jbrowse: jbrowse.py comparison

comparison jbrowse.py @ 25:1cfc579079a6 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f

author	iuc
date	Tue, 29 Jan 2019 05:34:16 -0500
parents	fa30df9b79c2
children	61ce21e36cb5

comparison

equal deleted inserted replaced

-:fa30df9b79c2
+:1cfc579079a6
 trackConfig['style']['color'] = color_function.replace('\n', '')
 return trackConfig
 def etree_to_dict(t):
+if t is None:
+return {}
 d = {t.tag: {} if t.attrib else None}
 children = list(t)
 if children:
 dd = defaultdict(list)
 for dc in map(etree_to_dict, children):
 def subprocess_check_call(self, 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)
+output, err = p.communicate()
+retcode = p.returncode
+if retcode != 0:
+log.error('cd %s && %s', self.outdir, command)
+log.error(output)
+log.error(err)
+raise RuntimeError("Command failed with exit code %s" % (retcode))
 def _jbrowse_bin(self, command):
 return os.path.realpath(os.path.join(self.jbrowse, 'bin', command))
 def process_genomes(self):
 for genome_node in self.genome_paths:
-# TODO: Waiting on https://github.com/GMOD/jbrowse/pull/884
+# We only expect one input genome per run. This for loop is just
+# easier to write than the alternative / catches any possible
+# issues.
+# Copy the file in workdir, prepare-refseqs.pl will copy it to jbrowse's data dir
+local_genome = os.path.realpath('./genome.fasta')
+shutil.copy(genome_node['path'], local_genome)
+cmd = ['samtools', 'faidx', local_genome]
+self.subprocess_check_call(cmd)
 self.subprocess_check_call([
 'perl', self._jbrowse_bin('prepare-refseqs.pl'),
-'--fasta', genome_node['path']])
+'--trackConfig', json.dumps({'metadata': genome_node['meta']}),
+'--indexed_fasta', os.path.realpath(local_genome)])
+os.unlink(local_genome)
+os.unlink(local_genome + '.fai')
 def generate_names(self):
 # Generate names
 args = [
 'perl', self._jbrowse_bin('generate-names.pl'),
 def _add_track_json(self, json_data):
 if len(json_data) == 0:
 return
 tmp = tempfile.NamedTemporaryFile(delete=False)
-tmp.write(json.dumps(json_data))
+json.dump(json_data, tmp)
 tmp.close()
 cmd = ['perl', self._jbrowse_bin('add-track-json.pl'), tmp.name,
 os.path.join('data', 'trackList.json')]
 self.subprocess_check_call(cmd)
 os.unlink(tmp.name)
 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', '--min_gap', str(min_gap), xml]
+'--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
 # Replace original gff3 file
 shutil.copy(gff3_rebased.name, gff3)
 os.unlink(gff3_rebased.name)
-config = {
+dest = os.path.join(self.outdir, 'data', 'raw', trackData['label'] + '.gff')
-'glyph': 'JBrowse/View/FeatureGlyph/Segments',
-"category": trackData['category'],
+self._sort_gff(gff3, dest)
-}
+url = os.path.join('raw', trackData['label'] + '.gff.gz')
-clientConfig = trackData['style']
+trackData.update({
+"urlTemplate": url,
-cmd = ['perl', self._jbrowse_bin('flatfile-to-json.pl'),
+"storeClass": "JBrowse/Store/SeqFeature/GFF3Tabix",
-'--gff', gff3,
+})
-'--trackLabel', trackData['label'],
-'--key', trackData['key'],
+trackData['glyph'] = 'JBrowse/View/FeatureGlyph/Segments'
-'--clientConfig', json.dumps(clientConfig),
-'--config', json.dumps(config),
+trackData['trackType'] = 'BlastView/View/Track/CanvasFeatures'
-'--trackType', 'BlastView/View/Track/CanvasFeatures'
+trackData['type'] = 'BlastView/View/Track/CanvasFeatures'
-]
+self._add_track_json(trackData)
-# className in --clientConfig is ignored, it needs to be set with --className
-if 'className' in trackData['style']:
-cmd += ['--className', trackData['style']['className']]
-self.subprocess_check_call(cmd)
 os.unlink(gff3)
 if blastOpts.get('index', 'false') == 'true':
 self.tracksToIndex.append("%s" % trackData['label'])
 trackData['scale'] = wiggleOpts['scale']
 self._add_track_json(trackData)
+def add_bigwig_multiple(self, data, trackData, wiggleOpts, **kwargs):
+urls = []
+for idx, bw in enumerate(data):
+dest = os.path.join('data', 'raw', trackData['label'] + '_' + str(idx) + '.bw')
+cmd = ['ln', '-s', bw[1], dest]
+self.subprocess_check_call(cmd)
+urls.append({"url": os.path.join('raw', trackData['label'] + '_' + str(idx) + '.bw'), "name": str(idx + 1) + ' - ' + bw[0]})
+trackData.update({
+"urlTemplates": urls,
+"showTooltips": "true",
+"storeClass": "MultiBigWig/Store/SeqFeature/MultiBigWig",
+"type": "MultiBigWig/View/Track/MultiWiggle/MultiDensity",
+})
+if 'XYPlot' in wiggleOpts['type']:
+trackData['type'] = "MultiBigWig/View/Track/MultiWiggle/MultiXYPlot"
+trackData['variance_band'] = True if wiggleOpts['variance_band'] == 'true' else False
+if 'min' in wiggleOpts and 'max' in wiggleOpts:
+trackData['min_score'] = wiggleOpts['min']
+trackData['max_score'] = wiggleOpts['max']
+else:
+trackData['autoscale'] = wiggleOpts.get('autoscale', 'local')
+trackData['scale'] = wiggleOpts['scale']
+self._add_track_json(trackData)
 def add_bam(self, data, trackData, bamOpts, bam_index=None, **kwargs):
 dest = os.path.join('data', 'raw', trackData['label'] + '.bam')
 cmd = ['ln', '-s', os.path.realpath(data), dest]
 self.subprocess_check_call(cmd)
 url = os.path.join('raw', trackData['label'] + '.bam')
 trackData.update({
 "urlTemplate": url,
 "type": "JBrowse/View/Track/Alignments2",
 "storeClass": "JBrowse/Store/SeqFeature/BAM",
+"chunkSizeLimit": bamOpts.get('chunkSizeLimit', '5000000')
 })
 # Apollo will only switch to the (prettier) 'bam-read' className if it's not set explicitly in the track config
 # So remove the default 'feature' value for these bam tracks
 if 'className' in trackData['style'] and trackData['style']['className'] == 'feature':
 trackData2 = copy.copy(trackData)
 trackData2.update({
 "type": "JBrowse/View/Track/SNPCoverage",
 "key": trackData['key'] + " - SNPs/Coverage",
 "label": trackData['label'] + "_autosnp",
+"chunkSizeLimit": bamOpts.get('chunkSizeLimit', '5000000')
 })
 self._add_track_json(trackData2)
 def add_vcf(self, data, trackData, vcfOpts={}, **kwargs):
 dest = os.path.join('data', 'raw', trackData['label'] + '.vcf')
 cmd = ['bgzip', dest]
 self.subprocess_check_call(cmd)
 cmd = ['tabix', '-p', 'vcf', dest + '.gz']
 self.subprocess_check_call(cmd)
-url = os.path.join('raw', trackData['label'] + '.vcf')
+url = os.path.join('raw', trackData['label'] + '.vcf.gz')
 trackData.update({
 "urlTemplate": url,
 "type": "JBrowse/View/Track/HTMLVariants",
 "storeClass": "JBrowse/Store/SeqFeature/VCFTabix",
 })
 self._add_track_json(trackData)
-def add_features(self, data, format, trackData, gffOpts, metadata=None, **kwargs):
+def _sort_gff(self, data, dest):
-cmd = [
-'perl', self._jbrowse_bin('flatfile-to-json.pl'),
+if not os.path.exists(dest):
-self.TN_TABLE.get(format, 'gff'),
+# Only index if not already done
-data,
+cmd = "grep ^\"#\" '%s' > '%s'" % (data, dest)
-'--trackLabel', trackData['label'],
+self.subprocess_popen(cmd)
-'--key', trackData['key']
-]
+cmd = "grep -v ^\"#\" '%s' | grep -v \"^$\" | grep \"\t\" | sort -k1,1 -k4,4n >> '%s'" % (data, dest)
+self.subprocess_popen(cmd)
-# className in --clientConfig is ignored, it needs to be set with --className
-if 'className' in trackData['style']:
+cmd = ['bgzip', '-f', dest]
-cmd += ['--className', trackData['style']['className']]
+self.subprocess_popen(' '.join(cmd))
+cmd = ['tabix', '-f', '-p', 'gff', dest + '.gz']
-config = copy.copy(trackData)
+self.subprocess_popen(' '.join(cmd))
-clientConfig = trackData['style']
-del config['style']
+def add_features(self, data, format, trackData, gffOpts, **kwargs):
+dest = os.path.join(self.outdir, 'data', 'raw', trackData['label'] + '.gff')
+self._sort_gff(data, dest)
+url = os.path.join('raw', trackData['label'] + '.gff.gz')
+trackData.update({
+"urlTemplate": url,
+"storeClass": "JBrowse/Store/SeqFeature/GFF3Tabix",
+})
 if 'match' in gffOpts:
-config['glyph'] = 'JBrowse/View/FeatureGlyph/Segments'
+trackData['glyph'] = 'JBrowse/View/FeatureGlyph/Segments'
-if bool(gffOpts['match']):
-# Can be empty for CanvasFeatures = will take all by default
-cmd += ['--type', gffOpts['match']]
-cmd += ['--clientConfig', json.dumps(clientConfig),
-]
 trackType = 'JBrowse/View/Track/CanvasFeatures'
 if 'trackType' in gffOpts:
 trackType = gffOpts['trackType']
+trackData['trackType'] = trackType
 if trackType == 'JBrowse/View/Track/CanvasFeatures':
 if 'transcriptType' in gffOpts and gffOpts['transcriptType']:
-config['transcriptType'] = gffOpts['transcriptType']
+trackData['transcriptType'] = gffOpts['transcriptType']
 if 'subParts' in gffOpts and gffOpts['subParts']:
-config['subParts'] = gffOpts['subParts']
+trackData['subParts'] = gffOpts['subParts']
 if 'impliedUTRs' in gffOpts and gffOpts['impliedUTRs']:
-config['impliedUTRs'] = gffOpts['impliedUTRs']
+trackData['impliedUTRs'] = gffOpts['impliedUTRs']
-elif trackType == 'JBrowse/View/Track/HTMLFeatures':
-if 'transcriptType' in gffOpts and gffOpts['transcriptType']:
+self._add_track_json(trackData)
-cmd += ['--type', gffOpts['transcriptType']]
-cmd += [
-'--trackType', gffOpts['trackType']
-]
-if metadata:
-config.update({'metadata': metadata})
-cmd.extend(['--config', json.dumps(config)])
-self.subprocess_check_call(cmd)
 if gffOpts.get('index', 'false') == 'true':
 self.tracksToIndex.append("%s" % trackData['label'])
 def add_rest(self, url, trackData):
 "label": trackData['label'],
 "key": trackData['key'],
 "category": trackData['category'],
 "type": "JBrowse/View/Track/HTMLFeatures",
 "storeClass": "JBrowse/Store/SeqFeature/REST",
-"baseUrl": url,
+"baseUrl": url
-"query": {
+}
-"organism": "tyrannosaurus"
+self._add_track_json(data)
-}
+def add_sparql(self, url, query, trackData):
+data = {
+"label": trackData['label'],
+"key": trackData['key'],
+"category": trackData['category'],
+"type": "JBrowse/View/Track/CanvasFeatures",
+"storeClass": "JBrowse/Store/SeqFeature/SPARQL",
+"urlTemplate": url,
+"queryTemplate": query
 }
 self._add_track_json(data)
 def process_annotations(self, track):
 category = track['category'].replace('__pd__date__pd__', TODAY)
 '[': '__ob__',
 ']': '__cb__',
 '{': '__oc__',
 '}': '__cc__',
 '@': '__at__',
-'#': '__pd__'
+'#': '__pd__',
+"": '__cn__'
 }
 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 %s / %s', category, track_human_label)
 outputTrackConfig['key'] = track_human_label
 # We add extra data to hash for the case of REST + SPARQL.
-try:
+if 'conf' in track and 'options' in track['conf'] and 'url' in track['conf']['options']:
 rest_url = track['conf']['options']['url']
-except KeyError:
+else:
 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 = [dataset_path, track_human_label, track['category'], rest_url]
+hashData = [str(dataset_path), track_human_label, track['category'], rest_url]
 hashData = '|'.join(hashData).encode('utf-8')
 outputTrackConfig['label'] = hashlib.md5(hashData).hexdigest() + '_%s' % i
+outputTrackConfig['metadata'] = extra_metadata
 # Colour parsing is complex due to different track types having
 # different colour options.
 colourOptions = self.cs.parse_colours(track['conf']['options'], track['format'], gff3=dataset_path)
 # This used to be done with a dict.update() call, however that wiped out any previous style settings...
 # import pprint; pprint.pprint(track)
 # import sys; sys.exit()
 if dataset_ext in ('gff', 'gff3', 'bed'):
 self.add_features(dataset_path, dataset_ext, outputTrackConfig,
-track['conf']['options']['gff'], metadata=extra_metadata)
+track['conf']['options']['gff'])
 elif dataset_ext == 'bigwig':
 self.add_bigwig(dataset_path, outputTrackConfig,
-track['conf']['options']['wiggle'], metadata=extra_metadata)
+track['conf']['options']['wiggle'])
+elif dataset_ext == 'bigwig_multiple':
+self.add_bigwig_multiple(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>
 # becomes a list. Fun!
 real_indexes = [real_indexes]
 self.add_bam(dataset_path, outputTrackConfig,
 track['conf']['options']['pileup'],
-bam_index=real_indexes[i], metadata=extra_metadata)
+bam_index=real_indexes[i])
 elif dataset_ext == 'blastxml':
-self.add_blastxml(dataset_path, outputTrackConfig, track['conf']['options']['blast'], metadata=extra_metadata)
+self.add_blastxml(dataset_path, outputTrackConfig, track['conf']['options']['blast'])
 elif dataset_ext == 'vcf':
-self.add_vcf(dataset_path, outputTrackConfig, metadata=extra_metadata)
+self.add_vcf(dataset_path, outputTrackConfig)
 elif dataset_ext == 'rest':
-self.add_rest(track['conf']['options']['url'], outputTrackConfig, metadata=extra_metadata)
+self.add_rest(track['conf']['options']['rest']['url'], outputTrackConfig)
+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)
+self.add_sparql(track['conf']['options']['sparql']['url'], sparql_query, outputTrackConfig)
 else:
 log.warn('Do not know how to handle %s', dataset_ext)
 # Return non-human label for use in other fields
 yield outputTrackConfig['label']
 viz_data.update(generalData)
 self._add_json(viz_data)
 if 'GCContent' in data['plugins_python']:
 self._add_track_json({
-"storeClass": "JBrowse/Store/SeqFeature/SequenceChunks",
+"storeClass": "JBrowse/Store/SeqFeature/IndexedFasta",
 "type": "GCContent/View/Track/GCContentXY",
-"label": "GCContentXY",
+"label": "GC Content",
-"urlTemplate": "seq/{refseq_dirpath}/{refseq}-",
+"key": "GCContentXY",
-"bicolor_pivot": 0.5
+"urlTemplate": "seq/genome.fasta",
+"bicolor_pivot": 0.5,
+"category": "GC Content",
+"metadata": {
+"tool_tool": '<a target="_blank" href="https://github.com/elsiklab/gccontent/commit/030180e75a19fad79478d43a67c566ec6">elsiklab/gccontent</a>',
+"tool_tool_version": "5c8b0582ecebf9edf684c76af8075fb3d30ec3fa",
+"dataset_edam_format": "",
+"dataset_size": "",
+"history_display_name": "",
+"history_user_email": "",
+"metadata_dbkey": "",
+}
+# TODO: Expose params for everyone.
+})
+self._add_track_json({
+"storeClass": "JBrowse/Store/SeqFeature/IndexedFasta",
+"type": "GCContent/View/Track/GCContentXY",
+"label": "GC skew",
+"key": "GCSkew",
+"urlTemplate": "seq/genome.fasta",
+"gcMode": "skew",
+"min_score": -1,
+"bicolor_pivot": 0,
+"category": "GC Content",
+"metadata": {
+"tool_tool": '<a target="_blank" href="https://github.com/elsiklab/gccontent/commit/030180e75a19fad79478d43a67c566ec6">elsiklab/gccontent</a>',
+"tool_tool_version": "5c8b0582ecebf9edf684c76af8075fb3d30ec3fa",
+"dataset_edam_format": "",
+"dataset_size": "",
+"history_display_name": "",
+"history_user_email": "",
+"metadata_dbkey": "",
+}
 # TODO: Expose params for everyone.
 })
 if 'ComboTrackSelector' in data['plugins_python']:
 with open(os.path.join(self.outdir, 'data', 'trackList.json'), 'r') as handle:
 "history_user_email",
 "metadata_dbkey",
 ],
 "type": "Faceted",
 "title": ["Galaxy Metadata"],
+"icon": "https://galaxyproject.org/images/logos/galaxy-icon-square.png",
 "escapeHTMLInData": False
 },
 "trackMetadata": {
 "indexFacets": [
 "category",
 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('--standalone', help='Standalone mode includes a copy of JBrowse', action='store_true')
-parser.add_argument('--version', '-V', action='version', version="%(prog)s 0.7.0")
+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
+# Sometimes this comes as `localhost` without a protocol
+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
 jc = JbrowseConnector(
 jbrowse=args.jbrowse,
 outdir=args.outdir,
 genomes=[
 'show_nav': root.find('metadata/general/show_nav').text,
 'show_overview': root.find('metadata/general/show_overview').text,
 'show_menu': root.find('metadata/general/show_menu').text,
 'hideGenomeOptions': root.find('metadata/general/hideGenomeOptions').text,
 },
-'plugins': [{
+'plugins': [],
-'location': 'https://cdn.jsdelivr.net/gh/TAMU-CPT/blastview@97572a21b7f011c2b4d9a0b5af40e292d694cbef/',
+'plugins_python': [],
-'name': 'BlastView'
-}],
-'plugins_python': ['BlastView'],
 }
 plugins = root.find('plugins').attrib
 if plugins['GCContent'] == 'True':
 extra_data['plugins_python'].append('GCContent')
 extra_data['plugins'].append({
 'location': 'https://cdn.jsdelivr.net/gh/elsiklab/gccontent@5c8b0582ecebf9edf684c76af8075fb3d30ec3fa/',
 'name': 'GCContent'
 })
-if plugins['Bookmarks'] == 'True':
+# Not needed in 1.16.1: it's built in the conda package now, and this plugin doesn't need to be enabled anywhere
-extra_data['plugins'].append({
+# if plugins['Bookmarks'] == 'True':
-'location': 'https://cdn.jsdelivr.net/gh/TAMU-CPT/bookmarks-jbrowse@5242694120274c86e1ccd5cb0e5e943e78f82393/',
+#    extra_data['plugins'].append({
-'name': 'Bookmarks'
+#        'location': 'https://cdn.jsdelivr.net/gh/TAMU-CPT/bookmarks-jbrowse@5242694120274c86e1ccd5cb0e5e943e78f82393/',
-})
+#        'name': 'Bookmarks'
+#    })
+# Not needed in 1.16.1: it's built in the conda package now, and this plugin doesn't need to be enabled anywhere
 if plugins['ComboTrackSelector'] == 'True':
 extra_data['plugins_python'].append('ComboTrackSelector')
-extra_data['plugins'].append({
+# Not needed in 1.16.1: it's built in the conda package now, and this plugin doesn't need to be enabled anywhere
-'location': 'https://cdn.jsdelivr.net/gh/Arabidopsis-Information-Portal/ComboTrackSelector@52403928d5ccbe2e3a86b0fa5eb8e61c0f2e2f57',
+# extra_data['plugins'].append({
-'icon': 'https://galaxyproject.org/images/logos/galaxy-icon-square.png',
+#    'location': 'https://cdn.jsdelivr.net/gh/Arabidopsis-Information-Portal/ComboTrackSelector@52403928d5ccbe2e3a86b0fa5eb8e61c0f2e2f57/',
-'name': 'ComboTrackSelector'
+#    'icon': 'https://galaxyproject.org/images/logos/galaxy-icon-square.png',
-})
+#    'name': 'ComboTrackSelector'
+# })
 if plugins['theme'] == 'Minimalist':
 extra_data['plugins'].append({
 'location': 'https://cdn.jsdelivr.net/gh/erasche/jbrowse-minimalist-theme@d698718442da306cf87f033c72ddb745f3077775/',
 'name': 'MinimalistTheme'
 extra_data['plugins'].append({
 'location': 'https://cdn.jsdelivr.net/gh/erasche/jbrowse-dark-theme@689eceb7e33bbc1b9b15518d45a5a79b2e5d0a26/',
 'name': 'DarkTheme'
 })
-GALAXY_INFRASTRUCTURE_URL = root.find('metadata/galaxyUrl').text
+if plugins['BlastView'] == 'True':
-# Sometimes this comes as `localhost` without a protocol
+extra_data['plugins_python'].append('BlastView')
-if not GALAXY_INFRASTRUCTURE_URL.startswith('http'):
+extra_data['plugins'].append({
-# so we'll prepend `http://` and hope for the best. Requests *should*
+'location': 'https://cdn.jsdelivr.net/gh/TAMU-CPT/blastview@97572a21b7f011c2b4d9a0b5af40e292d694cbef/',
-# be GET and not POST so it should redirect OK
+'name': 'BlastView'
-GALAXY_INFRASTRUCTURE_URL = 'http://' + GALAXY_INFRASTRUCTURE_URL
+})
 for track in root.findall('tracks/track'):
 track_conf = {}
 track_conf['trackfiles'] = []
-for x in track.findall('files/trackFile'):
+is_multi_bigwig = False
+try:
+if track.find('options/wiggle/multibigwig') and (track.find('options/wiggle/multibigwig').text == 'True'):
+is_multi_bigwig = True
+multi_bigwig_paths = []
+except KeyError:
+pass
+trackfiles = track.findall('files/trackFile')
+if trackfiles:
+for x in track.findall('files/trackFile'):
+if is_multi_bigwig:
+multi_bigwig_paths.append((x.attrib['label'], os.path.realpath(x.attrib['path'])))
+else:
+if trackfiles:
+metadata = metadata_from_node(x.find('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,
+{}
+))
+if is_multi_bigwig:
 metadata = metadata_from_node(x.find('metadata'))
 track_conf['trackfiles'].append((
-os.path.realpath(x.attrib['path']),
+multi_bigwig_paths,  # Passing an array of paths to represent as one track
-x.attrib['ext'],
+'bigwig_multiple',
-x.attrib['label'],
+'MultiBigWig',  # Giving an hardcoded name for now
-metadata
+{}  # No metadata for multiple bigwig
 ))
 track_conf['category'] = track.attrib['cat']
 track_conf['format'] = track.attrib['format']
 try:
 # Only pertains to gff3 + blastxml. TODO?
 track_conf['style'] = {t.tag: t.text for t in track.find('options/style')}
-except TypeError as te:
+except TypeError:
 track_conf['style'] = {}
 pass
 track_conf['conf'] = etree_to_dict(track.find('options'))
 keys = jc.process_annotations(track_conf)

Mercurial > repos > iuc > jbrowse

comparison jbrowse.py @ 25:1cfc579079a6 draft