jbrowse: jbrowse.py comparison

comparison jbrowse.py @ 17:ff11d442feed draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257

author	iuc
date	Wed, 15 Nov 2017 15:15:27 -0500
parents	b5c5470d7c09
children	558d652cd681

comparison

equal deleted inserted replaced

-:b5c5470d7c09
+:ff11d442feed
 #!/usr/bin/env python
 import argparse
-import codecs
+import binascii
 import copy
+import datetime
 import hashlib
 import json
 import logging
 import os
 import shutil
 import tempfile
 import xml.etree.ElementTree as ET
 from collections import defaultdict
 from Bio.Data import CodonTable
 logging.basicConfig(level=logging.INFO)
 log = logging.getLogger('jbrowse')
+TODAY = datetime.datetime.now().strftime("%Y-%m-%d")
+GALAXY_INFRASTRUCTURE_URL = None
 class ColorScaling(object):
 COLOR_FUNCTION_TEMPLATE = """
 }};
 var color = ({user_spec_color} || search_up(feature, 'color') || search_down(feature, 'color') || {auto_gen_color});
 var score = (search_up(feature, 'score') || search_down(feature, 'score'));
 {opacity}
+if(score === undefined){{ opacity = 1; }}
 var result = /^#?([a-f\d]{{2}})([a-f\d]{{2}})([a-f\d]{{2}})$/i.exec(color);
 var red = parseInt(result[1], 16);
 var green = parseInt(result[2], 16);
 var blue = parseInt(result[3], 16);
 if(isNaN(opacity) || opacity < 0){{ opacity = 0; }}
 var opacity = (score - ({min})) / (({max}) - ({min}));
 opacity = Math.log10(opacity) + Math.log10({max});
 """,
 'blast': """
 var opacity = 0;
-if(score == 0.0) {
+if(score == 0.0) {{
 opacity = 1;
-} else{
+}} else {{
 opacity = (20 - Math.log10(score)) / 180;
-}
+}}
 """
 }
 BREWER_COLOUR_IDX = 0
 BREWER_COLOUR_SCHEMES = [
 def __init__(self):
 self.brewer_colour_idx = 0
 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', codecs.decode(hexstr, 'hex'))
+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:
 # score comes from feature._parent.get('score') or feature.get('score')
 INSTALLED_TO = os.path.dirname(os.path.realpath(__file__))
+def metadata_from_node(node):
+metadata = {}
+try:
+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('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('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(
+galaxy=GALAXY_INFRASTRUCTURE_URL,
+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(
+galaxy=GALAXY_INFRASTRUCTURE_URL,
+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, standalone=False, gencode=1):
 self.TN_TABLE = {
 'gff3': '--gff',
 os.makedirs(self.outdir)
 except OSError:
 # Ignore if the folder exists
 pass
+try:
+os.makedirs(os.path.join(self.outdir, 'data', 'raw'))
+except OSError:
+# Ignore if the folder exists
+pass
 self.process_genomes()
 self.update_gencode()
 def update_gencode(self):
 table = CodonTable.unambiguous_dna_by_id[int(self.gencode)]
 def _jbrowse_bin(self, command):
 return os.path.realpath(os.path.join(self.jbrowse, 'bin', command))
 def process_genomes(self):
-for genome_path in self.genome_paths:
+for genome_node in self.genome_paths:
+# TODO: Waiting on https://github.com/GMOD/jbrowse/pull/884
 self.subprocess_check_call([
 'perl', self._jbrowse_bin('prepare-refseqs.pl'),
-'--fasta', genome_path])
+'--fasta', genome_node['path']])
 def generate_names(self):
 # Generate names
 args = [
 'perl', self._jbrowse_bin('generate-names.pl'),
 '--hashBits', '16'
 ]
 tracks = ','.join(self.tracksToIndex)
 if tracks:
 args += ['--tracks', tracks]
 else:
 # No tracks to index, index only the refseq
 args += ['--tracks', 'DNA']
 self.subprocess_check_call(args)
 def _add_json(self, json_data):
 cmd = [
 'perl', self._jbrowse_bin('add-json.pl'),
 json.dumps(json_data),
 os.path.join('data', 'trackList.json')
 ]
 '--gff', gff3,
 '--trackLabel', trackData['label'],
 '--key', trackData['key'],
 '--clientConfig', json.dumps(clientConfig),
 '--config', json.dumps(config),
-'--trackType', 'JBrowse/View/Track/CanvasFeatures'
+'--trackType', 'BlastView/View/Track/CanvasFeatures'
 ]
 # className in --clientConfig is ignored, it needs to be set with --className
 if 'className' in trackData['style']:
 cmd += ['--className', trackData['style']['className']]
 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')
 "type": "JBrowse/View/Track/HTMLVariants",
 "storeClass": "JBrowse/Store/SeqFeature/VCFTabix",
 })
 self._add_track_json(trackData)
-def add_features(self, data, format, trackData, gffOpts, **kwargs):
+def add_features(self, data, format, trackData, gffOpts, metadata=None, **kwargs):
 cmd = [
 'perl', self._jbrowse_bin('flatfile-to-json.pl'),
 self.TN_TABLE.get(format, 'gff'),
 data,
 '--trackLabel', trackData['label'],
 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):
+data = {
+"label": trackData['label'],
+"key": trackData['key'],
+"category": trackData['category'],
+"type": "JBrowse/View/Track/HTMLFeatures",
+"storeClass": "JBrowse/Store/SeqFeature/REST",
+"baseUrl": url,
+"query": {
+"organism": "tyrannosaurus"
+}
+}
+self._add_track_json(data)
 def process_annotations(self, track):
+category = track['category'].replace('__pd__date__pd__', TODAY)
 outputTrackConfig = {
 'style': {
 'label': track['style'].get('label', 'description'),
 'className': track['style'].get('className', 'feature'),
 'description': track['style'].get('description', ''),
 },
-'category': track['category'],
+'overridePlugins': track['style'].get('overridePlugins', False) == 'True',
+'overrideDraggable': track['style'].get('overrideDraggable', False) == 'True',
+'maxHeight': track['style'].get('maxHeight', '600'),
+'category': category,
 }
 mapped_chars = {
 '>': '__gt__',
 '<': '__lt__',
 '}': '__cc__',
 '@': '__at__',
 '#': '__pd__'
 }
-for i, (dataset_path, dataset_ext, track_human_label) 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 %s / %s', track['category'], track_human_label)
+log.info('Processing %s / %s', category, track_human_label)
 outputTrackConfig['key'] = track_human_label
-hashData = [dataset_path, track_human_label, track['category']]
+# We add extra data to hash for the case of REST + SPARQL.
-outputTrackConfig['label'] = hashlib.md5('|'.join(hashData).encode('utf-8')).hexdigest() + '_%s' % i
+try:
+rest_url = track['conf']['options']['url']
+except KeyError:
+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 = '|'.join(hashData).encode('utf-8')
+outputTrackConfig['label'] = hashlib.md5(hashData).hexdigest() + '_%s' % i
 # 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'])
+track['conf']['options']['gff'], metadata=extra_metadata)
 elif dataset_ext == 'bigwig':
 self.add_bigwig(dataset_path, outputTrackConfig,
-track['conf']['options']['wiggle'])
+track['conf']['options']['wiggle'], metadata=extra_metadata)
 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])
+bam_index=real_indexes[i], metadata=extra_metadata)
 elif dataset_ext == 'blastxml':
-self.add_blastxml(dataset_path, outputTrackConfig, track['conf']['options']['blast'])
+self.add_blastxml(dataset_path, outputTrackConfig, track['conf']['options']['blast'], metadata=extra_metadata)
 elif dataset_ext == 'vcf':
-self.add_vcf(dataset_path, outputTrackConfig)
+self.add_vcf(dataset_path, outputTrackConfig, metadata=extra_metadata)
+elif dataset_ext == 'rest':
+self.add_rest(track['conf']['options']['url'], outputTrackConfig, metadata=extra_metadata)
+else:
+log.warn('Do not know how to handle %s', dataset_ext)
 # Return non-human label for use in other fields
 yield outputTrackConfig['label']
 def add_final_data(self, data):
 generalData['show_tracklist'] = (data['general']['show_tracklist'] == 'true')
 generalData['show_nav'] = (data['general']['show_nav'] == 'true')
 generalData['show_overview'] = (data['general']['show_overview'] == 'true')
 generalData['show_menu'] = (data['general']['show_menu'] == 'true')
 generalData['hideGenomeOptions'] = (data['general']['hideGenomeOptions'] == 'true')
+generalData['plugins'] = data['plugins']
 viz_data.update(generalData)
 self._add_json(viz_data)
+if 'GCContent' in data['plugins_python']:
+self._add_track_json({
+"storeClass": "JBrowse/Store/SeqFeature/SequenceChunks",
+"type": "GCContent/View/Track/GCContentXY",
+"label": "GCContentXY",
+"urlTemplate": "seq/{refseq_dirpath}/{refseq}-",
+"bicolor_pivot": 0.5
+# TODO: Expose params for everyone.
+})
+if 'ComboTrackSelector' in data['plugins_python']:
+with open(os.path.join(self.outdir, 'data', 'trackList.json'), 'r') as handle:
+trackListJson = json.load(handle)
+trackListJson.update({
+"trackSelector": {
+"renameFacets": {
+"tool_tool": "Tool ID",
+"tool_tool_id": "Tool ID",
+"tool_tool_version": "Tool Version",
+"dataset_edam_format": "EDAM",
+"dataset_size": "Size",
+"history_display_name": "History Name",
+"history_user_email": "Owner",
+"metadata_dbkey": "Dbkey",
+},
+"displayColumns": [
+"key",
+"tool_tool",
+"tool_tool_version",
+"dataset_edam_format",
+"dataset_size",
+"history_display_name",
+"history_user_email",
+"metadata_dbkey",
+],
+"type": "Faceted",
+"title": ["Galaxy Metadata"],
+"escapeHTMLInData": False
+},
+"trackMetadata": {
+"indexFacets": [
+"category",
+"key",
+"tool_tool_id",
+"tool_tool_version",
+"dataset_edam_format",
+"history_user_email",
+"history_display_name"
+]
+}
+})
+with open(os.path.join(self.outdir, 'data', 'trackList2.json'), 'w') as handle:
+json.dump(trackListJson, handle)
 def clone_jbrowse(self, jbrowse_dir, destination):
 """Clone a JBrowse directory into a destination directory.
 """
 # JBrowse seems to have included some bad symlinks, cp ignores bad symlinks
 log.debug(' '.join(cmd))
 subprocess.check_call(cmd)
 # http://unix.stackexchange.com/a/38691/22785
 # JBrowse releases come with some broken symlinks
-cmd = ['find', destination, '-type', 'l', '-xtype', 'l', '-exec', 'rm', "'{}'", '+']
+cmd = ['find', destination, '-type', 'l', '-xtype', 'l']
 log.debug(' '.join(cmd))
-subprocess.check_call(cmd)
+symlinks = subprocess.check_output(cmd)
+for i in symlinks:
+try:
+os.unlink(i)
+except OSError:
+pass
 if __name__ == '__main__':
 parser = argparse.ArgumentParser(description="", epilog="")
 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")
 args = parser.parse_args()
 tree = ET.parse(args.xml.name)
 root = tree.getroot()
 jc = JbrowseConnector(
 jbrowse=args.jbrowse,
 outdir=args.outdir,
-genomes=[os.path.realpath(x.text) for x in root.findall('metadata/genomes/genome')],
+genomes=[
+{
+'path': os.path.realpath(x.attrib['path']),
+'meta': metadata_from_node(x.find('metadata'))
+}
+for x in root.findall('metadata/genomes/genome')
+],
 standalone=args.standalone,
 gencode=root.find('metadata/gencode').text
 )
 extra_data = {
 'show_tracklist': root.find('metadata/general/show_tracklist').text,
 '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': [{
+'location': 'https://cdn.rawgit.com/TAMU-CPT/blastview/97572a21b7f011c2b4d9a0b5af40e292d694cbef/',
+'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.rawgit.com/elsiklab/gccontent/5c8b0582ecebf9edf684c76af8075fb3d30ec3fa/',
+'name': 'GCContent'
+})
+if plugins['Bookmarks'] == 'True':
+extra_data['plugins'].append({
+'location': 'https://cdn.rawgit.com/TAMU-CPT/bookmarks-jbrowse/5242694120274c86e1ccd5cb0e5e943e78f82393/',
+'name': 'Bookmarks'
+})
+if plugins['ComboTrackSelector'] == 'True':
+extra_data['plugins_python'].append('ComboTrackSelector')
+extra_data['plugins'].append({
+'location': 'https://cdn.rawgit.com/Arabidopsis-Information-Portal/ComboTrackSelector/52403928d5ccbe2e3a86b0fa5eb8e61c0f2e2f57',
+'icon': 'https://galaxyproject.org/images/logos/galaxy-icon-square.png',
+'name': 'ComboTrackSelector'
+})
+if plugins['theme'] == 'Minimalist':
+extra_data['plugins'].append({
+'location': 'https://cdn.rawgit.com/erasche/jbrowse-minimalist-theme/d698718442da306cf87f033c72ddb745f3077775/',
+'name': 'MinimalistTheme'
+})
+elif plugins['theme'] == 'Dark':
+extra_data['plugins'].append({
+'location': 'https://cdn.rawgit.com/erasche/jbrowse-dark-theme/689eceb7e33bbc1b9b15518d45a5a79b2e5d0a26/',
+'name': 'DarkTheme'
+})
+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
 for track in root.findall('tracks/track'):
 track_conf = {}
-track_conf['trackfiles'] = [
+track_conf['trackfiles'] = []
-(os.path.realpath(x.attrib['path']), x.attrib['ext'], x.attrib['label'])
-for x in track.findall('files/trackFile')
+for x in track.findall('files/trackFile'):
-]
+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['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:
+except TypeError as te:
 track_conf['style'] = {}
 pass
 track_conf['conf'] = etree_to_dict(track.find('options'))
 keys = jc.process_annotations(track_conf)
 for key in keys:
 extra_data['visibility'][track.attrib.get('visibility', 'default_off')].append(key)
 jc.add_final_data(extra_data)
-jc.generate_names()

Mercurial > repos > iuc > jbrowse

comparison jbrowse.py @ 17:ff11d442feed draft