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Discussion list for biocommons users. Renamed from the hgvs-discuss list on 2025-12-01.

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Matt Ducar, Reece Hart4

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 Hart2

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 Hart5

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

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

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

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 Hart3

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

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 Hart2

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 Hart4

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 S3

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

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

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 Hart2

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

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 Hart2

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 Hart2

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 Hart4

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

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

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

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 Peacock8

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 Hart3

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

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 Roy2

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

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 Hinrichs6

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

6/2/18

Hi Jianfen- Sorry for the delay in replying. You're likely get a faster reply if you send to hgvs

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Hi Jianfen- Sorry for the delay in replying. You're likely get a faster reply if you send to hgvs

6/2/18

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