Commits · 0d858c63b265675fca37d8840a98a82daa9e17ae · Mirrors / mutalyzer

Jan 03, 2013

New version of the Mutalyzer 2.0 paper. · 0d858c63

Laros authored 12 years ago

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@660 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

0d858c63

Dec 20, 2012

Fix typo (thanks Gerard) · 17aa330d

Vermaat authored 12 years ago

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@659 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

17aa330d

NCBI mapping update command for build 37.5 · a439e9b1

Vermaat authored 12 years ago

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@658 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

a439e9b1

Fix bug in NCBI mapping update process · a61d9e83

Vermaat authored 12 years ago

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@657 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

a61d9e83

Dec 15, 2012

Fixed a highlighting bug in the text output. · 935340b1

Laros authored 12 years ago

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@656 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

935340b1

Added fancy printing of a protein to the console (handy for debugging). · 25b33ebe
Laros authored 12 years ago
```
git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@655 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1
```
25b33ebe

Dec 11, 2012

Only show experimental services if we have the info · 74f517c2

Vermaat authored 12 years ago

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@652 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

74f517c2

Merge protein-branch r397-r650 in trunk · 219bf6ea

Vermaat authored 12 years ago

This consists of an updated HGVS parser accepting protein level descriptions
and some checks in the name checker to disable them for now.

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@651 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

219bf6ea

Merge trunk r554-r649 in protein-branch · aab3de31

Vermaat authored 12 years ago

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/branches/protein-branch@650 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

aab3de31

Open development for 2.0.beta-25 · bcb2b65d

Vermaat authored 12 years ago

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@649 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

bcb2b65d

Release 2.0.beta-24 · e80fd858

Vermaat authored 12 years ago

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@647 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

e80fd858

Dec 06, 2012

Added a Makefile for compiling papers. · d2ddaa08

Laros authored 12 years ago

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@646 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

d2ddaa08

Updated the Mutalyzer 2.0 paper. · 30ba85ef

Laros authored 12 years ago

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@645 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

30ba85ef

Nov 29, 2012

Rename some warning codes · 823f5bc0

Vermaat authored 12 years ago

Changed codes:

    WCDSSELECTED    -> WCDS
    WCDS            -> WCDS_OTHER
    WSPLICESELECTED -> WSPLICE
    WSPLICE         -> WSPLICE_OTHER


git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@644 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

823f5bc0

Nov 28, 2012

Fixed the command line interface, it is not very pretty yet, but it now is · be574870

Laros authored 12 years ago

fully functional again.


git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@643 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

be574870

Frameshift detection error (#124) fixed. · 4e9bd5f2

Laros authored 12 years ago

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@642 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

4e9bd5f2

Nov 26, 2012

Have separate WCDS and WCDSSELECTED codes (#98) · 137474bd

Vermaat authored 12 years ago

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@641 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

137474bd

Nov 22, 2012

Create databases in install script (fixes #112) · 6a38f261

Vermaat authored 12 years ago

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@640 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

6a38f261

Nov 15, 2012

Some unit tests for mtDNA position converter · 455ae1e2

Vermaat authored 12 years ago

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@639 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

455ae1e2

Nov 14, 2012

Support organelle types in position converter · 095bea67

Vermaat authored 12 years ago

Keep organelle type ('chromosome' or 'mitochondrion') in chromosome database
table and use it to choose between g. and m. positioning.

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@638 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

095bea67

Use temporary directory in remote deployment · 75340eb2

Vermaat authored 12 years ago

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@637 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

75340eb2

Fix for incorrect SQL in r635 · efaaed66

Vermaat authored 12 years ago

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@636 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

efaaed66

Genomic reference transcript mappings · f17e991f

Vermaat authored 12 years ago

Support genomic references in the mapping database. At the moment, this is
only tested with mtDNA genes, but should in clear the way for NG_ mappings
as well.
Mappings for mtDNA genes can be added to the database using the command line
tool mutalyzer-mapping-import.


git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@635 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

f17e991f

Nov 08, 2012

Open development for 2.0.beta-24 · 5cfd21d8

Vermaat authored 12 years ago

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@634 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

5cfd21d8

Release 2.0.beta-23 · 905284e9

Vermaat authored 12 years ago

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@632 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

905284e9

Add new script to setup.py · 86f7e0ed

Vermaat authored 12 years ago

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@631 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

86f7e0ed

Script to load mapping info from UCSC · 9d0ceda1

Vermaat authored 12 years ago

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@630 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

9d0ceda1

Nov 05, 2012

Have latest refseq mapping in cron example · 03391977

Vermaat authored 12 years ago

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@629 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

03391977

Nov 02, 2012

Open development for 2.0.beta-23 · 36bde44c

Vermaat authored 12 years ago

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@628 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

36bde44c

Release 2.0.beta-22 · b9498dd9

Vermaat authored 12 years ago

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@626 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

b9498dd9

Oct 29, 2012

Catch IncompleteRead error in dbSNP communication · 1f22cc21

Vermaat authored 12 years ago

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@625 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

1f22cc21

Write monitor errors to stderr · f2448ac8

Vermaat authored 12 years ago

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@624 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

f2448ac8

Oct 26, 2012

Mutalyzer instance monitor script · 8c21b407

Vermaat authored 12 years ago

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@623 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

8c21b407

Oct 20, 2012

Added a first draft of the Mutalyzer 2.0 paper. · 6e5795bc

Laros authored 12 years ago


git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@622 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

6e5795bc

Oct 05, 2012

Webservice interface for submitting batch jobs · a7248a86

Vermaat authored 12 years ago

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@621 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

a7248a86

Fix unit test for restriction site analysis · 8f31e51d

Vermaat authored 12 years ago

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@620 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

8f31e51d

Use functools.wraps in decorators · 3a7c3a61

Vermaat authored 12 years ago

This makes sure docstring and name are inherited from the decorated
definition. Fixes decorated unit tests, which previously where skipped
since their name did not start with test_ after decorating.

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@619 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

3a7c3a61

Typo · be4bdc68

Vermaat authored 12 years ago

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@618 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

be4bdc68

Oct 04, 2012

Warn on missing positioning scheme (fixes #114) · 1ec48b68

Vermaat authored 12 years ago

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@617 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

1ec48b68

Do not crash on EST reference · b3ca7327

Vermaat authored 12 years ago

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@616 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

b3ca7327