In [4]:

import ipyigv as igv
from ipywidgets.widgets.trait_types import InstanceDict
from ipyigv.options import ReferenceGenome, Track
from ipywidgets import Output 

Initializing the browser¶

In [5]:

genomeDict=igv.PUBLIC_GENOMES.hg38

In [6]:

genome = ReferenceGenome(**genomeDict)

In [7]:

browser = igv.IgvBrowser(genome=genome)

In [8]:

browser

IgvBrowser(genome=ReferenceGenome(cytobandURL='https://s3.dualstack.us-east-1.amazonaws.com/igv.org.genomes/hg…

Adding or removing a track¶

In [9]:

trackDict = {'name': 'Refseq Genes',
   'format': 'refgene',
   'url': 'https://s3.dualstack.us-east-1.amazonaws.com/igv.org.genomes/hg38/refGene.txt.gz',
   'indexed': False,
   'visibilityWindow': -1,
   'removable': False,
   'order': 1000000}

In [10]:

oneMoreTrack = Track(**trackDict)

In [11]:

browser.add_track(oneMoreTrack)

In [12]:

browser.remove_track(oneMoreTrack)

Adding a Region of Interest¶

In [13]:

roiDict = {
        'name': 'ROI set 1',
        'url': 'https://s3.amazonaws.com/igv.org.test/data/roi/roi_bed_1.bed',
        'indexed': False,
        'color': "rgba(68, 134, 247, 0.25)"
}

In [14]:

roi=igv.options.AnnotationTrack(**roiDict)

In [15]:

browser.add_roi(roi)

Searching¶

In [16]:

browser.search('chr3:1-190,100,300')

search

Getting the browser configuration¶

We need to output the configuration in browser.out, which is an Output widget

In [17]:

browser.dump_json()

Dumping JSON to browser.out

In [18]:

browser.out

Output(outputs=({'output_type': 'stream', 'text': "{'version': '2.7.0', 'reference': {'id': 'hg38', 'name': 'H…

Charging local files¶

NB: igv.js tries to load a file undefined.fai which causes an error. Maybe due to the use of localhost:8000 -- activate it with python -m http.server in your files directory.

In [19]:

genome2 = {
 'name': 'Example chr6p',
 'fastaURL': 'http://localhost:8000/chr6p.fa',
 'indexURL': 'http://localhost:8000/chr6p.fa.fai',
}

In [20]:

pgf6p_on_chr6p_track = {'name': 'PGF 6p on chr6p',
   'format': 'refgene',
   'url': 'http://localhost:8000/PGF_6p_on_chr6p.bam',
   'indexURL': 'http://localhost:8000/PGF_6p_on_chr6p.bai',
   }

In [21]:

browser2 = igv.IgvBrowser(genome=ReferenceGenome(**genome2))

In [22]:

browser2

IgvBrowser(genome=ReferenceGenome(fastaURL='http://localhost:8000/chr6p.fa', indexURL='http://localhost:8000/c…

In [23]:

import urllib.request

In [24]:

url = urllib.request.urlopen('http://localhost:8000/chr6p.fa.fai')

---------------------------------------------------------------------------
ConnectionRefusedError                    Traceback (most recent call last)
~/opt/miniconda3/envs/widgets/lib/python3.9/urllib/request.py in do_open(self, http_class, req, **http_conn_args)
   1341             try:
-> 1342                 h.request(req.get_method(), req.selector, req.data, headers,
   1343                           encode_chunked=req.has_header('Transfer-encoding'))

~/opt/miniconda3/envs/widgets/lib/python3.9/http/client.py in request(self, method, url, body, headers, encode_chunked)
   1254         """Send a complete request to the server."""
-> 1255         self._send_request(method, url, body, headers, encode_chunked)
   1256 

~/opt/miniconda3/envs/widgets/lib/python3.9/http/client.py in _send_request(self, method, url, body, headers, encode_chunked)
   1300             body = _encode(body, 'body')
-> 1301         self.endheaders(body, encode_chunked=encode_chunked)
   1302 

~/opt/miniconda3/envs/widgets/lib/python3.9/http/client.py in endheaders(self, message_body, encode_chunked)
   1249             raise CannotSendHeader()
-> 1250         self._send_output(message_body, encode_chunked=encode_chunked)
   1251 

~/opt/miniconda3/envs/widgets/lib/python3.9/http/client.py in _send_output(self, message_body, encode_chunked)
   1009         del self._buffer[:]
-> 1010         self.send(msg)
   1011 

~/opt/miniconda3/envs/widgets/lib/python3.9/http/client.py in send(self, data)
    949             if self.auto_open:
--> 950                 self.connect()
    951             else:

~/opt/miniconda3/envs/widgets/lib/python3.9/http/client.py in connect(self)
    920         """Connect to the host and port specified in __init__."""
--> 921         self.sock = self._create_connection(
    922             (self.host,self.port), self.timeout, self.source_address)

~/opt/miniconda3/envs/widgets/lib/python3.9/socket.py in create_connection(address, timeout, source_address)
    842         try:
--> 843             raise err
    844         finally:

~/opt/miniconda3/envs/widgets/lib/python3.9/socket.py in create_connection(address, timeout, source_address)
    830                 sock.bind(source_address)
--> 831             sock.connect(sa)
    832             # Break explicitly a reference cycle

ConnectionRefusedError: [Errno 61] Connection refused

During handling of the above exception, another exception occurred:

URLError                                  Traceback (most recent call last)
<ipython-input-24-0ba9ddfa92c7> in <module>
----> 1 url = urllib.request.urlopen('http://localhost:8000/chr6p.fa.fai')

~/opt/miniconda3/envs/widgets/lib/python3.9/urllib/request.py in urlopen(url, data, timeout, cafile, capath, cadefault, context)
    212     else:
    213         opener = _opener
--> 214     return opener.open(url, data, timeout)
    215 
    216 def install_opener(opener):

~/opt/miniconda3/envs/widgets/lib/python3.9/urllib/request.py in open(self, fullurl, data, timeout)
    515 
    516         sys.audit('urllib.Request', req.full_url, req.data, req.headers, req.get_method())
--> 517         response = self._open(req, data)
    518 
    519         # post-process response

~/opt/miniconda3/envs/widgets/lib/python3.9/urllib/request.py in _open(self, req, data)
    532 
    533         protocol = req.type
--> 534         result = self._call_chain(self.handle_open, protocol, protocol +
    535                                   '_open', req)
    536         if result:

~/opt/miniconda3/envs/widgets/lib/python3.9/urllib/request.py in _call_chain(self, chain, kind, meth_name, *args)
    492         for handler in handlers:
    493             func = getattr(handler, meth_name)
--> 494             result = func(*args)
    495             if result is not None:
    496                 return result

~/opt/miniconda3/envs/widgets/lib/python3.9/urllib/request.py in http_open(self, req)
   1369 
   1370     def http_open(self, req):
-> 1371         return self.do_open(http.client.HTTPConnection, req)
   1372 
   1373     http_request = AbstractHTTPHandler.do_request_

~/opt/miniconda3/envs/widgets/lib/python3.9/urllib/request.py in do_open(self, http_class, req, **http_conn_args)
   1343                           encode_chunked=req.has_header('Transfer-encoding'))
   1344             except OSError as err: # timeout error
-> 1345                 raise URLError(err)
   1346             r = h.getresponse()
   1347         except:

URLError: <urlopen error [Errno 61] Connection refused>

In [25]:

print(url.read(100).decode('utf-8'))

---------------------------------------------------------------------------
NameError                                 Traceback (most recent call last)
<ipython-input-25-c0f5215b53c0> in <module>
----> 1 print(url.read(100).decode('utf-8'))

NameError: name 'url' is not defined

In [ ]: