffOpts, **kwargs): - rel_dest = os.path.join('data', trackData['label'] + '.gff') + rel_dest = os.path.join("data", trackData["label"] + ".gff") dest = os.path.join(self.outdir, rel_dest) self._sort_gff(data, dest) style_json = self._prepare_track_style(trackData) - self._add_track(trackData['label'], trackData['key'], trackData['category'], rel_dest + '.gz', config=style_json) + self._add_track( + trackData["label"], + trackData["key"], + trackData["category"], + rel_dest + ".gz", + config=style_json, + ) def add_bed(self, data, format, trackData, gffOpts, **kwargs): - rel_dest = os.path.join('data', trackData['label'] + '.bed') + rel_dest = os.path.join("data", trackData["label"] + ".bed") dest = os.path.join(self.outdir, rel_dest) self._sort_bed(data, dest) style_json = self._prepare_track_style(trackData) - self._add_track(trackData['label'], trackData['key'], trackData['category'], rel_dest + '.gz', config=style_json) + self._add_track( + trackData["label"], + trackData["key"], + trackData["category"], + rel_dest + ".gz", + config=style_json, + ) def add_paf(self, data, trackData, pafOpts, **kwargs): - rel_dest = os.path.join('data', trackData['label'] + '.paf') + rel_dest = os.path.join("data", trackData["label"] + ".paf") dest = os.path.join(self.outdir, rel_dest) self.symlink_or_copy(os.path.realpath(data), dest) - added_assembly = self.add_assembly(pafOpts['genome'], pafOpts['genome_label'], default=False) + added_assembly = self.add_assembly( + pafOpts["genome"], pafOpts["genome_label"], default=False + ) style_json = self._prepare_track_style(trackData) - self._add_track(trackData['label'], trackData['key'], trackData['category'], rel_dest, assemblies=[self.current_assembly_id, added_assembly], config=style_json) + self._add_track( + trackData["label"], + trackData["key"], + trackData["category"], + rel_dest, + assemblies=[self.current_assembly_id, added_assembly], + config=style_json, + ) def add_hic(self, data, trackData, hicOpts, **kwargs): - rel_dest = os.path.join('data', trackData['label'] + '.hic') + rel_dest = os.path.join("data", trackData["label"] + ".hic") dest = os.path.join(self.outdir, rel_dest) self.symlink_or_copy(os.path.realpath(data), dest) style_json = self._prepare_track_style(trackData) - self._add_track(trackData['label'], trackData['key'], trackData['category'], rel_dest, config=style_json) + self._add_track( + trackData["label"], + trackData["key"], + trackData["category"], + rel_dest, + config=style_json, + ) def add_sparql(self, url, query, query_refnames, trackData): json_track_data = { "type": "FeatureTrack", "trackId": id, - "name": trackData['label'], + "name": trackData["label"], "adapter": { "type": "SPARQLAdapter", - "endpoint": { - "uri": url, - "locationType": "UriLocation" - }, - "queryTemplate": query + "endpoint": {"uri": url, "locationType": "UriLocation"}, + "queryTemplate": query, }, - "category": [ - trackData['category'] - ], - "assemblyNames": [ - self.current_assembly_id - ] + "category": [trackData["category"]], + "assemblyNames": [self.current_assembly_id], } if query_refnames: - json_track_data['adapter']['refNamesQueryTemplate']: query_refnames + json_track_data["adapter"]["refNamesQueryTemplate"]: query_refnames - self.subprocess_check_call([ - 'jbrowse', 'add-track-json', - '--target', os.path.join(self.outdir, 'data'), - json_track_data]) + self.subprocess_check_call( + [ + "jbrowse", + "add-track-json", + "--target", + os.path.join(self.outdir, "data"), + json_track_data, + ] + ) # Doesn't work as of 1.6.4, might work in the future # self.subprocess_check_call([ @@ -666,20 +777,27 @@ assemblies_opt = self.current_assembly_id if assemblies: - assemblies_opt = ','.join(assemblies) + assemblies_opt = ",".join(assemblies) cmd = [ - 'jbrowse', 'add-track', - '--load', 'inPlace', - '--name', label, - '--category', category, - '--target', os.path.join(self.outdir, 'data'), - '--trackId', id, - '--assemblyNames', assemblies_opt + "jbrowse", + "add-track", + "--load", + "inPlace", + "--name", + label, + "--category", + category, + "--target", + os.path.join(self.outdir, "data"), + "--trackId", + id, + "--assemblyNames", + assemblies_opt, ] if config: - cmd.append('--config') + cmd.append("--config") cmd.append(json.dumps(config)) cmd.append(path) @@ -692,79 +810,110 @@ cmd = "gff3sort.pl --precise '%s' | grep -v \"^$\" > '%s'" % (data, dest) self.subprocess_popen(cmd) - self.subprocess_check_call(['bgzip', '-f', dest]) - self.subprocess_check_call(['tabix', '-f', '-p', 'gff', dest + '.gz']) + self.subprocess_check_call(["bgzip", "-f", dest]) + self.subprocess_check_call(["tabix", "-f", "-p", "gff", dest + ".gz"]) def _sort_bed(self, data, dest): # Only index if not already done if not os.path.exists(dest): - cmd = ['sort', '-k1,1', '-k2,2n', data] - with open(dest, 'w') as handle: + cmd = ["sort", "-k1,1", "-k2,2n", data] + with open(dest, "w") as handle: self.subprocess_check_call(cmd, output=handle) - self.subprocess_check_call(['bgzip', '-f', dest]) - self.subprocess_check_call(['tabix', '-f', '-p', 'bed', dest + '.gz']) + self.subprocess_check_call(["bgzip", "-f", dest]) + self.subprocess_check_call(["tabix", "-f", "-p", "bed", dest + ".gz"]) def process_annotations(self, track): - category = track['category'].replace('__pd__date__pd__', TODAY) + category = track["category"].replace("__pd__date__pd__", TODAY) outputTrackConfig = { - 'category': category, + "category": category, } mapped_chars = { - '>': '__gt__', - '<': '__lt__', - "'": '__sq__', - '"': '__dq__', - '[': '__ob__', - ']': '__cb__', - '{': '__oc__', - '}': '__cc__', - '@': '__at__', - '#': '__pd__', - "": '__cn__' + ">": "__gt__", + "<": "__lt__", + "'": "__sq__", + '"': "__dq__", + "[": "__ob__", + "]": "__cb__", + "{": "__oc__", + "}": "__cc__", + "@": "__at__", + "#": "__pd__", + "": "__cn__", } - for i, (dataset_path, dataset_ext, track_human_label, extra_metadata) in enumerate(track['trackfiles']): + for i, ( + dataset_path, + dataset_ext, + track_human_label, + extra_metadata, + ) in enumerate(track["trackfiles"]): # Unsanitize labels (element_identifiers are always sanitized by Galaxy) for key, value in mapped_chars.items(): track_human_label = track_human_label.replace(value, key) - log.info('Processing track %s / %s (%s)', category, track_human_label, dataset_ext) - outputTrackConfig['key'] = track_human_label + log.info( + "Processing track %s / %s (%s)", + category, + track_human_label, + dataset_ext, + ) + outputTrackConfig["key"] = track_human_label # We add extra data to hash for the case of REST + SPARQL. - if 'conf' in track and 'options' in track['conf'] and 'url' in track['conf']['options']: - rest_url = track['conf']['options']['url'] + if ( + "conf" in track + and "options" in track["conf"] + and "url" in track["conf"]["options"] + ): + rest_url = track["conf"]["options"]["url"] else: - rest_url = '' + rest_url = "" # I chose to use track['category'] instead of 'category' here. This # is intentional. This way re-running the tool on a different date # will not generate different hashes and make comparison of outputs # much simpler. - hashData = [str(dataset_path), track_human_label, track['category'], rest_url, self.current_assembly_id] - hashData = '|'.join(hashData).encode('utf-8') - outputTrackConfig['label'] = hashlib.md5(hashData).hexdigest() + '_%s' % i - outputTrackConfig['metadata'] = extra_metadata + hashData = [ + str(dataset_path), + track_human_label, + track["category"], + rest_url, + self.current_assembly_id, + ] + hashData = "|".join(hashData).encode("utf-8") + outputTrackConfig["label"] = hashlib.md5(hashData).hexdigest() + "_%s" % i + outputTrackConfig["metadata"] = extra_metadata - outputTrackConfig['style'] = track['style'] + outputTrackConfig["style"] = track["style"] - if 'menus' in track['conf']['options']: - menus = self.cs.parse_menus(track['conf']['options']) + if "menus" in track["conf"]["options"]: + menus = self.cs.parse_menus(track["conf"]["options"]) outputTrackConfig.update(menus) - if dataset_ext in ('gff', 'gff3'): - self.add_gff(dataset_path, dataset_ext, outputTrackConfig, - track['conf']['options']['gff']) - elif dataset_ext == 'bed': - self.add_bed(dataset_path, dataset_ext, outputTrackConfig, - track['conf']['options']['gff']) - elif dataset_ext == 'bigwig': - self.add_bigwig(dataset_path, outputTrackConfig, - track['conf']['options']['wiggle']) - elif dataset_ext == 'bam': - real_indexes = track['conf']['options']['pileup']['bam_indices']['bam_index'] + if dataset_ext in ("gff", "gff3"): + self.add_gff( + dataset_path, + dataset_ext, + outputTrackConfig, + track["conf"]["options"]["gff"], + ) + elif dataset_ext == "bed": + self.add_bed( + dataset_path, + dataset_ext, + outputTrackConfig, + track["conf"]["options"]["gff"], + ) + elif dataset_ext == "bigwig": + self.add_bigwig( + dataset_path, outputTrackConfig, track["conf"]["options"]["wiggle"] + ) + elif dataset_ext == "bam": + real_indexes = track["conf"]["options"]["pileup"]["bam_indices"][ + "bam_index" + ] if not isinstance(real_indexes, list): # <bam_indices> # <bam_index>/path/to/a.bam.bai</bam_index> @@ -775,11 +924,17 @@ # becomes a list. Fun! real_indexes = [real_indexes] - self.add_xam(dataset_path, outputTrackConfig, - track['conf']['options']['pileup'], - index=real_indexes[i], ext="bam") - elif dataset_ext == 'cram': - real_indexes = track['conf']['options']['cram']['cram_indices']['cram_index'] + self.add_xam( + dataset_path, + outputTrackConfig, + track["conf"]["options"]["pileup"], + index=real_indexes[i], + ext="bam", + ) + elif dataset_ext == "cram": + real_indexes = track["conf"]["options"]["cram"]["cram_indices"][ + "cram_index" + ] if not isinstance(real_indexes, list): # <bam_indices> # <bam_index>/path/to/a.bam.bai</bam_index> @@ -790,93 +945,104 @@ # becomes a list. Fun! real_indexes = [real_indexes] - self.add_xam(dataset_path, outputTrackConfig, - track['conf']['options']['cram'], - index=real_indexes[i], ext="cram") - elif dataset_ext == 'blastxml': - self.add_blastxml(dataset_path, outputTrackConfig, track['conf']['options']['blast']) - elif dataset_ext == 'vcf': + self.add_xam( + dataset_path, + outputTrackConfig, + track["conf"]["options"]["cram"], + index=real_indexes[i], + ext="cram", + ) + elif dataset_ext == "blastxml": + self.add_blastxml( + dataset_path, outputTrackConfig, track["conf"]["options"]["blast"] + ) + elif dataset_ext == "vcf": self.add_vcf(dataset_path, outputTrackConfig) - elif dataset_ext == 'vcf_bgzip': + elif dataset_ext == "vcf_bgzip": self.add_vcf(dataset_path, outputTrackConfig, zipped=True) - elif dataset_ext == 'rest': - self.add_rest(track['conf']['options']['rest']['url'], outputTrackConfig) - elif dataset_ext == 'synteny': - self.add_paf(dataset_path, outputTrackConfig, - track['conf']['options']['synteny']) - elif dataset_ext == 'hic': - self.add_hic(dataset_path, outputTrackConfig, - track['conf']['options']['hic']) - elif dataset_ext == 'sparql': - sparql_query = track['conf']['options']['sparql']['query'] + elif dataset_ext == "rest": + self.add_rest( + track["conf"]["options"]["rest"]["url"], outputTrackConfig + ) + elif dataset_ext == "synteny": + self.add_paf( + dataset_path, outputTrackConfig, track["conf"]["options"]["synteny"] + ) + elif dataset_ext == "hic": + self.add_hic( + dataset_path, outputTrackConfig, track["conf"]["options"]["hic"] + ) + elif dataset_ext == "sparql": + sparql_query = track["conf"]["options"]["sparql"]["query"] for key, value in mapped_chars.items(): sparql_query = sparql_query.replace(value, key) - sparql_query_refnames = track['conf']['options']['sparql']['query_refnames'] + sparql_query_refnames = track["conf"]["options"]["sparql"][ + "query_refnames" + ] for key, value in mapped_chars.items(): sparql_query_refnames = sparql_query_refnames.replace(value, key) - self.add_sparql(track['conf']['options']['sparql']['url'], sparql_query, sparql_query_refnames, outputTrackConfig) + self.add_sparql( + track["conf"]["options"]["sparql"]["url"], + sparql_query, + sparql_query_refnames, + outputTrackConfig, + ) else: - log.warn('Do not know how to handle %s', dataset_ext) + log.warn("Do not know how to handle %s", dataset_ext) # Return non-human label for use in other fields - yield outputTrackConfig['label'] + yield outputTrackConfig["label"] def add_default_session(self, data): """ - Add some default session settings: set some assemblies/tracks on/off + Add some default session settings: set some assemblies/tracks on/off """ 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 - config_path = os.path.join(self.outdir, 'data', 'config.json') + config_path = os.path.join(self.outdir, "data", "config.json") track_types = {} - with open(config_path, 'r') as config_file: + with open(config_path, "r") as config_file: config_json = json.load(config_file) - for track_conf in config_json['tracks']: - track_types[track_conf['trackId']] = track_conf['type'] + for track_conf in config_json["tracks"]: + track_types[track_conf["trackId"]] = track_conf["type"] - for on_track in data['visibility']['default_on']: + for on_track in data["visibility"]["default_on"]: # TODO several problems with this currently # - we are forced to copy the same kind of style config as the per track config from _prepare_track_style (not exactly the same though) # - we get an error when refreshing the page # - this could be solved by session specs, see https://github.com/GMOD/jbrowse-components/issues/2708 - style_data = { - "type": "LinearBasicDisplay", - "height": 100 - } + style_data = {"type": "LinearBasicDisplay", "height": 100} - if on_track in data['style']: - if 'display' in data['style'][on_track]: - style_data['type'] = data['style'][on_track]['display'] - del data['style'][on_track]['display'] + if on_track in data["style"]: + if "display" in data["style"][on_track]: + style_data["type"] = data["style"][on_track]["display"] + del data["style"][on_track]["display"] - style_data.update(data['style'][on_track]) + style_data.update(data["style"][on_track]) - if on_track in data['style_labels']: + if on_track in data["style_labels"]: # TODO fix this: it should probably go in a renderer block (SvgFeatureRenderer) but still does not work # TODO move this to per track displays? - style_data['labels'] = data['style_labels'][on_track] + style_data["labels"] = data["style_labels"][on_track] - tracks_data.append({ - "type": track_types[on_track], - "configuration": on_track, - "displays": [ - style_data - ] - }) + tracks_data.append( + { + "type": track_types[on_track], + "configuration": on_track, + "displays": [style_data], + } + ) # The view for the assembly we're adding - view_json = { - "type": "LinearGenomeView", - "tracks": tracks_data - } + view_json = {"type": "LinearGenomeView", "tracks": tracks_data} refName = None - if data.get('defaultLocation', ''): - loc_match = re.search(r'^(\w+):(\d+)\.+(\d+)$', data['defaultLocation']) + if data.get("defaultLocation", ""): + loc_match = re.search(r"^(\w+):(\d+)\.+(\d+)$", data["defaultLocation"]) if loc_match: refName = loc_match.group(1) start = int(loc_match.group(2)) @@ -888,90 +1054,81 @@ if refName is not None: # TODO displayedRegions is not just zooming to the region, it hides the rest of the chromosome - view_json['displayedRegions'] = [{ - "refName": refName, - "start": start, - "end": end, - "reversed": False, - "assemblyName": self.current_assembly_id - }] + view_json["displayedRegions"] = [ + { + "refName": refName, + "start": start, + "end": end, + "reversed": False, + "assemblyName": self.current_assembly_id, + } + ] - session_name = data.get('session_name', "New session") + session_name = data.get("session_name", "New session") if not session_name: session_name = "New session" # Merge with possibly existing defaultSession (if upgrading a jbrowse instance) session_json = {} - if 'defaultSession' in config_json: - session_json = config_json['defaultSession'] + if "defaultSession" in config_json: + session_json = config_json["defaultSession"] session_json["name"] = session_name - if 'views' not in session_json: - session_json['views'] = [] + if "views" not in session_json: + session_json["views"] = [] - session_json['views'].append(view_json) + session_json["views"].append(view_json) - config_json['defaultSession'] = session_json + config_json["defaultSession"] = session_json - with open(config_path, 'w') as config_file: + with open(config_path, "w") as config_file: json.dump(config_json, config_file, indent=2) def add_general_configuration(self, data): """ - Add some general configuration to the config.json file + Add some general configuration to the config.json file """ - config_path = os.path.join(self.outdir, 'data', 'config.json') - with open(config_path, 'r') as config_file: + config_path = os.path.join(self.outdir, "data", "config.json") + with open(config_path, "r") as config_file: config_json = json.load(config_file) config_data = {} - config_data['disableAnalytics'] = data.get('analytics', 'false') == 'true' + config_data["disableAnalytics"] = data.get("analytics", "false") == "true" - config_data['theme'] = { + config_data["theme"] = { "palette": { - "primary": { - "main": data.get('primary_color', '#0D233F') - }, - "secondary": { - "main": data.get('secondary_color', '#721E63') - }, - "tertiary": { - "main": data.get('tertiary_color', '#135560') - }, - "quaternary": { - "main": data.get('quaternary_color', '#FFB11D') - }, + "primary": {"main": data.get("primary_color", "#0D233F")}, + "secondary": {"main": data.get("secondary_color", "#721E63")}, + "tertiary": {"main": data.get("tertiary_color", "#135560")}, + "quaternary": {"main": data.get("quaternary_color", "#FFB11D")}, }, - "typography": { - "fontSize": int(data.get('font_size', 10)) - }, + "typography": {"fontSize": int(data.get("font_size", 10))}, } - config_json['configuration'].update(config_data) + config_json["configuration"].update(config_data) - with open(config_path, 'w') as config_file: + with open(config_path, "w") as config_file: json.dump(config_json, config_file, indent=2) def clone_jbrowse(self, jbrowse_dir, destination): - """Clone a JBrowse directory into a destination directory. - """ + """Clone a JBrowse directory into a destination directory.""" copytree(jbrowse_dir, destination) try: - shutil.rmtree(os.path.join(destination, 'test_data')) + shutil.rmtree(os.path.join(destination, "test_data")) except OSError as e: log.error("Error: %s - %s." % (e.filename, e.strerror)) - if not os.path.exists(os.path.join(destination, 'data')): + if not os.path.exists(os.path.join(destination, "data")): # It can already exist if upgrading an instance - os.makedirs(os.path.join(destination, 'data')) - log.info("makedir %s" % (os.path.join(destination, 'data'))) + os.makedirs(os.path.join(destination, "data")) + log.info("makedir %s" % (os.path.join(destination, "data"))) - os.symlink('./data/config.json', os.path.join(destination, 'config.json')) + os.symlink("./data/config.json", os.path.join(destination, "config.json")) def copytree(src, dst, symlinks=False, ignore=None): @@ -985,113 +1142,131 @@ def parse_style_conf(item): - if 'type' in item.attrib and item.attrib['type'] in ['boolean', 'integer']: - if item.attrib['type'] == 'boolean': + if "type" in item.attrib and item.attrib["type"] in ["boolean", "integer"]: + if item.attrib["type"] == "boolean": return item.text in ("yes", "true", "True") - elif item.attrib['type'] == 'integer': + elif item.attrib["type"] == "integer": return int(item.text) else: return item.text -if __name__ == '__main__': +if __name__ == "__main__": parser = argparse.ArgumentParser(description="", epilog="") - parser.add_argument('xml', type=argparse.FileType('r'), help='Track Configuration') + parser.add_argument("xml", type=argparse.FileType("r"), help="Track Configuration") - parser.add_argument('--jbrowse', help='Folder containing a jbrowse release') - parser.add_argument('--outdir', help='Output directory', default='out') - parser.add_argument('--version', '-V', action='version', version="%(prog)s 0.8.0") + parser.add_argument("--jbrowse", help="Folder containing a jbrowse release") + parser.add_argument("--outdir", help="Output directory", default="out") + parser.add_argument("--version", "-V", action="version", version="%(prog)s 0.8.0") args = parser.parse_args() tree = ET.parse(args.xml.name) root = tree.getroot() # This should be done ASAP - GALAXY_INFRASTRUCTURE_URL = root.find('metadata/galaxyUrl').text + GALAXY_INFRASTRUCTURE_URL = root.find("metadata/galaxyUrl").text # Sometimes this comes as `localhost` without a protocol - if not GALAXY_INFRASTRUCTURE_URL.startswith('http'): + if not GALAXY_INFRASTRUCTURE_URL.startswith("http"): # so we'll prepend `http://` and hope for the best. Requests *should* # be GET and not POST so it should redirect OK - GALAXY_INFRASTRUCTURE_URL = 'http://' + GALAXY_INFRASTRUCTURE_URL + GALAXY_INFRASTRUCTURE_URL = "http://" + GALAXY_INFRASTRUCTURE_URL jc = JbrowseConnector( jbrowse=args.jbrowse, outdir=args.outdir, genomes=[ { - 'path': os.path.realpath(x.attrib['path']), - 'meta': metadata_from_node(x.find('metadata')), - 'label': x.attrib['label'] + "path": os.path.realpath(x.attrib["path"]), + "meta": metadata_from_node(x.find("metadata")), + "label": x.attrib["label"], } - for x in root.findall('metadata/genomes/genome') - ] + for x in root.findall("metadata/genomes/genome") + ], ) default_session_data = { - 'visibility': { - 'default_on': [], - 'default_off': [], + "visibility": { + "default_on": [], + "default_off": [], }, - 'style': {}, - 'style_labels': {} + "style": {}, + "style_labels": {}, } # TODO add metadata to tracks - for track in root.findall('tracks/track'): + for track in root.findall("tracks/track"): track_conf = {} - track_conf['trackfiles'] = [] + track_conf["trackfiles"] = [] - trackfiles = track.findall('files/trackFile') + trackfiles = track.findall("files/trackFile") if trackfiles: - for x in track.findall('files/trackFile'): + for x in track.findall("files/trackFile"): if trackfiles: - metadata = metadata_from_node(x.find('metadata')) + metadata = metadata_from_node(x.find("metadata")) - track_conf['trackfiles'].append(( - os.path.realpath(x.attrib['path']), - x.attrib['ext'], - x.attrib['label'], - metadata - )) + track_conf["trackfiles"].append( + ( + os.path.realpath(x.attrib["path"]), + x.attrib["ext"], + x.attrib["label"], + metadata, + ) + ) else: # For tracks without files (rest, sparql) - track_conf['trackfiles'].append(( - '', # N/A, no path for rest or sparql - track.attrib['format'], - track.find('options/label').text, - {} - )) + track_conf["trackfiles"].append( + ( + "", # N/A, no path for rest or sparql + track.attrib["format"], + track.find("options/label").text, + {}, + ) + ) - track_conf['category'] = track.attrib['cat'] - track_conf['format'] = track.attrib['format'] - track_conf['style'] = {item.tag: parse_style_conf(item) for item in track.find('options/style')} + track_conf["category"] = track.attrib["cat"] + track_conf["format"] = track.attrib["format"] + track_conf["style"] = { + item.tag: parse_style_conf(item) for item in track.find("options/style") + } - track_conf['style'] = {item.tag: parse_style_conf(item) for item in track.find('options/style')} + track_conf["style"] = { + item.tag: parse_style_conf(item) for item in track.find("options/style") + } - track_conf['style_labels'] = {item.tag: parse_style_conf(item) for item in 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["conf"] = etree_to_dict(track.find("options")) keys = jc.process_annotations(track_conf) for key in keys: - default_session_data['visibility'][track.attrib.get('visibility', 'default_off')].append(key) + default_session_data["visibility"][ + track.attrib.get("visibility", "default_off") + ].append(key) - default_session_data['style'][key] = track_conf['style'] # TODO do we need this anymore? - default_session_data['style_labels'][key] = track_conf['style_labels'] + default_session_data["style"][key] = track_conf[ + "style" + ] # TODO do we need this anymore? + default_session_data["style_labels"][key] = track_conf["style_labels"] - default_session_data['defaultLocation'] = root.find('metadata/general/defaultLocation').text - default_session_data['session_name'] = root.find('metadata/general/session_name').text + default_session_data["defaultLocation"] = root.find( + "metadata/general/defaultLocation" + ).text + default_session_data["session_name"] = root.find( + "metadata/general/session_name" + ).text general_data = { - 'analytics': root.find('metadata/general/analytics').text, - 'primary_color': root.find('metadata/general/primary_color').text, - 'secondary_color': root.find('metadata/general/secondary_color').text, - 'tertiary_color': root.find('metadata/general/tertiary_color').text, - 'quaternary_color': root.find('metadata/general/quaternary_color').text, - 'font_size': root.find('metadata/general/font_size').text, + "analytics": root.find("metadata/general/analytics").text, + "primary_color": root.find("metadata/general/primary_color").text, + "secondary_color": root.find("metadata/general/secondary_color").text, + "tertiary_color": root.find("metadata/general/tertiary_color").text, + "quaternary_color": root.find("metadata/general/quaternary_color").text, + "font_size": root.find("metadata/general/font_size").text, } jc.add_default_session(default_session_data) jc.add_general_configuration(general_data) jc.text_index() -
--- a/jbrowse2.py Mon Jan 22 11:52:19 2024 +0000 +++ b/jbrowse2.py Mon Jan 22 12:05:09 2024 +0000 @@ -1188,7 +1188,6 @@ % ddl ) elif self.genome_name is not None: - refName = self.genome_name start = 0 end = 10000 # Booh, hard coded! waiting for https://github.com/GMOD/jbrowse-components/issues/2708 logging.info(