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ENCSR2viz.py
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ENCSR2viz.py
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#!/usr/bin/env python
# -*- coding: latin-1 -*-
'''Take a list of ENCODE experiments and visualize them'''
import requests
import json
import sys, os.path
EPILOG = '''Examples:
'''
'''force return from the server in JSON format'''
HEADERS = {'content-type': 'application/json'}
def get_ENCODE(obj_id, frame='object'):
'''GET an ENCODE object as JSON and return as dict'''
if obj_id.rfind('?') == -1:
url = ENCODED_SERVER+obj_id+'?limit=all&frame=%s' %(frame)
else:
url = ENCODED_SERVER+obj_id+'&limit=all&frame=%s' %(frame)
if DEBUG:
print "DEBUG: GET %s" %(url)
response = requests.get(url, auth=(AUTHID, AUTHPW), headers=HEADERS)
if DEBUG:
print "DEBUG: GET RESPONSE code %s" %(response.status_code)
try:
if response.json():
print "DEBUG: GET RESPONSE JSON"
print json.dumps(response.json(), indent=4, separators=(',', ': '))
except:
print "DEBUG: GET RESPONSE text %s" %(response.text)
if not response.status_code == 200:
print >> sys.stderr, response.text
return response.json()
def processkeys(args):
keysf = open(args.keyfile,'r')
keys_json_string = keysf.read()
keysf.close()
keys = json.loads(keys_json_string)
key_dict = keys[args.key]
global AUTHID
global AUTHPW
global ENCODED_SERVER
if not args.authid:
AUTHID = key_dict['key']
else:
AUTHID = args.authid
if not args.authpw:
AUTHPW = key_dict['secret']
else:
AUTHPW = args.authpw
if not args.server:
ENCODED_SERVER = key_dict['server']
else:
ENCODED_SERVER = args.server
if not ENCODED_SERVER.endswith("/"):
ENCODED_SERVER += "/"
def flat_one(JSON_obj):
try:
return [JSON_obj[identifier] for identifier in \
['accession', 'name', 'email', 'title', 'uuid', 'href'] \
if identifier in JSON_obj][0]
except:
return JSON_obj
def flat_ENCODE(JSON_obj):
flat_obj = {}
for key in JSON_obj:
if isinstance(JSON_obj[key], dict):
flat_obj.update({key:flat_one(JSON_obj[key])})
elif isinstance(JSON_obj[key], list) and JSON_obj[key] != [] and isinstance(JSON_obj[key][0], dict):
newlist = []
for obj in JSON_obj[key]:
newlist.append(flat_one(obj))
flat_obj.update({key:newlist})
else:
flat_obj.update({key:JSON_obj[key]})
return flat_obj
def pprint_ENCODE(JSON_obj):
if ('type' in JSON_obj) and (JSON_obj['type'] == "object"):
print json.dumps(JSON_obj['properties'], sort_keys=True, indent=4, separators=(',', ': '))
else:
print json.dumps(flat_ENCODE(JSON_obj), sort_keys=True, indent=4, separators=(',', ': '))
def ENCSR2viz(experiments_to_visualize):
if DEBUG:
print "Visualizing"
print experiments_to_visualize
from trackhub import Hub, GenomesFile, Genome, TrackDb, Track
from trackhub.upload import upload_hub
HUBHOST = 'https://cherry-vm45.stanford.edu'
HUBDIR = 'jseth/trackhubs'
USER = 'jseth'
URLBASE = os.path.join(HUBHOST, HUBDIR)
EDWBASE = 'https://encodedcc.sdsc.edu/warehouse'
GENOME = 'hg19'
hub = Hub(
hub='ENCODE',
short_label='ENCODE',
long_label='ENCODE',
email='[email protected]')
genomes_file = GenomesFile()
genome = Genome(GENOME)
trackdb = TrackDb()
for accession in experiments_to_visualize:
experiment_obj = get_ENCODE(accession)
if DEBUG:
print experiment_obj
for file_id in experiment_obj['files']:
file_obj = get_ENCODE(file_id)
if file_obj['file_format'] in ['bigWig', 'bigBed', 'broadPeak', 'narrowPeak']:
if file_obj['file_format'] in ['bigWig']:
track_type = 'bigWig'
elif file_obj['file_format'] in ['bigBed', 'broadPeak', 'narrowPeak']:
track_type = 'bigBed'
track = Track(
name=str(file_obj['accession']),
url=os.path.join(EDWBASE, str(file_obj['download_path'])),
tracktype=track_type,
long_label=str(file_obj['accession']),
short_label=str(file_obj['output_type']),
color='128,0,0',
visibility='dense',
metadata='cell_type=primary')
print file_obj['accession']
trackdb.add_tracks([track])
genome.add_trackdb(trackdb)
genomes_file.add_genome(genome)
hub.add_genomes_file(genomes_file)
results=hub.render()
if DEBUG:
print hub
print '...'
print genomes_file
print '...'
print genome
print '...'
print trackdb
#upload_hub(hub=hub, host=HUBHOST, user=USER) #doesn't seem to work
import subprocess
subprocess.call("cd .. && rsync -r trackhub [email protected]:/www/html/jseth/trackhubs", shell=True)
import webbrowser
hubfile = str(hub.hub) + '.hub.txt'
UCSC_url = 'https://genome.ucsc.edu/cgi-bin/hgTracks?udcTimeout=1&db=hg19' + \
'&hubUrl=' + os.path.join(HUBHOST,HUBDIR,'trackhub',hubfile) # + \
#'&hsS_doLoadUrl=submit&hgS_loadUrlName=' + os.path.join(HUBHOST,HUBDIR,'trackhub','session.txt')
print UCSC_url
webbrowser.open(UCSC_url)
def main():
import argparse
parser = argparse.ArgumentParser(
description=__doc__, epilog=EPILOG,
formatter_class=argparse.RawDescriptionHelpFormatter,
)
parser.add_argument('experiments', metavar='ENCSR', nargs='*',
default=None,
help="Experiment(s) to visualize by ENCODE experiment accession, (default or '-': take list from stdin)")
parser.add_argument('--infile', '-i', metavar='file', nargs='*',
help="File(s) containing a (possibly multi-line) whitspace-delimited list of ENCODE experiment accessions")
parser.add_argument('--server',
help="Full URL of the server.")
parser.add_argument('--key',
default='default',
help="The keypair identifier from the keyfile. Default is --key=default")
parser.add_argument('--keyfile',
default=os.path.expanduser("~/keypairs.json"),
help="The keypair file. Default is --keyfile=%s" %(os.path.expanduser("~/keypairs.json")))
parser.add_argument('--authid',
help="The HTTP auth ID.")
parser.add_argument('--authpw',
help="The HTTP auth PW.")
parser.add_argument('--debug',
default=False,
action='store_true',
help="Print debug messages. Default is False.")
args = parser.parse_args()
processkeys(args)
global DEBUG
DEBUG = args.debug
if args.infile == None:
infilenames = []
else:
infilenames = args.infile
if args.experiments == '-':
infilenames.append('-')
if infilenames != []:
import fileinput
ENCODE_experiments = []
for line in fileinput.input(infilenames):
ENCODE_experiments.extend(line.split())
else:
ENCODE_experiments = args.experiments
result = ENCSR2viz(ENCODE_experiments)
if __name__ == '__main__':
main()