python's HGVS module UTA connection error
1
0
Entering edit mode
6.4 years ago
wrel2015 • 0

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 SNP software error • 2.4k views
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Entering edit mode

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

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I've been trying this for weeks :(

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

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Entering edit mode
6.2 years ago
Reece ▴ 310

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.

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