Skip to content
GitLab
Projects
Groups
Snippets
/
Help
Help
Support
Community forum
Keyboard shortcuts
?
Submit feedback
Contribute to GitLab
Sign in
Toggle navigation
Menu
Open sidebar
Mirrors
mutalyzer
Commits
60c2f919
Unverified
Commit
60c2f919
authored
Nov 08, 2021
by
Mihai
Committed by
GitHub
Nov 08, 2021
Browse files
Pre repository renaming (#526)
* Update GitHub links * Clean the about page * Update dependencies
parent
079c7c62
Changes
24
Hide whitespace changes
Inline
Side-by-side
CHANGES.rst
View file @
60c2f919
...
...
@@ -15,7 +15,7 @@ Version 2.0.34
Released on March 15th 2021.
- Update article link and point towards the new release website (`#518
<https://github.com/mutalyzer/mutalyzer/pull/518>`_).
<https://github.com/mutalyzer/mutalyzer
2
/pull/518>`_).
Version 2.0.33
...
...
@@ -24,11 +24,11 @@ Version 2.0.33
Released on November 24th 2020.
- Update links (`#514
<https://github.com/mutalyzer/mutalyzer/pull/514>`_).
<https://github.com/mutalyzer/mutalyzer
2
/pull/514>`_).
- Improve warning messages (`#513
<https://github.com/mutalyzer/mutalyzer/pull/513>`_).
<https://github.com/mutalyzer/mutalyzer
2
/pull/513>`_).
- Add legacy crossmapper module (`#508
<https://github.com/mutalyzer/mutalyzer/pull/508>`_).
<https://github.com/mutalyzer/mutalyzer
2
/pull/508>`_).
Version 2.0.32
...
...
@@ -37,13 +37,13 @@ Version 2.0.32
Released on December 9th 2019.
- Update email address and wiki link (`#498
<https://github.com/mutalyzer/mutalyzer/pull/498>`_).
<https://github.com/mutalyzer/mutalyzer
2
/pull/498>`_).
- Fix erroneous message for mtDNA m. coordinate system (`#497
<https://github.com/mutalyzer/mutalyzer/pull/497>`_).
<https://github.com/mutalyzer/mutalyzer
2
/pull/497>`_).
- Update requirements (`#496
<https://github.com/mutalyzer/mutalyzer/pull/496>`_).
<https://github.com/mutalyzer/mutalyzer
2
/pull/496>`_).
- Fix invalid LRG record issue (`#495
<https://github.com/mutalyzer/mutalyzer/pull/495>`_).
<https://github.com/mutalyzer/mutalyzer
2
/pull/495>`_).
Version 2.0.31
...
...
@@ -52,15 +52,15 @@ Version 2.0.31
Released on August 21st 2019.
- Update requirements (`#486
<https://github.com/mutalyzer/mutalyzer/pull/486>`_).
<https://github.com/mutalyzer/mutalyzer
2
/pull/486>`_).
- Add support for NCBI E-utilities API key (`#485
<https://github.com/mutalyzer/mutalyzer/pull/485>`_).
<https://github.com/mutalyzer/mutalyzer
2
/pull/485>`_).
- Update HGVS descriptions retrieval for SNP converter (`#482
<https://github.com/mutalyzer/mutalyzer/issues/482>`_)
<https://github.com/mutalyzer/mutalyzer
2
/issues/482>`_)
- Make file selection mandatory in the batch job web page (`#481
<https://github.com/mutalyzer/mutalyzer/issues/481>`_).
<https://github.com/mutalyzer/mutalyzer
2
/issues/481>`_).
- Update Travis configuration (`#483
<https://github.com/mutalyzer/mutalyzer/pull/483>`_)
<https://github.com/mutalyzer/mutalyzer
2
/pull/483>`_)
Version 2.0.30
...
...
@@ -69,11 +69,11 @@ Version 2.0.30
Released on May 24th 2019.
- Update requirements (`#475
<https://github.com/mutalyzer/mutalyzer/pull/475>`_).
<https://github.com/mutalyzer/mutalyzer
2
/pull/475>`_).
- Update documentation links (`#474
<https://github.com/mutalyzer/mutalyzer/pull/474>`_).
<https://github.com/mutalyzer/mutalyzer
2
/pull/474>`_).
- Fix the genbank parser to perform loci objects creation in two steps (`#468
<https://github.com/mutalyzer/mutalyzer/issues/468>`_).
<https://github.com/mutalyzer/mutalyzer
2
/issues/468>`_).
Version 2.0.29
...
...
@@ -82,15 +82,15 @@ Version 2.0.29
Released on December 4th 2018.
- Improve user feedback for incorrect specific locus (`#459
<https://github.com/mutalyzer/mutalyzer/pull/459>`_).
<https://github.com/mutalyzer/mutalyzer
2
/pull/459>`_).
- Improve some position converter warning (`#458
<https://github.com/mutalyzer/mutalyzer/pull/458>`_).
<https://github.com/mutalyzer/mutalyzer
2
/pull/458>`_).
- Update requirements (`#457
<https://github.com/mutalyzer/mutalyzer/pull/457>`_).
<https://github.com/mutalyzer/mutalyzer
2
/pull/457>`_).
- Make API more consistent between UDs and NCs (`#456
<https://github.com/mutalyzer/mutalyzer/pull/456>`_).
<https://github.com/mutalyzer/mutalyzer
2
/pull/456>`_).
- Fix internal server error on IVS variant (`#452
<https://github.com/mutalyzer/mutalyzer/pull/452>`_).
<https://github.com/mutalyzer/mutalyzer
2
/pull/452>`_).
Version 2.0.28
...
...
@@ -99,7 +99,7 @@ Version 2.0.28
Released on June 11th 2018.
- Support for LRG XML schema version 1.9 (`#449
<https://github.com/mutalyzer/mutalyzer/pull/449>`_).
<https://github.com/mutalyzer/mutalyzer
2
/pull/449>`_).
Version 2.0.27
...
...
@@ -108,19 +108,19 @@ Version 2.0.27
Released on May 25th 2018.
- Accept variant descriptions with NC files as references (`#445
<https://github.com/mutalyzer/mutalyzer/pull/445>`_).
<https://github.com/mutalyzer/mutalyzer
2
/pull/445>`_).
- Removed support for pending LRG reference files (`#444
<https://github.com/mutalyzer/mutalyzer/pull/444>`_).
<https://github.com/mutalyzer/mutalyzer
2
/pull/444>`_).
- Add link to wiki page with differences between Mutalyzer and HGVS (`#443
<https://github.com/mutalyzer/mutalyzer/pull/443>`_).
<https://github.com/mutalyzer/mutalyzer
2
/pull/443>`_).
- Fix for batch processor crash due to NCBI server timeout (`#442
<https://github.com/mutalyzer/mutalyzer/pull/442>`_).
<https://github.com/mutalyzer/mutalyzer
2
/pull/442>`_).
- Update genbank retriever parameters according to NCBI recommendations (`#439
<https://github.com/mutalyzer/mutalyzer/pull/439>`_).
<https://github.com/mutalyzer/mutalyzer
2
/pull/439>`_).
- Update getGeneLocation` to use standard strategy to select mapping (`#437
<https://github.com/mutalyzer/mutalyzer/pull/437>`_).
<https://github.com/mutalyzer/mutalyzer
2
/pull/437>`_).
- Add link to website changelog (`#434
<https://github.com/mutalyzer/mutalyzer/pull/434>`_).
<https://github.com/mutalyzer/mutalyzer
2
/pull/434>`_).
Version 2.0.26
...
...
@@ -129,9 +129,9 @@ Version 2.0.26
Released on July 19th 2017.
- Description-extractor dependency updated to version 2.35 (`#429
<https://github.com/mutalyzer/mutalyzer/pull/429>`_).
<https://github.com/mutalyzer/mutalyzer
2
/pull/429>`_).
- Fix for negative cCDSStop due to wrong transcript to protein link (`#430
<https://github.com/mutalyzer/mutalyzer/issues/430>`_).
<https://github.com/mutalyzer/mutalyzer
2
/issues/430>`_).
Version 2.0.25
...
...
@@ -141,7 +141,7 @@ Released on May 17th 2017.
- Fix for batch processor crash when trying to alter an "item" column of the
"batch_queue_items" database table (`#426
<https://github.com/mutalyzer/mutalyzer/pull/426>`_).
<https://github.com/mutalyzer/mutalyzer
2
/pull/426>`_).
Version 2.0.24
---------------
...
...
@@ -150,7 +150,7 @@ Released on April 12th 2017.
- Fix for SNP converter crash when called with 'rs0' as parameter.
SNP converter displays now more warning messages (`#419
<https://github.com/mutalyzer/mutalyzer/issues/419>`_).
<https://github.com/mutalyzer/mutalyzer
2
/issues/419>`_).
Version 2.0.23
...
...
@@ -160,7 +160,7 @@ Released on November 9th 2016.
- Fix for internal server error in the position converter triggered by
non-variant description (`#333
<https://github.com/mutalyzer/mutalyzer/issues/333>`_).
<https://github.com/mutalyzer/mutalyzer
2
/issues/333>`_).
Version 2.0.22
...
...
@@ -169,7 +169,7 @@ Version 2.0.22
Released on September 20th 2016.
- Biopython dependency updated to version 1.68 (`#411
<https://github.com/mutalyzer/mutalyzer/pull/411>`_).
<https://github.com/mutalyzer/mutalyzer
2
/pull/411>`_).
Version 2.0.21
...
...
@@ -178,7 +178,7 @@ Version 2.0.21
Released on June 24th 2016.
- Fix typo in batch SNP converter, causing all batch jobs to stall (`#409
<https://github.com/mutalyzer/mutalyzer/pull/409>`_).
<https://github.com/mutalyzer/mutalyzer
2
/pull/409>`_).
Version 2.0.20
...
...
@@ -187,11 +187,11 @@ Version 2.0.20
Released on June 22th 2016.
- Accept accession number as transcript selector (`#405
<https://github.com/mutalyzer/mutalyzer/pull/405>`_).
<https://github.com/mutalyzer/mutalyzer
2
/pull/405>`_).
- Add legend to the output of runMutalyzer service (`#404
<https://github.com/mutalyzer/mutalyzer/pull/404>`_).
<https://github.com/mutalyzer/mutalyzer
2
/pull/404>`_).
- Remove support for GI numbers (`#396
<https://github.com/mutalyzer/mutalyzer/pull/396>`_).
<https://github.com/mutalyzer/mutalyzer
2
/pull/396>`_).
Version 2.0.19
...
...
@@ -200,9 +200,9 @@ Version 2.0.19
Released on June 9th 2016.
- Fix reference file loading by URL (`#383
<https://github.com/mutalyzer/mutalyzer/pull/383>`_).
<https://github.com/mutalyzer/mutalyzer
2
/pull/383>`_).
- Consider accession version in `getGeneName` webservice method (`#390
<https://github.com/mutalyzer/mutalyzer/pull/390>`_).
<https://github.com/mutalyzer/mutalyzer
2
/pull/390>`_).
Version 2.0.18
...
...
@@ -211,13 +211,13 @@ Version 2.0.18
Released on May 23rd 2016.
- Fixed installation on CentOS 6 (`#358
<https://github.com/mutalyzer/mutalyzer/pull/358>`_).
<https://github.com/mutalyzer/mutalyzer
2
/pull/358>`_).
- Auto focus primary form input on page load (`#363
<https://github.com/mutalyzer/mutalyzer/pull/363>`_).
<https://github.com/mutalyzer/mutalyzer
2
/pull/363>`_).
- Check optional argument for ``dup`` (`#369
<https://github.com/mutalyzer/mutalyzer/pull/369>`_).
<https://github.com/mutalyzer/mutalyzer
2
/pull/369>`_).
- Fixes for chromosome slicing by gene symbol (`#371
<https://github.com/mutalyzer/mutalyzer/pull/371>`_).
<https://github.com/mutalyzer/mutalyzer
2
/pull/371>`_).
Version 2.0.17
...
...
@@ -226,12 +226,12 @@ Version 2.0.17
Released on March 24th 2016.
- Position converter now checks for selection of gene/transcript (`#346
<https://github.com/mutalyzer/mutalyzer/pull/346>`_).
<https://github.com/mutalyzer/mutalyzer
2
/pull/346>`_).
- Update about page and link to `new mailing list
<https://groups.google.com/forum/#!forum/mutalyzer>`_ (`#353
<https://github.com/mutalyzer/mutalyzer/pull/353>`_).
<https://github.com/mutalyzer/mutalyzer
2
/pull/353>`_).
- Batch jobs processor is more robust on errors (`#356
<https://github.com/mutalyzer/mutalyzer/pull/356>`_).
<https://github.com/mutalyzer/mutalyzer
2
/pull/356>`_).
Version 2.0.16
...
...
@@ -240,12 +240,12 @@ Version 2.0.16
Released on February 25th 2016.
- Fixed transcript naming in mapping webservices (`#147
<https://github.com/mutalyzer/mutalyzer/pull/147>`_). See below for
<https://github.com/mutalyzer/mutalyzer
2
/pull/147>`_). See below for
:ref:`details <changelog_2016_details>`.
- Support LRG transcripts in the position converter (`#147
<https://github.com/mutalyzer/mutalyzer/pull/147>`_).
<https://github.com/mutalyzer/mutalyzer
2
/pull/147>`_).
- Don't report ``ext*?`` when variant RNA has stop codon (`#146
<https://github.com/mutalyzer/mutalyzer/pull/146>`_).
<https://github.com/mutalyzer/mutalyzer
2
/pull/146>`_).
.. _changelog_2016_details:
...
...
@@ -274,14 +274,14 @@ Version 2.0.15
Released on January 6th 2016.
- Speedup NCBI mapview file import (`#124
<https://github.com/mutalyzer/mutalyzer/pull/124>`_).
<https://github.com/mutalyzer/mutalyzer
2
/pull/124>`_).
- Parse genbank file without VERSION field (`#126
<https://github.com/mutalyzer/mutalyzer/pull/126>`_).
<https://github.com/mutalyzer/mutalyzer
2
/pull/126>`_).
- Fix issue where some transcripts would not show in the legend (`#136
<https://github.com/mutalyzer/mutalyzer/pull/136>`_).
<https://github.com/mutalyzer/mutalyzer
2
/pull/136>`_).
- Don't discard complete gene from GenBank file when it has incomplete but
also complete features annotated (`#138
<https://github.com/mutalyzer/mutalyzer/pull/138>`_)
<https://github.com/mutalyzer/mutalyzer
2
/pull/138>`_)
Version 2.0.14
...
...
@@ -290,24 +290,24 @@ Version 2.0.14
Released on November 9th 2015.
- E-mail address is now optional in batch job website interface (`#119
<https://github.com/mutalyzer/mutalyzer/pull/119>`_).
<https://github.com/mutalyzer/mutalyzer
2
/pull/119>`_).
- Use Mailcheck in the batch jobs form (`#107
<https://github.com/mutalyzer/mutalyzer/pull/107>`_).
<https://github.com/mutalyzer/mutalyzer
2
/pull/107>`_).
- Optional email for batch jobs from webservices (`#104
<https://github.com/mutalyzer/mutalyzer/pull/104>`_).
<https://github.com/mutalyzer/mutalyzer
2
/pull/104>`_).
- Process batch jobs grouped by email address (`#101
<https://github.com/mutalyzer/mutalyzer/pull/101>`_).
<https://github.com/mutalyzer/mutalyzer
2
/pull/101>`_).
- Use interval binning scheme on transcript mappings (`#100
<https://github.com/mutalyzer/mutalyzer/pull/100>`_).
<https://github.com/mutalyzer/mutalyzer
2
/pull/100>`_).
- Back translator interface (`#74
<https://github.com/mutalyzer/mutalyzer/pull/74>`_).
<https://github.com/mutalyzer/mutalyzer
2
/pull/74>`_).
- Transcript-protein links are now cached in Redis (`#94
<https://github.com/mutalyzer/mutalyzer/pull/94>`_).
<https://github.com/mutalyzer/mutalyzer
2
/pull/94>`_).
- Added `Ter` as a valid amino acid in the HGVS grammar (`#90
<https://github.com/mutalyzer/mutalyzer/pull/90>`_).
<https://github.com/mutalyzer/mutalyzer
2
/pull/90>`_).
- Refactoring of unit tests (`#88
<https://github.com/mutalyzer/mutalyzer/pull/88>`_, `#89
<https://github.com/mutalyzer/mutalyzer/pull/89>`_).
<https://github.com/mutalyzer/mutalyzer
2
/pull/88>`_, `#89
<https://github.com/mutalyzer/mutalyzer
2
/pull/89>`_).
Version 2.0.13
...
...
@@ -316,7 +316,7 @@ Version 2.0.13
Released on October 1st 2015.
- Fix query bug in update transcript-protein links (`#85
<https://github.com/mutalyzer/mutalyzer/pull/85>`_).
<https://github.com/mutalyzer/mutalyzer
2
/pull/85>`_).
Version 2.0.12
...
...
@@ -325,17 +325,17 @@ Version 2.0.12
Released on September 30th 2015.
- Fix off-by-one in slicing chromosome by gene name (`#79
<https://github.com/mutalyzer/mutalyzer/pull/79>`_).
<https://github.com/mutalyzer/mutalyzer
2
/pull/79>`_).
- Document scheme used for all positions and ranges (`#79
<https://github.com/mutalyzer/mutalyzer/pull/79>`_).
<https://github.com/mutalyzer/mutalyzer
2
/pull/79>`_).
- Show diff for variant protein from non-reference start codon (`#78
<https://github.com/mutalyzer/mutalyzer/pull/78>`_).
<https://github.com/mutalyzer/mutalyzer
2
/pull/78>`_).
- Visualise protein change, also with alternative start (`#72
<https://github.com/mutalyzer/mutalyzer/pull/72>`_).
<https://github.com/mutalyzer/mutalyzer
2
/pull/72>`_).
- Translate alternative start to M, also in variant (`#72
<https://github.com/mutalyzer/mutalyzer/pull/72>`_).
<https://github.com/mutalyzer/mutalyzer
2
/pull/72>`_).
- Added Baker's yeast (SacCer_Apr2011/sacCer3) assembly (`#73
<https://github.com/mutalyzer/mutalyzer/pull/73>`_).
<https://github.com/mutalyzer/mutalyzer
2
/pull/73>`_).
Version 2.0.11
...
...
@@ -344,7 +344,7 @@ Version 2.0.11
Released on August 6th 2015.
- Fix bug in recognizing ``p.(=)`` (was reported as ``p.?``) (`#65
<https://github.com/mutalyzer/mutalyzer/pull/65>`_).
<https://github.com/mutalyzer/mutalyzer
2
/pull/65>`_).
Version 2.0.10
...
...
@@ -354,13 +354,13 @@ Released on July 21st 2015.
- Don't crash the position converter on transcript mappings containing no
exons (`#63
<https://github.com/mutalyzer/mutalyzer/pull/63>`_).
<https://github.com/mutalyzer/mutalyzer
2
/pull/63>`_).
- Use the notation for an uncertain stop codon, e.g., ``p.(Gln730Profs*?)``
instead of ``p.(Gln730Profs*96)`` when a variant results in a frame shift or
extension and we don't see a new stop codon in the RNA (`#57
<https://github.com/mutalyzer/mutalyzer/pull/57>`_).
<https://github.com/mutalyzer/mutalyzer
2
/pull/57>`_).
- Added Dog (Broad CanFam3.1/canFam3) assembly for position converter (`#56
<https://github.com/mutalyzer/mutalyzer/pull/56>`_).
<https://github.com/mutalyzer/mutalyzer
2
/pull/56>`_).
Version 2.0.9
...
...
@@ -372,7 +372,7 @@ Released on July 9th 2015.
<https://github.com/LUMC/mutalyzer/pull/52>`_, `#53
<https://github.com/LUMC/mutalyzer/pull/53>`_).
- Usability improvements in reading DNA for description extractor (`#54
<https://github.com/mutalyzer/mutalyzer/pull/54>`_).
<https://github.com/mutalyzer/mutalyzer
2
/pull/54>`_).
Version 2.0.8
...
...
README.rst
View file @
60c2f919
...
...
@@ -9,17 +9,17 @@ Documentation
-------------
User documentation can be found on the `wiki
<https://github.com/mutalyzer/mutalyzer/wiki>`_.
<https://github.com/mutalyzer/mutalyzer
2
/wiki>`_.
Developer documentation is `hosted at Read The Docs
<http://mutalyzer.readthedocs.org>`_.
<http://mutalyzer
2
.readthedocs.org>`_.
Submit your bug reports and feature requests `here
<https://github.com/mutalyzer/mutalyzer/issues>`_.
<https://github.com/mutalyzer/mutalyzer
2
/issues>`_.
If you're interested in running your own Mutalyzer installation, please have a
look at our `Mutalyzer Ansible role
<https://github.com/mutalyzer/ansible-role
-mutalyzer
>`_ for a completely
<https://github.com/mutalyzer/
mutalyzer2-
ansible-role>`_ for a completely
automated deployment.
...
...
@@ -31,7 +31,7 @@ reports, bug fixes, unit tests, documentation updates, or anything els you may
come up with.
Please refer to the documentation for `more information on contributions
<http://mutalyzer.readthedocs.org/en/latest/contributing.html>`_.
<http://mutalyzer
2
.readthedocs.org/en/latest/contributing.html>`_.
Copyright
...
...
doc/contributing.rst
View file @
60c2f919
...
...
@@ -10,7 +10,7 @@ reports, bug fixes, unit tests, documentation updates, or anything els you may
come up with.
Development of Mutalyzer happens on GitHub:
https://github.com/mutalyzer/mutalyzer
https://github.com/mutalyzer/mutalyzer
2
Coding style
...
...
doc/deploy.rst
View file @
60c2f919
...
...
@@ -166,7 +166,7 @@ error-prone. Several systems exist to automate this, such as `Puppet`_,
`Chef`_, and `Ansible`_.
An automated `deployment of Mutalyzer with Ansible
<https://github.com/mutalyzer/ansible-role
-mutalyzer
>`_ is available on
<https://github.com/mutalyzer/
mutalyzer2-
ansible-role>`_ is available on
GitHub. This includes installation of the website, SOAP and HTTP/RPC+JSON
webservices, and the batch processor, similar to the setup described above.
...
...
doc/download.rst
View file @
60c2f919
...
...
@@ -5,11 +5,11 @@
Downloading Mutalyzer
=====================
The Mutalyzer source code is `hosted on GitHub
<https://github.com/mutalyzer/mutalyzer>`_. The recommended way to get the
The Mutalyzer
2
source code is `hosted on GitHub
<https://github.com/mutalyzer/mutalyzer
2
>`_. The recommended way to get the
Mutalyzer source code is by cloning the `Git`_ repository::
git clone https://github.com/mutalyzer/mutalyzer.git
git clone https://github.com/mutalyzer/mutalyzer
2
.git
This will give you the current development version. See below for working with
other versions.
...
...
@@ -34,9 +34,9 @@ Archive downloads
If for whatever reason you don't want to use Git, you can download the source
code directly as a zip archive or tarball. The current development version can
be found from the `project homepage
<https://github.com/mutalyzer/mutalyzer>`_. Archive downloads for release versions
<https://github.com/mutalyzer/mutalyzer
2
>`_. Archive downloads for release versions
can be found on the `releases page
<https://github.com/mutalyzer/mutalyzer/releases>`_.
<https://github.com/mutalyzer/mutalyzer
2
/releases>`_.
.. _Git: http://git-scm.com/
doc/index.rst
View file @
60c2f919
...
...
@@ -8,7 +8,7 @@ installation can be found at `mutalyzer.nl <https://mutalyzer.nl>`_.
might be interested in :ref:`deploy_ansible`.
This is the developer documentation for Mutalyzer. User documentation can be
found on the `wiki <https://github.com/mutalyzer/mutalyzer/wiki>`_.
found on the `wiki <https://github.com/mutalyzer/mutalyzer
2
/wiki>`_.
Managing Mutalyzer
...
...
doc/requirements.txt
View file @
60c2f919
docutils<0.18
Sphinx
alembic
biopython
...
...
doc/testing.rst
View file @
60c2f919
...
...
@@ -38,7 +38,7 @@ Similarly, ``--redis-uri`` (only one allowed) specifies a Redis server to use
for testing. If unspecified, a mock Redis server is used.
Tests are `run automatically on Travis CI
<https://travis-ci.org/mutalyzer/mutalyzer>`_ with SQLite, PostgreSQL, and
<https://travis-ci.org/mutalyzer/mutalyzer
2
>`_ with SQLite, PostgreSQL, and
MySQL, for each pull request and push on GitHub.
...
...
mutalyzer/db/models.py
View file @
60c2f919
...
...
@@ -155,7 +155,7 @@ class Reference(db.Base):
#: Accession number for this reference, including the version number if
#: applicable (e.g., ``AL449423.14``, ``NM_000059.3``,
#: ``UD_138781341344``).
# See: https://github.com/mutalyzer/mutalyzer/issues/399
# See: https://github.com/mutalyzer/mutalyzer
2
/issues/399
accession
=
Column
(
String
(
20
),
nullable
=
False
,
index
=
True
,
unique
=
True
)
#: MD5 checksum of the reference file.
...
...
mutalyzer/mapping.py
View file @
60c2f919
...
...
@@ -1125,7 +1125,7 @@ def import_from_lrgmap_file(assembly, lrgmap_file):
# TODO: Also take protein into account. For example, in LRG_321 (TP53)
# some transcripts occur twice (with different CDSs and different
# protein numbers).
# https://github.com/mutalyzer/mutalyzer/issues/372
# https://github.com/mutalyzer/mutalyzer
2
/issues/372
return
TranscriptMapping
.
create_or_update
(
chromosome
,
'lrg'
,
accession
,
record
[
'gene'
],
orientation
,
record
[
'start'
],
record
[
'stop'
],
...
...
mutalyzer/website/templates/about.html
View file @
60c2f919
...
...
@@ -14,50 +14,23 @@ posted to this list via the Google Groups interface or by sending an email
to
<a
href=
"mutalyzer@googlegroups.com"
>
mutalyzer@googlegroups.com
</a>
.
</p>
<p>
Bugs and concrete feature requests may also be filed directly in
the
<a
href=
"https://github.com/mutalyzer/mutalyzer/issues"
>
GitHub issue
tracker
</a>
.
</p>
<p>
If you are a regular user of the Mutalyzer webservices or are maintaining your
own Mutalyzer installation, consider subscribing to
the
<a
href=
"https://groups.google.com/forum/#!forum/mutalyzer-announce"
>
Mutalyzer
Announcements mailing list
</a>
. This is a low-volume mailing list for
announcing updates to Mutalyzer and its infrastructure.
</p>
<p>
If you have a private question or a security related issue to discuss, please
use the private
address
<a
href=
"info@mutalyzer.nl"
>
info@mutalyzer.nl
</a>
.
</p>
<h2>
Open Source
</h2>
<p>
Mutalyzer is Open Source and available under
the
<a
href=
"http://www.gnu.org/licenses/agpl-3.0.html"
>
GNU Affero General
Public License
</a>
. Please
<a
href=
"mailto:info@mutalyzer.nl"
>
contact the
authors
</a>
if you want to discuss custom licensing.
</p>
<p>
Contributions to Mutalyzer are very welcome! They can be feature requests, bug
reports, bug fixes, unit tests, documentation updates, or anything else you may
come up with.
Public License
</a>
.
</p>
<p>
Development of Mutalyzer happens
on
GitHub:
<a
href=
"https://github.com/mutalyzer/mutalyzer"
>
github.com/mutalyzer/mutalyzer
</a>
Mutalyzer source code is available
on
GitHub:
<a
href=
"https://github.com/mutalyzer/mutalyzer
2
"
>
github.com/mutalyzer/mutalyzer
2
</a>
</p>
<p>
If you're interested in running your own Mutalyzer installation, please have a
look at
our
<a
href=
"https://github.com/mutalyzer/ansible-role
-mutalyzer
"
>
Mutalyzer
our
<a
href=
"https://github.com/mutalyzer/
mutalyzer2-
ansible-role"
>
Mutalyzer
Ansible role
</a>
for a completely automated deployment.
</p>
...
...
mutalyzer/website/templates/back-translator.html
View file @
60c2f919
...
...
@@ -38,7 +38,7 @@ Please supply an amino acid substitution.
</div>
<div
class=
"form-group button-group"
>
<input
type=
"submit"
class=
"btn btn-primary"
value=
"Back translate"
>
<a
href=
"https://github.com/mutalyzer/mutalyzer/wiki/Back-Translator"
target=
"new"
class=
"btn btn-default pull-right"
>
Help
</a>
<a
href=
"https://github.com/mutalyzer/mutalyzer
2
/wiki/Back-Translator"
target=
"new"
class=
"btn btn-default pull-right"
>
Help
</a>
</div>
</form>
...
...
mutalyzer/website/templates/base.html
View file @
60c2f919
...
...
@@ -108,13 +108,13 @@
<ul
class=
"dropdown-menu"
>
<li>
<a
href=
"https://github.com/mutalyzer/mutalyzer/wiki/Documentation"
target=
"_blank"
>
Documentation
</a>
<a
href=
"https://github.com/mutalyzer/mutalyzer
2
/wiki/Documentation"
target=
"_blank"
>
Documentation
</a>
</li>
<li>
<a
href=
"https://github.com/mutalyzer/mutalyzer/wiki/Mutalyzer-FAQ"
target=
"_blank"
>
FAQ
</a>
<a
href=
"https://github.com/mutalyzer/mutalyzer
2
/wiki/Mutalyzer-FAQ"
target=
"_blank"
>
FAQ
</a>
</li>
<li>
<a
href=
"https://github.com/mutalyzer/mutalyzer/wiki/Mutalyzer-Exercise"
target=
"_blank"
>
Exercise
</a>
<a
href=
"https://github.com/mutalyzer/mutalyzer
2
/wiki/Mutalyzer-Exercise"
target=
"_blank"
>
Exercise
</a>
</li>
<li>
<a
href=
"https://groups.google.com/forum/#!forum/mutalyzer"
target=
"_blank"
>
Mailing list
</a>
...
...
@@ -129,7 +129,7 @@
</ul>
<ul
class=
"nav navbar-nav navbar-right"
>
<li>
<a
class=
"navbar-brand"
href=
"https://github.com/mutalyzer/mutalyzer"
target=
"_blank"
><img
<a
class=
"navbar-brand"
href=
"https://github.com/mutalyzer/mutalyzer
2
"
target=
"_blank"
><img
src=
"{{ url_for('static', filename='images/github_logo.png') }}"
title=
"Mutalyzer on GitHub"
></a>
</li>
</ul>
...
...
@@ -185,14 +185,14 @@
{% endif %}
</span>
<br>
<a
href=
"https://github.com/mutalyzer/mutalyzer/blob/master/CHANGES.rst"
>
<a
href=
"https://github.com/mutalyzer/mutalyzer
2
/blob/master/CHANGES.rst"
>
Changelog
</a>
</p>
</div>
<div
class=
"col-md-4"
>
<p
class=
"text-muted"
>
HGVS nomenclature version {{ nomenclature_version }}
(
<a
href=
"https://github.com/mutalyzer/mutalyzer/wiki/HGVS-Mutalyzer-Differences"
>
notes
</a>
)
(
<a
href=
"https://github.com/mutalyzer/mutalyzer
2
/wiki/HGVS-Mutalyzer-Differences"
>
notes
</a>
)
<br>
<a
href=
"{{ url_for('website.about') }}#recommended-by"
name=
"recommended-by"
>
Recommended by
...
...
mutalyzer/website/templates/batch-jobs.html
View file @
60c2f919
...
...
@@ -52,7 +52,7 @@
<div
class=
"form-group"
>
<input
type=
"submit"
class=
"btn btn-primary"
value=
"Submit batch job"
>
<a
href=
"https://github.com/mutalyzer/mutalyzer/wiki/Batch-Checkers"
target=
"new"
class=
"btn btn-default pull-right"
>
Help
</a>
<a
href=
"https://github.com/mutalyzer/mutalyzer
2
/wiki/Batch-Checkers"
target=
"new"
class=
"btn btn-default pull-right"
>
Help
</a>
<a
href=
"#"
onclick=
"toggle_visibility('help');"
class=
"btn btn-default pull-right"
>
File format help
<span
class=
"caret"
></span></a>
</div>
</form>
...
...
mutalyzer/website/templates/description-extractor.html
View file @
60c2f919
...
...
@@ -151,7 +151,7 @@ Please supply a reference sequence and an observed sequence.
</div>
<div
class=
"form-group"
>
<input
type=
"submit"
class=
"btn btn-primary"
value=
"Extract variant description"
>
<a
href=
"https://github.com/mutalyzer/mutalyzer/wiki/Description-Extractor"
target=
"new"
class=
"btn btn-default pull-right"
>
Help
</a>
<a
href=
"https://github.com/mutalyzer/mutalyzer
2
/wiki/Description-Extractor"
target=
"new"
class=
"btn btn-default pull-right"
>
Help
</a>
</div>
</form>
...
...
mutalyzer/website/templates/name-checker.html
View file @
60c2f919
...
...
@@ -61,7 +61,7 @@
<div
class=
"form-group button-group"
>
<input
type=
"submit"
class=
"btn btn-primary"
value=
"Check variant description"
>
<a
href=
"https://github.com/mutalyzer/mutalyzer/wiki/Name-Checker"
target=
"new"
class=
"btn btn-default pull-right"
>
Help
</a>
<a
href=
"https://github.com/mutalyzer/mutalyzer
2
/wiki/Name-Checker"
target=
"new"
class=
"btn btn-default pull-right"
>
Help
</a>
</div>
</form>
...
...
@@ -96,7 +96,7 @@
{% if parse_error %}
<div
class=
"alert alert-info"
>
Please note that Mutalyzer does not cover the entire HGVS nomenclature. You can find more information
<a
href=
"https://github.com/mutalyzer/mutalyzer/wiki/HGVS-Mutalyzer-Differences"
>
here
</a>
.
<a
href=
"https://github.com/mutalyzer/mutalyzer
2
/wiki/HGVS-Mutalyzer-Differences"
>
here
</a>
.
</div>
{% endif %}
...
...
mutalyzer/website/templates/name-generator.html
View file @
60c2f919
...
...
@@ -134,7 +134,7 @@
<div
class=
"form-group"
>
<div
class=
"col-sm-12"
>
<input
type=
"button"
onclick=
"addVariant();"
class=
"btn btn-success"
value=
"Add variant +"
>
<a
href=
"https://github.com/mutalyzer/mutalyzer/wiki/Name-Generator"
target=
"new"
class=
"btn btn-default pull-right"
>
Help
</a>