-
Notifications
You must be signed in to change notification settings - Fork 4
/
Copy pathfiles2viz.py
executable file
·206 lines (181 loc) · 5.71 KB
/
files2viz.py
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
#!/usr/bin/env python
# -*- coding: latin-1 -*-
'''Take a list of ENCODE files 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):
'''GET an ENCODE object as JSON and return as dict'''
if obj_id.rfind('?') == -1:
url = ENCODED_SERVER+obj_id+'?limit=all'
else:
url = ENCODED_SERVER+obj_id+'&limit=all'
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 files2viz(files_to_visualize):
if DEBUG:
print "Visualizing"
print files_to_visualize
from trackhub import Hub, GenomesFile, Genome, TrackDb, Track
from trackhub.upload import upload_hub
HUBHOST = 'http://cherry-vm45.stanford.edu'
HUBDIR = 'trackhubs'
USER = 'jseth'
URLBASE = os.path.join(HUBHOST, HUBDIR)
EDWBASE = 'http://encodedcc.sdsc.edu/warehouse'
GENOME = 'hg19'
hub = Hub(
hub='Selected_ENCODE_Tracks',
short_label='Selected_ENCODE_Tracks_short',
long_label='Selected_ENCODE_Tracks_long',
email='[email protected]')
genomes_file = GenomesFile()
genome = Genome(GENOME)
trackdb = TrackDb()
for accession in files_to_visualize:
file_obj = get_ENCODE(accession)
if DEBUG:
print file_obj
if file_obj['file_format'] == 'bigWig':
track = Track(
name=accession,
url=os.path.join(EDWBASE, str(file_obj['download_path'])),
tracktype='bigWig',
short_label=accession,
long_label=accession,
color='128,0,0',
visibility='full')
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/trackhubs", shell=True)
import webbrowser
hubfile = str(hub.hub) + '.hub.txt'
UCSC_url = 'http://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('files', metavar='ENCFF', nargs='*',
default=None,
help="File(s) to visualize by ENCODE file accession, (default or '-': take list of files from stdin)")
parser.add_argument('--infile', '-i', metavar='file', nargs='*',
help="File(s) containing a (possibly multi-line) whitspace-delimited list of ENCODE file 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.files == '-':
infilenames.append('-')
if infilenames != []:
import fileinput
ENCODE_files = []
for line in fileinput.input(infilenames):
ENCODE_files.extend(line.split())
else:
ENCODE_files = args.files
result = files2viz(ENCODE_files)
if __name__ == '__main__':
main()