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1–30 of 103
The hgvs-discuss list is for discussing the
hgvs
library for parsing and formatting biological sequence variants.
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Matt Ducar
,
Reece Hart
4
9/29/22
Annotation for intronic variants
Hi Matt- Everything you wrote is correct. And, to be clearer (I hope): hgvs will neither parse nor
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Annotation for intronic variants
Hi Matt- Everything you wrote is correct. And, to be clearer (I hope): hgvs will neither parse nor
9/29/22
Linoy Tsaban
,
Reece Hart
2
12/9/21
question about hgvs.exceptions.HGVSDataNotAvailableError
Hi Linoy- A connection timeout is mostly likely a temporary failure, which happens from time to time.
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question about hgvs.exceptions.HGVSDataNotAvailableError
Hi Linoy- A connection timeout is mostly likely a temporary failure, which happens from time to time.
12/9/21
Sheila Reynolds
12/3/20
question about get_similar_transcripts
Hi all, when I see "None" as the value for cds_eq (for example, I am looking for
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question about get_similar_transcripts
Hi all, when I see "None" as the value for cds_eq (for example, I am looking for
12/3/20
Somak Roy
,
Reece Hart
5
5/26/20
UTA transcripts obsolete in RefSeq
Hi Reece, No worries, these are busy times for everyone. Thank you for offering to help with my
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UTA transcripts obsolete in RefSeq
Hi Reece, No worries, these are busy times for everyone. Thank you for offering to help with my
5/26/20
Reece Hart
4/13/20
seqrepo release
Hi All- biocommons.seqrepo 0.5.5 was released yesterday and there's a new data release, 2020-04-
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seqrepo release
Hi All- biocommons.seqrepo 0.5.5 was released yesterday and there's a new data release, 2020-04-
4/13/20
Reece Hart
3/28/20
hgvs 1.5.1 released
hgvs 1.5.1 was just released. This patch releases fixes bugs of omission related to the recent
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hgvs 1.5.1 released
hgvs 1.5.1 was just released. This patch releases fixes bugs of omission related to the recent
3/28/20
Reece Hart
3/17/20
hgvs 1.5.0 released
hgvs 1.5.0 was just released. See the changelog for details. The major feature added in this release
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hgvs 1.5.0 released
hgvs 1.5.0 was just released. See the changelog for details. The major feature added in this release
3/17/20
Tarun karthik kumar Mamidi
,
Reece Hart
3
2/10/20
How to ignore errors when working with multiple variants?
Thanks for the help. I still get an error. Please see below. NameError: ("name 'HGVSError
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How to ignore errors when working with multiple variants?
Thanks for the help. I still get an error. Please see below. NameError: ("name 'HGVSError
2/10/20
Reece Hart
1/27/20
hgvs 1.4.0 is out!
hgvs 1.4.0 was just released. See the changelog at https://hgvs.readthedocs.io/en/stable/changelog/
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hgvs 1.4.0 is out!
hgvs 1.4.0 was just released. See the changelog at https://hgvs.readthedocs.io/en/stable/changelog/
1/27/20
Naomi Fox
,
Reece Hart
2
1/3/20
Backtranslation support?
Hi Naomi- Yes, this has been raised before. Please add your ideas to https://github.com/biocommons/
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Backtranslation support?
Hi Naomi- Yes, this has been raised before. Please add your ideas to https://github.com/biocommons/
1/3/20
Ouhao Lin
,
Reece Hart
4
12/8/19
how to use locally
I just do as the guide told me , first docker pull, then export the port the default setting. the
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how to use locally
I just do as the guide told me , first docker pull, then export the port the default setting. the
12/8/19
Reece Hart
,
Sue S
3
10/30/19
Re: [hgvs-discuss] reference genome for minus strand is not revese_complemented
You're welcome. The CDS length is 2094, so valid c. coordinates are 1-2094 (inclusive, 1-based).
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Re: [hgvs-discuss] reference genome for minus strand is not revese_complemented
You're welcome. The CDS length is 2094, so valid c. coordinates are 1-2094 (inclusive, 1-based).
10/30/19
Sue S
10/29/19
c_to_g g.variant for minus strand is not revese_complemented
Hello, when I convert c_to_g for variant "NM_181714.3:c.4105_4117dupGCACTATGACTCT", I got
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c_to_g g.variant for minus strand is not revese_complemented
Hello, when I convert c_to_g for variant "NM_181714.3:c.4105_4117dupGCACTATGACTCT", I got
10/29/19
Andreas Prlić
10/21/19
Upcoming uta.biocommons.org maintenance Oct 23rd 6-8pm PT
Hi, We will need to perform maintenance on uta.biocommons.org (AWS reported that the system that runs
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Upcoming uta.biocommons.org maintenance Oct 23rd 6-8pm PT
Hi, We will need to perform maintenance on uta.biocommons.org (AWS reported that the system that runs
10/21/19
Sheila Reynolds
,
Reece Hart
2
9/27/19
newbie here, having trouble with install
Hi Sheila- In the future, please send the error that you're seeing and information about your
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newbie here, having trouble with install
Hi Sheila- In the future, please send the error that you're seeing and information about your
9/27/19
Reece Hart
9/10/19
RFC: Supporting partial alignments
This is a request for comments on a technical issue with transcript-genome alignments. As some of you
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RFC: Supporting partial alignments
This is a request for comments on a technical issue with transcript-genome alignments. As some of you
9/10/19
Sue S
,
Reece Hart
2
9/9/19
HGVS package 1.3 del and dup sequence omitted
Hi Sue- Documentation for configuration is weak right now. (PR's welcome!) For now, see these:
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HGVS package 1.3 del and dup sequence omitted
Hi Sue- Documentation for configuration is weak right now. (PR's welcome!) For now, see these:
9/9/19
Dario Beraldi
,
Reece Hart
2
8/5/19
Edit protein sequence given HGVS.p
Hi Dario- Sorry, this query was lost during my vacation. The hgvs package doesn't have a way to
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Edit protein sequence given HGVS.p
Hi Dario- Sorry, this query was lost during my vacation. The hgvs package doesn't have a way to
8/5/19
Felicia Ng
, …
Reece Hart
4
6/26/19
hgvs uta connection
Hi Felicia- Sorry for not replying earlier. I'm glad you found the solution. -Reece On Wed, Jun
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hgvs uta connection
Hi Felicia- Sorry for not replying earlier. I'm glad you found the solution. -Reece On Wed, Jun
6/26/19
Reece Hart
5/16/19
hgvs 1.3.0 released
Hi all- hgvs 1.3.0 was released last night. It contains a few new features, mostly experimental. As
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hgvs 1.3.0 released
Hi all- hgvs 1.3.0 was released last night. It contains a few new features, mostly experimental. As
5/16/19
andrea...@invitae.com
5/7/19
uta.biocommons.org maintenance: Wed May 8th 3 PM PDT
Hi, We will perform some maintenance work on the publicly hosted UTA postgres instances on Wed May
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uta.biocommons.org maintenance: Wed May 8th 3 PM PDT
Hi, We will perform some maintenance work on the publicly hosted UTA postgres instances on Wed May
5/7/19
Reece Hart
2/1/19
hgvs 1.2.5 is out
hgvs 1.2.5 was just released to pypi. Please see the changelog at https://hgvs.readthedocs.io/en/
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hgvs 1.2.5 is out
hgvs 1.2.5 was just released to pypi. Please see the changelog at https://hgvs.readthedocs.io/en/
2/1/19
Reece Hart
1/24/19
Reminder: Migrating to Python 3.6
Reminder: biocommons packages will be migrating to Python 3.6. Here's the plan: https://github.
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Reminder: Migrating to Python 3.6
Reminder: biocommons packages will be migrating to Python 3.6. Here's the plan: https://github.
1/24/19
Keith Callenberg
, …
Jake Peacock
8
1/15/19
SQLite object error using hgvs 0.5
Hi Reece and Peter, We have been running into this issue when utilizing celery to asynchronously
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SQLite object error using hgvs 0.5
Hi Reece and Peter, We have been running into this issue when utilizing celery to asynchronously
1/15/19
Jonathan Freidin
,
Reece Hart
3
12/9/18
How to translate TERT NM_198253 promoter -124C>T?
As for what you should do about it... At this time, the only thing you can do is to compute it
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How to translate TERT NM_198253 promoter -124C>T?
As for what you should do about it... At this time, the only thing you can do is to compute it
12/9/18
Reece Hart
10/6/18
biocommons packages dropping support for Python 2.7
All biocommons packages — hgvs, uta, seqrepo, bioutils, and eutils — currently support Python 2.7 and
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biocommons packages dropping support for Python 2.7
All biocommons packages — hgvs, uta, seqrepo, bioutils, and eutils — currently support Python 2.7 and
10/6/18
Reece Hart
,
Somak Roy
2
9/25/18
Just out: hgvs 2018 update paper
Hi Reece, Many congrats to you and all coauthors on this manuscript! Thanks for sharing the link.
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Just out: hgvs 2018 update paper
Hi Reece, Many congrats to you and all coauthors on this manuscript! Thanks for sharing the link.
9/25/18
Reece Hart
8/24/18
Re: Does the hgvs library have support for one-letter hgvs representations?
Hi Melissa- We got you covered! (I think) hgvs always uses 1-letter internally. It will always parse
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Re: Does the hgvs library have support for one-letter hgvs representations?
Hi Melissa- We got you covered! (I think) hgvs always uses 1-letter internally. It will always parse
8/24/18
Somak Roy
, …
Angie Hinrichs
6
8/20/18
hgvs package clinical validation study
Dear Reece, Raymond, and Angie, Thank you for your comments and feedback on the manuscript. Sorry for
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hgvs package clinical validation study
Dear Reece, Raymond, and Angie, Thank you for your comments and feedback on the manuscript. Sorry for
8/20/18
Reece Hart
6/2/18
Re: hgvs
Hi Jianfen- Sorry for the delay in replying. You're likely get a faster reply if you send to hgvs
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Re: hgvs
Hi Jianfen- Sorry for the delay in replying. You're likely get a faster reply if you send to hgvs
6/2/18