from IPython.display import HTML, SVG, display
from ipykernel.comm import Comm
import json
import random
import time
class _IGVComm:
def __init__(self, id):
# Use comm to send a message from the kernel
self.comm = Comm(target_name=id, data={})
def send(self, message):
self.comm.send(message)
class Browser(object):
# Always remember the *self* argument
def __init__(self, config):
"""Initialize an igv Browser object.
:param: config - A dictionary specifying the browser configuration. This will be converted to JSON and passed
to igv.js "igv.createBrowser(config)" as described in the igv.js documentation. See
https://github.com/igvteam/igv.js/wiki/Browser-Configuration-2.0 for configuration options.
:type dict
"""
# Check for minimal igv.js requirements (the only required field for all tracks is url, which must be a string)
if isinstance(config, dict) == False:
raise Exception("config parameter must be a dictionary")
has_genome = "genome" in config or "reference" in config
if not has_genome:
raise Exception("config must specify either 'genome' or 'reference'")
id = self._gen_id()
config["id"] = id
self.igv_id = id
self.config = config
self.comm = _IGVComm("igvcomm")
self._status = "initializing"
self.locus = None
self.eventHandlers = {}
self.svg = None
self.message_queue = []
# Add a callback for received messages.
@self.comm.comm.on_msg
def _recv(msg):
data = json.loads(msg['content']['data'])
if 'status' in data:
self.status = data['status']
elif 'locus' in data:
self.locus = data['locus']
elif 'svg' in data:
self.svg = data['svg']
elif 'event' in data:
if data['event'] in self.eventHandlers:
handler = self.eventHandlers[data['event']]
eventData = None
if 'data' in data:
eventData = data['data']
handler(eventData)
@property
def status(self):
return self._status
@status.setter
def status(self, value):
self._status = value
if value == "ready" and len(self.message_queue) > 0:
time.sleep(0.5)
self._send(self.message_queue.pop(0))
def show(self):
"""
Create an igv.js "Browser" instance on the front end.
"""
display(HTML("""<div id="%s"></div>""" % (self.igv_id)))
# DON'T check status before showing browser,
msg = json.dumps({
"id": self.igv_id,
"command": "create",
"options": self.config
})
self.comm.send(msg)
def search(self, locus):
"""
Go to the specified locus.
:param locus: Chromosome location of the form "chromsosome:start-end", or for supported genomes (hg38, hg19, and mm10) a gene name.
:type str
"""
self._send({
"id": self.igv_id,
"command": "search",
"locus": locus
})
def zoom_in(self):
"""
Zoom in by a factor of 2
"""
self._send({
"id": self.igv_id,
"command": "zoomIn"
})
def zoom_out(self):
"""
Zoom out by a factor of 2
"""
self._send({
"id": self.igv_id,
"command": "zoomOut"
})
def load_track(self, track):
"""
Load a track. Corresponds to the igv.js Browser function loadTrack (see https://github.com/igvteam/igv.js/wiki/Browser-Control-2.0#loadtrack).
:param track: A dictionary specifying track options. See https://github.com/igvteam/igv.js/wiki/Tracks-2.0.
:type dict
"""
# Check for minimal igv.js requirements (the only required field for all tracks is url, which must be a string)
if isinstance(track, dict) == False:
raise Exception("track parameter must be a dictionary")
self._send({
"id": self.igv_id,
"command": "loadTrack",
"track": track
})
def to_svg(self):
"""
Fetch the current IGV view as an SVG image and display it in this cell
"""
div_id = self._gen_id();
display(HTML("""<div id="%s"></div>""" % div_id))
self._send({
"id": self.igv_id,
"div": div_id,
"command": "toSVG"
})
def get_svg(self):
"""
Fetch the current IGV view as an SVG image. To display the message call display_svg()
"""
self.svg = "FETCHING"
return self._send({
"id": self.igv_id,
"command": "toSVG"
})
def display_svg(self):
"""
Display the current SVG image. You must call get_svg() before calling this method.
"""
if self.svg == None:
return "Must call get_svg() first"
elif self.svg == "FETCHING":
return 'Awaiting SVG - try again in a few seconds'
else:
svg = self.svg
self.svg == None
display(SVG(svg))
def on(self, eventName, cb):
"""
Subscribe to an igv.js event.
:param Name of the event. Currently only "locuschange" is supported.
:type str
:param cb - callback function taking a single argument. For the locuschange event this argument will contain
a dictionary of the form {chr, start, end}
:type function
"""
self.eventHandlers[eventName] = cb
self._send({
"id": self.igv_id,
"command": "on",
"eventName": eventName
})
def remove(self):
"""
Remove the igv.js Browser instance from the front end. The server Browser object should be disposed of after calling
this method.
"""
self._send({
"id": self.igv_id,
"command": "remove"
})
def _send(self, msg):
if self.status == "ready":
self.status = "busy"
self.comm.send(json.dumps(msg))
else:
self.message_queue.append(msg)
def _gen_id(self):
return 'igv_' + str(random.randint(1, 10000000))
