Question: python's HGVS module UTA connection error
0
gravatar for wrel2015
4.0 years ago by
wrel20150
wrel20150 wrote:

Hi,

I am getting an error whenever I try to connect to the public UTA database hosted by Invitae as part of the HGVS module to try and get the genomic location of the Refseq transcript HGVS term using publicly available data.

Here is what I entered in terminal, if anyone has come across this I would really appreciate your help. Thanks!

>>> import hgvs
>>> import hgvs.parser
>>> hgvsparser = hgvs.parser.Parser()
>>> var_c1 = hgvsparser.parse_hgvs_variant('NM_001197320.1:c.281C>T')
>>> var_c1
SequenceVariant(ac=NM_001197320.1, type=c, posedit=281C>T)
>>> import hgvs.dataproviders.uta
>>> hdp = hgvs.dataproviders.uta.connect()
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "/location/users/bla/bla_user/.local/lib/python2.7/site-packages/hgvs-0.3.6-py2.7.egg/hgvs/dataproviders/uta.py", line 71, in connect
    conn = UTA_postgresql(url, pooling)
  File "/location/users/bla/bla_user/.local/lib/python2.7/site-packages/hgvs-0.3.6-py2.7.egg/hgvs/dataproviders/uta.py", line 390, in __init__
    super(UTA_postgresql, self).__init__(url)
  File "/location/users/bla/bla_user/.local/lib/python2.7/site-packages/hgvs-0.3.6-py2.7.egg/hgvs/dataproviders/uta.py", line 146, in __init__
    self._connect()
  File "/location/users/bla/bla_user/.local/lib/python2.7/site-packages/hgvs-0.3.6-py2.7.egg/hgvs/dataproviders/uta.py", line 405, in _connect
    password=self.url.password)
  File "/software/title/python2/lib/python2.7/site-packages/psycopg2/__init__.py", line 164, in connect
    conn = _connect(dsn, connection_factory=connection_factory, async=async)
psycopg2.OperationalError: could not connect to server: Connection refused
    Is the server running on host "uta.invitae.com" (54.237.120.108) and accepting

    TCP/IP connections on port 5432?

 

snp software error • 1.7k views
ADD COMMENTlink modified 19 months ago by Biostar ♦♦ 20 • written 4.0 years ago by wrel20150

The site might be down. Try again after a while maybe?

ADD REPLYlink written 4.0 years ago by RamRS24k

I've been trying this for weeks :(

ADD REPLYlink written 4.0 years ago by wrel20150

Ohh. Maybe a network problem on your end then? Maybe raise an issue on their bitbucket? They are pretty responsive.

ADD REPLYlink written 4.0 years ago by RamRS24k
1
gravatar for Reece
3.9 years ago by
Reece260
United States
Reece260 wrote:

The OP also asked at the hgvs bitbucket page and the issue was solved there. The problem appears to be that the user's institution began blocking outgoing ports.

 

 

ADD COMMENTlink written 3.9 years ago by Reece260
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