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question about hgvs.exceptions.HGVSDataNotAvailableError

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Linoy Tsaban

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Dec 8, 2021, 4:42:29 AM12/8/21
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Hello,

I'm new to hgvs.  Been using the parser and g_to_c, c_to_p and c_to_g functions.  I start with input of genomic variants in the form of  NC_000017.11:g.7674244_7674245insT for example.

I get this error when I call c_to_g on the return value from the g_to_c (it has worked in the past and specifically on NC_000017.11, so I'm not sure what went wrong now):

hgvs.exceptions.HGVSDataNotAvailableError: Failed to fetch NC_000017.11 from bioutils.seqfetcher (network fetching) (Failed to fetch NC_000017.11 (HTTPSConnectionPool(host='eutils.ncbi.nlm.nih.gov', port=443): Max retries exceeded with url: /entrez/eutils/efetch.fcgi?db=nucleotide&id=NC_000017.11&rettype=fasta&seq_start=7676210&seq_stop=7676210&tool=bioutils&email=biocomm...@googlegroups.com (Caused by NewConnectionError('<urllib3.connection.HTTPSConnection object at 0x7f327cc18ba8>: Failed to establish a new connection: [Errno 110] Connection timed out'))))

Thank you!

Linoy

Reece Hart

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Dec 9, 2021, 1:00:01 AM12/9/21
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Hi Linoy-

A connection timeout is mostly likely a temporary failure, which happens from time to time.

As an alternative, you can install SeqRepo, which is a local sequence repository (and ~40-50x faster than network fetching). Please see the hgvs installation instructions for details.

Good luck,
Reece



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