| Name | hgvs JSON |
| Version |
1.5.4
JSON |
| download |
| home_page | |
| Summary | HGVS Parser, Formatter, Mapper, Validator |
| upload_time | 2022-11-21 20:03:51 |
| maintainer | |
| docs_url | https://pythonhosted.org/hgvs/ |
| author | |
| requires_python | >=3.6 |
| license | Apache License Version 2.0, January 2004 http://www.apache.org/licenses/ TERMS AND CONDITIONS FOR USE, REPRODUCTION, AND DISTRIBUTION 1. Definitions. "License" shall mean the terms and conditions for use, reproduction, and distribution as defined by Sections 1 through 9 of this document. "Licensor" shall mean the copyright owner or entity authorized by the copyright owner that is granting the License. "Legal Entity" shall mean the union of the acting entity and all other entities that control, are controlled by, or are under common control with that entity. For the purposes of this definition, "control" means (i) the power, direct or indirect, to cause the direction or management of such entity, whether by contract or otherwise, or (ii) ownership of fifty percent (50%) or more of the outstanding shares, or (iii) beneficial ownership of such entity. "You" (or "Your") shall mean an individual or Legal Entity exercising permissions granted by this License. "Source" form shall mean the preferred form for making modifications, including but not limited to software source code, documentation source, and configuration files. "Object" form shall mean any form resulting from mechanical transformation or translation of a Source form, including but not limited to compiled object code, generated documentation, and conversions to other media types. "Work" shall mean the work of authorship, whether in Source or Object form, made available under the License, as indicated by a copyright notice that is included in or attached to the work (an example is provided in the Appendix below). "Derivative Works" shall mean any work, whether in Source or Object form, that is based on (or derived from) the Work and for which the editorial revisions, annotations, elaborations, or other modifications represent, as a whole, an original work of authorship. For the purposes of this License, Derivative Works shall not include works that remain separable from, or merely link (or bind by name) to the interfaces of, the Work and Derivative Works thereof. "Contribution" shall mean any work of authorship, including the original version of the Work and any modifications or additions to that Work or Derivative Works thereof, that is intentionally submitted to Licensor for inclusion in the Work by the copyright owner or by an individual or Legal Entity authorized to submit on behalf of the copyright owner. For the purposes of this definition, "submitted" means any form of electronic, verbal, or written communication sent to the Licensor or its representatives, including but not limited to communication on electronic mailing lists, source code control systems, and issue tracking systems that are managed by, or on behalf of, the Licensor for the purpose of discussing and improving the Work, but excluding communication that is conspicuously marked or otherwise designated in writing by the copyright owner as "Not a Contribution." "Contributor" shall mean Licensor and any individual or Legal Entity on behalf of whom a Contribution has been received by Licensor and subsequently incorporated within the Work. 2. Grant of Copyright License. Subject to the terms and conditions of this License, each Contributor hereby grants to You a perpetual, worldwide, non-exclusive, no-charge, royalty-free, irrevocable copyright license to reproduce, prepare Derivative Works of, publicly display, publicly perform, sublicense, and distribute the Work and such Derivative Works in Source or Object form. 3. Grant of Patent License. Subject to the terms and conditions of this License, each Contributor hereby grants to You a perpetual, worldwide, non-exclusive, no-charge, royalty-free, irrevocable (except as stated in this section) patent license to make, have made, use, offer to sell, sell, import, and otherwise transfer the Work, where such license applies only to those patent claims licensable by such Contributor that are necessarily infringed by their Contribution(s) alone or by combination of their Contribution(s) with the Work to which such Contribution(s) was submitted. If You institute patent litigation against any entity (including a cross-claim or counterclaim in a lawsuit) alleging that the Work or a Contribution incorporated within the Work constitutes direct or contributory patent infringement, then any patent licenses granted to You under this License for that Work shall terminate as of the date such litigation is filed. 4. Redistribution. You may reproduce and distribute copies of the Work or Derivative Works thereof in any medium, with or without modifications, and in Source or Object form, provided that You meet the following conditions: (a) You must give any other recipients of the Work or Derivative Works a copy of this License; and (b) You must cause any modified files to carry prominent notices stating that You changed the files; and (c) You must retain, in the Source form of any Derivative Works that You distribute, all copyright, patent, trademark, and attribution notices from the Source form of the Work, excluding those notices that do not pertain to any part of the Derivative Works; and (d) If the Work includes a "NOTICE" text file as part of its distribution, then any Derivative Works that You distribute must include a readable copy of the attribution notices contained within such NOTICE file, excluding those notices that do not pertain to any part of the Derivative Works, in at least one of the following places: within a NOTICE text file distributed as part of the Derivative Works; within the Source form or documentation, if provided along with the Derivative Works; or, within a display generated by the Derivative Works, if and wherever such third-party notices normally appear. The contents of the NOTICE file are for informational purposes only and do not modify the License. You may add Your own attribution notices within Derivative Works that You distribute, alongside or as an addendum to the NOTICE text from the Work, provided that such additional attribution notices cannot be construed as modifying the License. You may add Your own copyright statement to Your modifications and may provide additional or different license terms and conditions for use, reproduction, or distribution of Your modifications, or for any such Derivative Works as a whole, provided Your use, reproduction, and distribution of the Work otherwise complies with the conditions stated in this License. 5. Submission of Contributions. Unless You explicitly state otherwise, any Contribution intentionally submitted for inclusion in the Work by You to the Licensor shall be under the terms and conditions of this License, without any additional terms or conditions. Notwithstanding the above, nothing herein shall supersede or modify the terms of any separate license agreement you may have executed with Licensor regarding such Contributions. 6. Trademarks. This License does not grant permission to use the trade names, trademarks, service marks, or product names of the Licensor, except as required for reasonable and customary use in describing the origin of the Work and reproducing the content of the NOTICE file. 7. Disclaimer of Warranty. Unless required by applicable law or agreed to in writing, Licensor provides the Work (and each Contributor provides its Contributions) on an "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied, including, without limitation, any warranties or conditions of TITLE, NON-INFRINGEMENT, MERCHANTABILITY, or FITNESS FOR A PARTICULAR PURPOSE. You are solely responsible for determining the appropriateness of using or redistributing the Work and assume any risks associated with Your exercise of permissions under this License. 8. Limitation of Liability. In no event and under no legal theory, whether in tort (including negligence), contract, or otherwise, unless required by applicable law (such as deliberate and grossly negligent acts) or agreed to in writing, shall any Contributor be liable to You for damages, including any direct, indirect, special, incidental, or consequential damages of any character arising as a result of this License or out of the use or inability to use the Work (including but not limited to damages for loss of goodwill, work stoppage, computer failure or malfunction, or any and all other commercial damages or losses), even if such Contributor has been advised of the possibility of such damages. 9. Accepting Warranty or Additional Liability. While redistributing the Work or Derivative Works thereof, You may choose to offer, and charge a fee for, acceptance of support, warranty, indemnity, or other liability obligations and/or rights consistent with this License. However, in accepting such obligations, You may act only on Your own behalf and on Your sole responsibility, not on behalf of any other Contributor, and only if You agree to indemnify, defend, and hold each Contributor harmless for any liability incurred by, or claims asserted against, such Contributor by reason of your accepting any such warranty or additional liability. END OF TERMS AND CONDITIONS APPENDIX: How to apply the Apache License to your work. To apply the Apache License to your work, attach the following boilerplate notice, with the fields enclosed by brackets "[]" replaced with your own identifying information. (Don't include the brackets!) The text should be enclosed in the appropriate comment syntax for the file format. We also recommend that a file or class name and description of purpose be included on the same "printed page" as the copyright notice for easier identification within third-party archives. Copyright [yyyy] [name of copyright owner] Licensed under the Apache License, Version 2.0 (the "License"); you may not use this file except in compliance with the License. You may obtain a copy of the License at http://www.apache.org/licenses/LICENSE-2.0 Unless required by applicable law or agreed to in writing, software distributed under the License is distributed on an "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the License for the specific language governing permissions and limitations under the License. |
| keywords |
biocommons
bioinformatics
computational biology
genome variation
genomics
hgvs
variation
|
| VCS |
|
| bugtrack_url |
|
| requirements |
No requirements were recorded.
|
| Travis-CI |
No Travis.
|
| coveralls test coverage |
No coveralls.
|
*hgvs* - manipulate biological sequence variants according to Human Genome Variation Society recommendations
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
**Important:** biocommons packages require Python 3.6+.
`More
<https://groups.google.com/forum/#!topic/hgvs-discuss/iLUzjzoD-28>`__
The *hgvs* package provides a Python library to parse, format,
validate, normalize, and map sequence variants according to `Variation
Nomenclature`_ (aka Human Genome Variation Society) recommendations.
Specifically, the hgvs package focuses on the subset of the HGVS
recommendations that precisely describe sequence-level variation
relevant to the application of high-throughput sequencing to clinical
diagnostics. The package does not attempt to cover the full scope of
HGVS recommendations. Please refer to `issues
<https://github.com/biocommons/hgvs/issues>`_ for limitations.
+--------------------+--------------------------------------------------------------------+
| **Information** | | |rtd| |changelog| |getting_help| |
| | | |github_license| |binder| |
+--------------------+--------------------------------------------------------------------+
| **Latest Release** | |github_tag| |pypi_rel| |hit| |
+--------------------+--------------------------------------------------------------------+
| **Development** | | |status_rel| |coveralls| |
| (main branch) | | | |issues| |github_open_pr| |github_contrib| |
| | | |github_stars| |github_forks| |
+--------------------+--------------------------------------------------------------------+
Features
@@@@@@@@
* Parsing is based on formal grammar.
* An easy-to-use object model that represents
most variant types (SNVs, indels, dups, inverstions, etc) and
concepts (intronic offsets, uncertain positions, intervals)
* A variant normalizer that rewrites variants in canoncial forms and
substitutes reference sequences (if reference and transcript
sequences differ)
* Formatters that generate HGVS strings from internal representations
* Tools to map variants between genome, transcript, and protein sequences
* Reliable handling of regions genome-transcript discrepancies
* Pluggable data providers support alternative sources of transcript mapping
data
* Extensive automated tests, including those for all variant types and
"problematic" transcripts
* Easily installed using remote data sources. Installation with local
data sources is straightforward and completely obviates network
access
Important Notes
@@@@@@@@@@@@@@@
* **You are encouraged to** `browse issues
<https://github.com/biocommons/hgvs/issues>`_. All known issues are
listed there. Please report any issues you find.
* **Use a pip package specification to stay within minor releases.**
For example, ``hgvs>=1.5,<1.6``. `hgvs` uses `Semantic Versioning
<http://semver.org/>`__.
Examples
@@@@@@@@
Installation
#############
By default, `hgvs` uses remote data sources, which makes installation
easy.
::
$ mkvirtualenv hgvs-test
(hgvs-test)$ pip install --upgrade setuptools
(hgvs-test)$ pip install hgvs
(hgvs-test)$ python
See `Installation instructions
<http://hgvs.readthedocs.org/en/stable/installation.html>`__ for
details, including instructions for installing `Universal Transcript
Archive (UTA) <https://github.com/biocommons/uta/>`__ and `SeqRepo
<https://github.com/biocommons/biocommons.seqrepo/>`__ locally.
Configuration
#############
`hgvs` will use publicly available data sources unless directed
otherwise through environment variables, like so::
# N.B. These are examples. The correct values will depend on your installation
$ export UTA_DB_URL=postgresql://anonymous:anonymous@localhost:5432/uta/uta_20210129
$ export HGVS_SEQREPO_DIR=/usr/local/share/seqrepo/latest
Alternatively, if you are unable to pass the postgresql password in the
UTA_DB_URL environment variable (i.e., generating an auth token), you can set
UTA_DB_URL to ``postgresql://<user>@<host>/<db>/<schema>`` and set PGPASSWORD. For example::
$ export UTA_DB_URL=postgresql://anonymous@localhost:5432/uta/uta_20210129 PGPASSWORD=anonymous
See the installation instructions for details.
Parsing and Formating
#####################
`hgvs` parses HGVS variants (as strings) into an object model, and can format
object models back into HGVS strings.
.. code-block:: python
>>> import hgvs.parser
# start with these variants as strings
>>> hgvs_g = 'NC_000007.13:g.36561662C>T'
>>> hgvs_c = 'NM_001637.3:c.1582G>A'
# parse the genomic variant into a Python structure
>>> hp = hgvs.parser.Parser()
>>> var_g = hp.parse_hgvs_variant(hgvs_g)
>>> var_g
SequenceVariant(ac=NC_000007.13, type=g, posedit=36561662C>T, gene=None)
# SequenceVariants are composed of structured objects, e.g.,
>>> var_g.posedit.pos.start
SimplePosition(base=36561662, uncertain=False)
# format by stringification
>>> str(var_g)
'NC_000007.13:g.36561662C>T'
Projecting ("Mapping") variants between aligned genome and transcript sequences
###############################################################################
`hgvs` provides tools to project variants between genome, transcript,
and protein sequences. Non-coding and intronic variants are
supported. Alignment data come from the `Universal Transcript Archive
(UTA) <https://github.com/biocommons/uta/>`__.
.. code-block:: python
>>> import hgvs.dataproviders.uta
>>> import hgvs.assemblymapper
# initialize the mapper for GRCh37 with splign-based alignments
>>> hdp = hgvs.dataproviders.uta.connect()
>>> am = hgvs.assemblymapper.AssemblyMapper(hdp,
... assembly_name='GRCh37', alt_aln_method='splign',
... replace_reference=True)
# identify transcripts that overlap this genomic variant
>>> transcripts = am.relevant_transcripts(var_g)
>>> sorted(transcripts)
['NM_001177506.1', 'NM_001177507.1', 'NM_001637.3']
# map genomic variant to one of these transcripts
>>> var_c = am.g_to_c(var_g, 'NM_001637.3')
>>> var_c
SequenceVariant(ac=NM_001637.3, type=c, posedit=1582G>A, gene=None)
>>> str(var_c)
'NM_001637.3:c.1582G>A'
# CDS coordinates use BaseOffsetPosition to support intronic offsets
>>> var_c.posedit.pos.start
BaseOffsetPosition(base=1582, offset=0, datum=Datum.CDS_START, uncertain=False)
Translating coding variants to protein sequences
################################################
Coding variants may be translated to their protein consequences. HGVS
uses the same pairing of transcript and protein accessions as seen in
NCBI and Ensembl.
.. code-block:: python
# translate var_c to its protein consequence
# The object structure of protein variants is nearly identical to
# that of nucleic acid variants and is converted to a string form
# by stringification. Per HGVS recommendations, inferred consequences
# must have parentheses to indicate uncertainty.
>>> var_p = am.c_to_p(var_c)
>>> var_p
SequenceVariant(ac=NP_001628.1, type=p, posedit=(Gly528Arg), gene=None)
>>> str(var_p)
'NP_001628.1:p.(Gly528Arg)'
# setting uncertain to False removes the parentheses on the
# stringified form
>>> var_p.posedit.uncertain = False
>>> str(var_p)
'NP_001628.1:p.Gly528Arg'
# formatting can be customized, e.g., use 1 letter amino acids to
# format a specific variant
# (configuration may also be set globally)
>>> var_p.format(conf={"p_3_letter": False})
'NP_001628.1:p.G528R'
Normalizing variants
####################
Some variants have multiple representations due to instrinsic
biological ambiguity (e.g., inserting a G in a poly-G run) or due to
misunderstanding HGVS recommendations. Normalization rewrites certain
veriants into a single representation.
.. code-block:: python
# rewrite ins as dup (depends on sequence context)
>>> import hgvs.normalizer
>>> hn = hgvs.normalizer.Normalizer(hdp)
>>> hn.normalize(hp.parse_hgvs_variant('NM_001166478.1:c.35_36insT'))
SequenceVariant(ac=NM_001166478.1, type=c, posedit=35dup, gene=None)
# during mapping, variants are normalized (by default)
>>> c1 = hp.parse_hgvs_variant('NM_001166478.1:c.31del')
>>> c1
SequenceVariant(ac=NM_001166478.1, type=c, posedit=31del, gene=None)
>>> c1n = hn.normalize(c1)
>>> c1n
SequenceVariant(ac=NM_001166478.1, type=c, posedit=35del, gene=None)
>>> g = am.c_to_g(c1)
>>> g
SequenceVariant(ac=NC_000006.11, type=g, posedit=49917127del, gene=None)
>>> c2 = am.g_to_c(g, c1.ac)
>>> c2
SequenceVariant(ac=NM_001166478.1, type=c, posedit=35del, gene=None)
There are `more examples in the documentation
<http://hgvs.readthedocs.org/en/stable/examples.html>`_.
Citing hgvs (the package)
@@@@@@@@@@@@@@@@@@@@@@@@@
| **hgvs: A Python package for manipulating sequence variants using HGVS nomenclature: 2018 Update.**
| Wang M, Callenberg KM, Dalgleish R, Fedtsov A, Fox N, Freeman PJ, Jacobs KB, Kaleta P, McMurry AJ, Prlić A, Rajaraman V, Hart RK
| Human Mutation. 2018 `Pubmed <https://www.ncbi.nlm.nih.gov/pubmed/30129167>`__ | `Open Access PDF <https://doi.org/10.1002/humu.23615>`__
| **A Python Package for Parsing, Validating, Mapping, and Formatting Sequence Variants Using HGVS Nomenclature.**
| Hart RK, Rico R, Hare E, Garcia J, Westbrook J, Fusaro VA.
| *Bioinformatics*. 2014 Sep 30. `PubMed <http://www.ncbi.nlm.nih.gov/pubmed/25273102>`__ | `Open Access PDF <http://bioinformatics.oxfordjournals.org/content/31/2/268.full.pdf>`__
Contributing
@@@@@@@@@@@@
The hgvs package is intended to be a community project. Please see
`Contributing
<http://hgvs.readthedocs.org/en/stable/contributing.html>`__ to get
started in submitting source code, tests, or documentation. Thanks
for getting involved!
See Also
@@@@@@@@
Other packages that manipulate HGVS variants:
* `pyhgvs <https://github.com/counsyl/hgvs>`__
* `Mutalyzer <https://mutalyzer.nl/>`__
.. _docs: http://hgvs.readthedocs.org/
.. _Variation Nomenclature: http://varnomen.hgvs.org/
.. |getting_help| image:: https://img.shields.io/badge/!-help%20me-red.svg
:target: https://hgvs.readthedocs.io/en/stable/getting_help.html
.. |rtd| image:: https://img.shields.io/badge/docs-readthedocs-green.svg
:target: http://hgvs.readthedocs.io/
.. |changelog| image:: https://img.shields.io/badge/docs-changelog-green.svg
:target: https://hgvs.readthedocs.io/en/stable/changelog/
.. |github_license| image:: https://img.shields.io/github/license/biocommons/hgvs.svg
:alt: GitHub license
:target: https://github.com/biocommons/hgvs/blob/main/LICENSE)
.. |group| image:: https://img.shields.io/badge/group-hgvs%20discuss-green.svg
:alt: Mailing list
:target: https://groups.google.com/forum/#!forum/hgvs-discuss
.. |chat| image:: https://img.shields.io/badge/chat-gitter-green.svg
:alt: Join the chat at https://gitter.im/biocommons/hgvs
:target: https://gitter.im/biocommons/hgvs?utm_source=badge&utm_medium=badge&utm_campaign=pr-badge&utm_content=badge
.. |github_tag| image:: https://img.shields.io/github/tag/biocommons/hgvs.svg
:alt: GitHub tag
:target: https://github.com/biocommons/hgvs
.. |pypi_rel| image:: https://img.shields.io/pypi/v/hgvs.svg
:target: https://pypi.org/project/hgvs/
.. |status_rel| image:: https://img.shields.io/travis/biocommons/hgvs/main.svg
:target: https://travis-ci.org/biocommons/hgvs?branch=main
.. |coveralls| image:: https://img.shields.io/coveralls/github/biocommons/hgvs.svg
:target: https://coveralls.io/github/biocommons/hgvs
.. |issues| image:: https://img.shields.io/github/issues-raw/biocommons/hgvs.svg
:alt: issues
:target: https://github.com/biocommons/hgvs/issues
.. |github_open_pr| image:: https://img.shields.io/github/issues-pr/biocommons/hgvs.svg
:alt: GitHub Open Pull Requests
:target: https://github.com/biocommons/hgvs/pull/
.. |github_stars| image:: https://img.shields.io/github/stars/biocommons/hgvs.svg?style=social&label=Stars
:alt: GitHub stars
:target: https://github.com/biocommons/hgvs/stargazers
.. |github_forks| image:: https://img.shields.io/github/forks/biocommons/hgvs.svg?style=social&label=Forks
:alt: GitHub forks
:target: https://github.com/biocommons/hgvs/network
.. |github_contrib| image:: https://img.shields.io/github/contributors/biocommons/hgvs.svg
:alt: GitHub license
:target: https://github.com/biocommons/hgvs/graphs/contributors/
.. |install_status| image:: https://travis-ci.org/reece/hgvs-integration-test.png?branch=main
:target: https://travis-ci.org/reece/hgvs-integration-test
.. |binder| image:: https://mybinder.org/badge_logo.svg
:target: https://mybinder.org/v2/gh/biocommons/hgvs/main?filepath=examples
.. |hit| image:: https://travis-ci.org/biocommons/hgvs-installation-test.svg?branch=main
:alt: nightly test of ability to pip install, import, and parse a variant
:target: https://travis-ci.org/biocommons/hgvs-installation-test
Raw data
{
"_id": null,
"home_page": "",
"name": "hgvs",
"maintainer": "",
"docs_url": "https://pythonhosted.org/hgvs/",
"requires_python": ">=3.6",
"maintainer_email": "",
"keywords": "biocommons,bioinformatics,computational biology,genome variation,genomics,hgvs,variation",
"author": "",
"author_email": "HGVS Contributors <biocommons-dev@googlegroups.com>",
"download_url": "https://files.pythonhosted.org/packages/f9/35/15d86f2e862a697626fdfc7c91d6ccf862bdbb7a7c595b428bf9dddb6c3c/hgvs-1.5.4.tar.gz",
"platform": null,
"description": "*hgvs* - manipulate biological sequence variants according to Human Genome Variation Society recommendations\n!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!\n\n**Important:** biocommons packages require Python 3.6+.\n`More\n<https://groups.google.com/forum/#!topic/hgvs-discuss/iLUzjzoD-28>`__\n\n\nThe *hgvs* package provides a Python library to parse, format,\nvalidate, normalize, and map sequence variants according to `Variation\nNomenclature`_ (aka Human Genome Variation Society) recommendations.\n\nSpecifically, the hgvs package focuses on the subset of the HGVS\nrecommendations that precisely describe sequence-level variation\nrelevant to the application of high-throughput sequencing to clinical\ndiagnostics. The package does not attempt to cover the full scope of\nHGVS recommendations. Please refer to `issues\n<https://github.com/biocommons/hgvs/issues>`_ for limitations.\n\n\n+--------------------+--------------------------------------------------------------------+\n| **Information** | | |rtd| |changelog| |getting_help| |\n| | | |github_license| |binder| |\n+--------------------+--------------------------------------------------------------------+\n| **Latest Release** | |github_tag| |pypi_rel| |hit| |\n+--------------------+--------------------------------------------------------------------+\n| **Development** | | |status_rel| |coveralls| |\n| (main branch) | | | |issues| |github_open_pr| |github_contrib| |\n| | | |github_stars| |github_forks| |\n+--------------------+--------------------------------------------------------------------+\n\n\n\nFeatures\n@@@@@@@@\n\n* Parsing is based on formal grammar.\n* An easy-to-use object model that represents\n most variant types (SNVs, indels, dups, inverstions, etc) and\n concepts (intronic offsets, uncertain positions, intervals)\n* A variant normalizer that rewrites variants in canoncial forms and\n substitutes reference sequences (if reference and transcript\n sequences differ)\n* Formatters that generate HGVS strings from internal representations\n* Tools to map variants between genome, transcript, and protein sequences\n* Reliable handling of regions genome-transcript discrepancies\n* Pluggable data providers support alternative sources of transcript mapping\n data\n* Extensive automated tests, including those for all variant types and\n \"problematic\" transcripts\n* Easily installed using remote data sources. Installation with local\n data sources is straightforward and completely obviates network\n access\n\n\nImportant Notes\n@@@@@@@@@@@@@@@\n\n* **You are encouraged to** `browse issues\n <https://github.com/biocommons/hgvs/issues>`_. All known issues are\n listed there. Please report any issues you find.\n* **Use a pip package specification to stay within minor releases.**\n For example, ``hgvs>=1.5,<1.6``. `hgvs` uses `Semantic Versioning\n <http://semver.org/>`__.\n\n\nExamples\n@@@@@@@@\n\nInstallation\n#############\n\nBy default, `hgvs` uses remote data sources, which makes installation\neasy. \n\n::\n\n $ mkvirtualenv hgvs-test\n (hgvs-test)$ pip install --upgrade setuptools\n (hgvs-test)$ pip install hgvs\n (hgvs-test)$ python\n\nSee `Installation instructions\n<http://hgvs.readthedocs.org/en/stable/installation.html>`__ for\ndetails, including instructions for installing `Universal Transcript\nArchive (UTA) <https://github.com/biocommons/uta/>`__ and `SeqRepo\n<https://github.com/biocommons/biocommons.seqrepo/>`__ locally.\n\n\nConfiguration\n#############\n\n`hgvs` will use publicly available data sources unless directed\notherwise through environment variables, like so::\n\n # N.B. These are examples. The correct values will depend on your installation\n $ export UTA_DB_URL=postgresql://anonymous:anonymous@localhost:5432/uta/uta_20210129\n $ export HGVS_SEQREPO_DIR=/usr/local/share/seqrepo/latest\n\nAlternatively, if you are unable to pass the postgresql password in the\nUTA_DB_URL environment variable (i.e., generating an auth token), you can set\nUTA_DB_URL to ``postgresql://<user>@<host>/<db>/<schema>`` and set PGPASSWORD. For example::\n\n $ export UTA_DB_URL=postgresql://anonymous@localhost:5432/uta/uta_20210129 PGPASSWORD=anonymous\n\nSee the installation instructions for details.\n\n\nParsing and Formating\n#####################\n\n`hgvs` parses HGVS variants (as strings) into an object model, and can format\nobject models back into HGVS strings.\n\n.. code-block:: python\n\n >>> import hgvs.parser\n\n # start with these variants as strings\n >>> hgvs_g = 'NC_000007.13:g.36561662C>T'\n >>> hgvs_c = 'NM_001637.3:c.1582G>A'\n\n # parse the genomic variant into a Python structure\n >>> hp = hgvs.parser.Parser()\n >>> var_g = hp.parse_hgvs_variant(hgvs_g)\n >>> var_g\n SequenceVariant(ac=NC_000007.13, type=g, posedit=36561662C>T, gene=None)\n\n # SequenceVariants are composed of structured objects, e.g.,\n >>> var_g.posedit.pos.start\n SimplePosition(base=36561662, uncertain=False)\n\n # format by stringification \n >>> str(var_g)\n 'NC_000007.13:g.36561662C>T'\n\n\nProjecting (\"Mapping\") variants between aligned genome and transcript sequences\n###############################################################################\n\n`hgvs` provides tools to project variants between genome, transcript,\nand protein sequences. Non-coding and intronic variants are\nsupported. Alignment data come from the `Universal Transcript Archive\n(UTA) <https://github.com/biocommons/uta/>`__.\n\n.. code-block:: python\n\n >>> import hgvs.dataproviders.uta\n >>> import hgvs.assemblymapper\n\n # initialize the mapper for GRCh37 with splign-based alignments\n >>> hdp = hgvs.dataproviders.uta.connect()\n >>> am = hgvs.assemblymapper.AssemblyMapper(hdp,\n ... assembly_name='GRCh37', alt_aln_method='splign',\n ... replace_reference=True)\n \n # identify transcripts that overlap this genomic variant\n >>> transcripts = am.relevant_transcripts(var_g)\n >>> sorted(transcripts)\n ['NM_001177506.1', 'NM_001177507.1', 'NM_001637.3']\n\n # map genomic variant to one of these transcripts\n >>> var_c = am.g_to_c(var_g, 'NM_001637.3')\n >>> var_c\n SequenceVariant(ac=NM_001637.3, type=c, posedit=1582G>A, gene=None)\n >>> str(var_c)\n 'NM_001637.3:c.1582G>A'\n\n # CDS coordinates use BaseOffsetPosition to support intronic offsets\n >>> var_c.posedit.pos.start\n BaseOffsetPosition(base=1582, offset=0, datum=Datum.CDS_START, uncertain=False)\n\n\nTranslating coding variants to protein sequences\n################################################\n\nCoding variants may be translated to their protein consequences. HGVS\nuses the same pairing of transcript and protein accessions as seen in\nNCBI and Ensembl.\n\n.. code-block:: python\n\n # translate var_c to its protein consequence\n # The object structure of protein variants is nearly identical to\n # that of nucleic acid variants and is converted to a string form\n # by stringification. Per HGVS recommendations, inferred consequences\n # must have parentheses to indicate uncertainty.\n >>> var_p = am.c_to_p(var_c)\n >>> var_p\n SequenceVariant(ac=NP_001628.1, type=p, posedit=(Gly528Arg), gene=None)\n >>> str(var_p)\n 'NP_001628.1:p.(Gly528Arg)'\n\n # setting uncertain to False removes the parentheses on the\n # stringified form\n >>> var_p.posedit.uncertain = False\n >>> str(var_p)\n 'NP_001628.1:p.Gly528Arg'\n\n # formatting can be customized, e.g., use 1 letter amino acids to\n # format a specific variant\n # (configuration may also be set globally)\n >>> var_p.format(conf={\"p_3_letter\": False})\n 'NP_001628.1:p.G528R'\n\n\n\nNormalizing variants\n####################\n\nSome variants have multiple representations due to instrinsic\nbiological ambiguity (e.g., inserting a G in a poly-G run) or due to\nmisunderstanding HGVS recommendations. Normalization rewrites certain\nveriants into a single representation.\n\n.. code-block:: python\n\n # rewrite ins as dup (depends on sequence context)\n >>> import hgvs.normalizer\n >>> hn = hgvs.normalizer.Normalizer(hdp)\n >>> hn.normalize(hp.parse_hgvs_variant('NM_001166478.1:c.35_36insT'))\n SequenceVariant(ac=NM_001166478.1, type=c, posedit=35dup, gene=None)\n\n # during mapping, variants are normalized (by default)\n >>> c1 = hp.parse_hgvs_variant('NM_001166478.1:c.31del')\n >>> c1\n SequenceVariant(ac=NM_001166478.1, type=c, posedit=31del, gene=None)\n >>> c1n = hn.normalize(c1)\n >>> c1n\n SequenceVariant(ac=NM_001166478.1, type=c, posedit=35del, gene=None)\n >>> g = am.c_to_g(c1)\n >>> g\n SequenceVariant(ac=NC_000006.11, type=g, posedit=49917127del, gene=None)\n >>> c2 = am.g_to_c(g, c1.ac)\n >>> c2\n SequenceVariant(ac=NM_001166478.1, type=c, posedit=35del, gene=None)\n\n\nThere are `more examples in the documentation\n<http://hgvs.readthedocs.org/en/stable/examples.html>`_.\n\n\nCiting hgvs (the package)\n@@@@@@@@@@@@@@@@@@@@@@@@@\n\n| **hgvs: A Python package for manipulating sequence variants using HGVS nomenclature: 2018 Update.**\n| Wang M, Callenberg KM, Dalgleish R, Fedtsov A, Fox N, Freeman PJ, Jacobs KB, Kaleta P, McMurry AJ, Prli\u0107 A, Rajaraman V, Hart RK\n| Human Mutation. 2018 `Pubmed <https://www.ncbi.nlm.nih.gov/pubmed/30129167>`__ | `Open Access PDF <https://doi.org/10.1002/humu.23615>`__\n\n| **A Python Package for Parsing, Validating, Mapping, and Formatting Sequence Variants Using HGVS Nomenclature.**\n| Hart RK, Rico R, Hare E, Garcia J, Westbrook J, Fusaro VA.\n| *Bioinformatics*. 2014 Sep 30. `PubMed <http://www.ncbi.nlm.nih.gov/pubmed/25273102>`__ | `Open Access PDF <http://bioinformatics.oxfordjournals.org/content/31/2/268.full.pdf>`__\n\n\nContributing\n@@@@@@@@@@@@\n\nThe hgvs package is intended to be a community project. Please see\n`Contributing\n<http://hgvs.readthedocs.org/en/stable/contributing.html>`__ to get\nstarted in submitting source code, tests, or documentation. Thanks\nfor getting involved!\n\n\nSee Also\n@@@@@@@@\n\nOther packages that manipulate HGVS variants:\n\n* `pyhgvs <https://github.com/counsyl/hgvs>`__\n* `Mutalyzer <https://mutalyzer.nl/>`__\n\n\n.. _docs: http://hgvs.readthedocs.org/\n.. _Variation Nomenclature: http://varnomen.hgvs.org/\n\n.. |getting_help| image:: https://img.shields.io/badge/!-help%20me-red.svg\n :target: https://hgvs.readthedocs.io/en/stable/getting_help.html\n\n.. |rtd| image:: https://img.shields.io/badge/docs-readthedocs-green.svg\n :target: http://hgvs.readthedocs.io/\n\n.. |changelog| image:: https://img.shields.io/badge/docs-changelog-green.svg\n :target: https://hgvs.readthedocs.io/en/stable/changelog/\n\n.. |github_license| image:: https://img.shields.io/github/license/biocommons/hgvs.svg\n :alt: GitHub license\n :target: https://github.com/biocommons/hgvs/blob/main/LICENSE)\n\n.. |group| image:: https://img.shields.io/badge/group-hgvs%20discuss-green.svg\n :alt: Mailing list\n :target: https://groups.google.com/forum/#!forum/hgvs-discuss\n\n.. |chat| image:: https://img.shields.io/badge/chat-gitter-green.svg\n :alt: Join the chat at https://gitter.im/biocommons/hgvs\n :target: https://gitter.im/biocommons/hgvs?utm_source=badge&utm_medium=badge&utm_campaign=pr-badge&utm_content=badge\n\n\n.. |github_tag| image:: https://img.shields.io/github/tag/biocommons/hgvs.svg\n :alt: GitHub tag\n :target: https://github.com/biocommons/hgvs\n\n.. |pypi_rel| image:: https://img.shields.io/pypi/v/hgvs.svg\n :target: https://pypi.org/project/hgvs/\n\n\n.. |status_rel| image:: https://img.shields.io/travis/biocommons/hgvs/main.svg\n :target: https://travis-ci.org/biocommons/hgvs?branch=main\n\n.. |coveralls| image:: https://img.shields.io/coveralls/github/biocommons/hgvs.svg\n :target: https://coveralls.io/github/biocommons/hgvs\n\n.. |issues| image:: https://img.shields.io/github/issues-raw/biocommons/hgvs.svg\n :alt: issues\n :target: https://github.com/biocommons/hgvs/issues\n\n.. |github_open_pr| image:: https://img.shields.io/github/issues-pr/biocommons/hgvs.svg\n :alt: GitHub Open Pull Requests\n :target: https://github.com/biocommons/hgvs/pull/\n\n.. |github_stars| image:: https://img.shields.io/github/stars/biocommons/hgvs.svg?style=social&label=Stars\n :alt: GitHub stars\n :target: https://github.com/biocommons/hgvs/stargazers\n\n.. |github_forks| image:: https://img.shields.io/github/forks/biocommons/hgvs.svg?style=social&label=Forks\n :alt: GitHub forks\n :target: https://github.com/biocommons/hgvs/network\n\n.. |github_contrib| image:: https://img.shields.io/github/contributors/biocommons/hgvs.svg\n :alt: GitHub license\n :target: https://github.com/biocommons/hgvs/graphs/contributors/\n\n.. |install_status| image:: https://travis-ci.org/reece/hgvs-integration-test.png?branch=main\n :target: https://travis-ci.org/reece/hgvs-integration-test\n\n.. |binder| image:: https://mybinder.org/badge_logo.svg\n :target: https://mybinder.org/v2/gh/biocommons/hgvs/main?filepath=examples\n\n.. |hit| image:: https://travis-ci.org/biocommons/hgvs-installation-test.svg?branch=main\n :alt: nightly test of ability to pip install, import, and parse a variant\n :target: https://travis-ci.org/biocommons/hgvs-installation-test\t \n",
"bugtrack_url": null,
"license": " Apache License Version 2.0, January 2004 http://www.apache.org/licenses/ TERMS AND CONDITIONS FOR USE, REPRODUCTION, AND DISTRIBUTION 1. Definitions. \"License\" shall mean the terms and conditions for use, reproduction, and distribution as defined by Sections 1 through 9 of this document. \"Licensor\" shall mean the copyright owner or entity authorized by the copyright owner that is granting the License. \"Legal Entity\" shall mean the union of the acting entity and all other entities that control, are controlled by, or are under common control with that entity. For the purposes of this definition, \"control\" means (i) the power, direct or indirect, to cause the direction or management of such entity, whether by contract or otherwise, or (ii) ownership of fifty percent (50%) or more of the outstanding shares, or (iii) beneficial ownership of such entity. \"You\" (or \"Your\") shall mean an individual or Legal Entity exercising permissions granted by this License. \"Source\" form shall mean the preferred form for making modifications, including but not limited to software source code, documentation source, and configuration files. \"Object\" form shall mean any form resulting from mechanical transformation or translation of a Source form, including but not limited to compiled object code, generated documentation, and conversions to other media types. \"Work\" shall mean the work of authorship, whether in Source or Object form, made available under the License, as indicated by a copyright notice that is included in or attached to the work (an example is provided in the Appendix below). \"Derivative Works\" shall mean any work, whether in Source or Object form, that is based on (or derived from) the Work and for which the editorial revisions, annotations, elaborations, or other modifications represent, as a whole, an original work of authorship. For the purposes of this License, Derivative Works shall not include works that remain separable from, or merely link (or bind by name) to the interfaces of, the Work and Derivative Works thereof. \"Contribution\" shall mean any work of authorship, including the original version of the Work and any modifications or additions to that Work or Derivative Works thereof, that is intentionally submitted to Licensor for inclusion in the Work by the copyright owner or by an individual or Legal Entity authorized to submit on behalf of the copyright owner. For the purposes of this definition, \"submitted\" means any form of electronic, verbal, or written communication sent to the Licensor or its representatives, including but not limited to communication on electronic mailing lists, source code control systems, and issue tracking systems that are managed by, or on behalf of, the Licensor for the purpose of discussing and improving the Work, but excluding communication that is conspicuously marked or otherwise designated in writing by the copyright owner as \"Not a Contribution.\" \"Contributor\" shall mean Licensor and any individual or Legal Entity on behalf of whom a Contribution has been received by Licensor and subsequently incorporated within the Work. 2. Grant of Copyright License. Subject to the terms and conditions of this License, each Contributor hereby grants to You a perpetual, worldwide, non-exclusive, no-charge, royalty-free, irrevocable copyright license to reproduce, prepare Derivative Works of, publicly display, publicly perform, sublicense, and distribute the Work and such Derivative Works in Source or Object form. 3. Grant of Patent License. Subject to the terms and conditions of this License, each Contributor hereby grants to You a perpetual, worldwide, non-exclusive, no-charge, royalty-free, irrevocable (except as stated in this section) patent license to make, have made, use, offer to sell, sell, import, and otherwise transfer the Work, where such license applies only to those patent claims licensable by such Contributor that are necessarily infringed by their Contribution(s) alone or by combination of their Contribution(s) with the Work to which such Contribution(s) was submitted. If You institute patent litigation against any entity (including a cross-claim or counterclaim in a lawsuit) alleging that the Work or a Contribution incorporated within the Work constitutes direct or contributory patent infringement, then any patent licenses granted to You under this License for that Work shall terminate as of the date such litigation is filed. 4. Redistribution. You may reproduce and distribute copies of the Work or Derivative Works thereof in any medium, with or without modifications, and in Source or Object form, provided that You meet the following conditions: (a) You must give any other recipients of the Work or Derivative Works a copy of this License; and (b) You must cause any modified files to carry prominent notices stating that You changed the files; and (c) You must retain, in the Source form of any Derivative Works that You distribute, all copyright, patent, trademark, and attribution notices from the Source form of the Work, excluding those notices that do not pertain to any part of the Derivative Works; and (d) If the Work includes a \"NOTICE\" text file as part of its distribution, then any Derivative Works that You distribute must include a readable copy of the attribution notices contained within such NOTICE file, excluding those notices that do not pertain to any part of the Derivative Works, in at least one of the following places: within a NOTICE text file distributed as part of the Derivative Works; within the Source form or documentation, if provided along with the Derivative Works; or, within a display generated by the Derivative Works, if and wherever such third-party notices normally appear. The contents of the NOTICE file are for informational purposes only and do not modify the License. You may add Your own attribution notices within Derivative Works that You distribute, alongside or as an addendum to the NOTICE text from the Work, provided that such additional attribution notices cannot be construed as modifying the License. You may add Your own copyright statement to Your modifications and may provide additional or different license terms and conditions for use, reproduction, or distribution of Your modifications, or for any such Derivative Works as a whole, provided Your use, reproduction, and distribution of the Work otherwise complies with the conditions stated in this License. 5. Submission of Contributions. Unless You explicitly state otherwise, any Contribution intentionally submitted for inclusion in the Work by You to the Licensor shall be under the terms and conditions of this License, without any additional terms or conditions. Notwithstanding the above, nothing herein shall supersede or modify the terms of any separate license agreement you may have executed with Licensor regarding such Contributions. 6. Trademarks. This License does not grant permission to use the trade names, trademarks, service marks, or product names of the Licensor, except as required for reasonable and customary use in describing the origin of the Work and reproducing the content of the NOTICE file. 7. Disclaimer of Warranty. Unless required by applicable law or agreed to in writing, Licensor provides the Work (and each Contributor provides its Contributions) on an \"AS IS\" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied, including, without limitation, any warranties or conditions of TITLE, NON-INFRINGEMENT, MERCHANTABILITY, or FITNESS FOR A PARTICULAR PURPOSE. You are solely responsible for determining the appropriateness of using or redistributing the Work and assume any risks associated with Your exercise of permissions under this License. 8. Limitation of Liability. In no event and under no legal theory, whether in tort (including negligence), contract, or otherwise, unless required by applicable law (such as deliberate and grossly negligent acts) or agreed to in writing, shall any Contributor be liable to You for damages, including any direct, indirect, special, incidental, or consequential damages of any character arising as a result of this License or out of the use or inability to use the Work (including but not limited to damages for loss of goodwill, work stoppage, computer failure or malfunction, or any and all other commercial damages or losses), even if such Contributor has been advised of the possibility of such damages. 9. Accepting Warranty or Additional Liability. While redistributing the Work or Derivative Works thereof, You may choose to offer, and charge a fee for, acceptance of support, warranty, indemnity, or other liability obligations and/or rights consistent with this License. However, in accepting such obligations, You may act only on Your own behalf and on Your sole responsibility, not on behalf of any other Contributor, and only if You agree to indemnify, defend, and hold each Contributor harmless for any liability incurred by, or claims asserted against, such Contributor by reason of your accepting any such warranty or additional liability. END OF TERMS AND CONDITIONS APPENDIX: How to apply the Apache License to your work. To apply the Apache License to your work, attach the following boilerplate notice, with the fields enclosed by brackets \"[]\" replaced with your own identifying information. (Don't include the brackets!) The text should be enclosed in the appropriate comment syntax for the file format. We also recommend that a file or class name and description of purpose be included on the same \"printed page\" as the copyright notice for easier identification within third-party archives. Copyright [yyyy] [name of copyright owner] Licensed under the Apache License, Version 2.0 (the \"License\"); you may not use this file except in compliance with the License. You may obtain a copy of the License at http://www.apache.org/licenses/LICENSE-2.0 Unless required by applicable law or agreed to in writing, software distributed under the License is distributed on an \"AS IS\" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the License for the specific language governing permissions and limitations under the License. ",
"summary": "HGVS Parser, Formatter, Mapper, Validator",
"version": "1.5.4",
"split_keywords": [
"biocommons",
"bioinformatics",
"computational biology",
"genome variation",
"genomics",
"hgvs",
"variation"
],
"urls": [
{
"comment_text": "",
"digests": {
"blake2b_256": "c8b78950a1ce90093f2f1342cb745d50028553a587f6d0973e1e7a97e364b348",
"md5": "16cdaa06110fcd3f0d9bc73943906e3f",
"sha256": "598640bae0de34ff29c58440904fc9156d7a1bc750ddef5894edd415c772b957"
},
"downloads": -1,
"filename": "hgvs-1.5.4-py2.py3-none-any.whl",
"has_sig": false,
"md5_digest": "16cdaa06110fcd3f0d9bc73943906e3f",
"packagetype": "bdist_wheel",
"python_version": "py2.py3",
"requires_python": ">=3.6",
"size": 107263,
"upload_time": "2022-11-21T20:03:49",
"upload_time_iso_8601": "2022-11-21T20:03:49.302657Z",
"url": "https://files.pythonhosted.org/packages/c8/b7/8950a1ce90093f2f1342cb745d50028553a587f6d0973e1e7a97e364b348/hgvs-1.5.4-py2.py3-none-any.whl",
"yanked": false,
"yanked_reason": null
},
{
"comment_text": "",
"digests": {
"blake2b_256": "f93515d86f2e862a697626fdfc7c91d6ccf862bdbb7a7c595b428bf9dddb6c3c",
"md5": "9e5fb1a56334792abae168ec5352aac2",
"sha256": "06abb6363bb0c8ef9f3f8f9dc333d3a346ab5f9ebcb20a5bb56c69256262559f"
},
"downloads": -1,
"filename": "hgvs-1.5.4.tar.gz",
"has_sig": false,
"md5_digest": "9e5fb1a56334792abae168ec5352aac2",
"packagetype": "sdist",
"python_version": "source",
"requires_python": ">=3.6",
"size": 2223400,
"upload_time": "2022-11-21T20:03:51",
"upload_time_iso_8601": "2022-11-21T20:03:51.412259Z",
"url": "https://files.pythonhosted.org/packages/f9/35/15d86f2e862a697626fdfc7c91d6ccf862bdbb7a7c595b428bf9dddb6c3c/hgvs-1.5.4.tar.gz",
"yanked": false,
"yanked_reason": null
}
],
"upload_time": "2022-11-21 20:03:51",
"github": false,
"gitlab": false,
"bitbucket": false,
"lcname": "hgvs"
}
