Commits · 8464555bb12c0720277dc88697a03ce5be760329 · Mirrors / mutalyzer

Aug 20, 2012

Fix unit tests for description extractor update · 8464555b

Vermaat authored 12 years ago

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@598 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

8464555b

Aug 19, 2012

Optimised the description extractor by: · c8f66129

Laros authored 12 years ago

- Calculating the LCS matrices only for the affected region.
- Reusing the LCS matrices.



git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@597 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

c8f66129

Added description extractor functionality to the name checker as an · 646ce812

Laros authored 12 years ago

experimental service.

describe.py:
- Added an `unknown' type to the possible types of raw variants.
- Disabled the experimental LCSMatrix() code.



git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@596 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

646ce812

Aug 18, 2012

Added functionality for generating complex protein descriptions. · 93920052

Laros authored 12 years ago

describe.py:
- Added functionality to detect frame shifts.
- Modified the RawVar class to support protein descriptions.
- Added the core protein description function.

models.py:
- Modified the RawVar class to support protein descriptions.


git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@595 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

93920052

Minor (punctuation) changes in the about page. · 0dcb662d

Laros authored 12 years ago

Modified describe.py to comply with the preferred programming style.


git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@594 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

0dcb662d

Aug 06, 2012

Made the description generation slightly more insightful. · fcf63867

Laros authored 12 years ago

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@593 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

fcf63867

Added a hgvs field to the RawVar class. · cabd73ed

Laros authored 12 years ago

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@592 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

cabd73ed

Aug 04, 2012

Added a webservice function for the description extractor. · 8131c606

Laros authored 12 years ago

rpc.py:
- Added the function descriptionExtract().
- Standardised indentation.

models.py:
- Added a RawVar and an Allele class for the webservices.

describe.py:
- Made the RawVar class a child of models.RawVar. This is convenient for
  webservices since we can simply return this object.



git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@591 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

8131c606

Jul 26, 2012

Unit test for issue #108 · 7e6dd859

Vermaat authored 12 years ago

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@590 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

7e6dd859

Removed erroneous optional argument check for DelIns. (Fixes #108). · 5952b8a0
Laros authored 12 years ago
```
git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@589 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1
```
5952b8a0

Jul 25, 2012

Allow leading whitespace in batch input (#107) · 6030c8b7

Vermaat authored 12 years ago

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@588 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

6030c8b7

Merge spyne branch back in trunk · 76e90a4c

Vermaat authored 12 years ago

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@586 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

76e90a4c

Jul 23, 2012

Open development for 2.0.beta-22 · 2b47e863

Vermaat authored 12 years ago

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/branches/spyne@585 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

2b47e863

Release 2.0.beta-21 · 6cf159f5

Vermaat authored 12 years ago

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/branches/spyne@583 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

6cf159f5

Use spyne instead of rpclib in install script · b5ae751b

Vermaat authored 12 years ago

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/branches/spyne@582 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

b5ae751b

Only apply spyne monkey patch if needed · 7b48d010

Vermaat authored 12 years ago

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/branches/spyne@581 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

7b48d010

Jul 16, 2012

Better Json-serialized Fault objects · bdf95fab

Vermaat authored 12 years ago

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/branches/spyne@580 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

bdf95fab

Monkey patch spyne to Json-serialize Fault objects · 68ffe865

Vermaat authored 12 years ago

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/branches/spyne@579 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

68ffe865

Update tests for wrapped json responses · 7f986b76

Vermaat authored 12 years ago

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/branches/spyne@578 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

7f986b76

Fix for primitive JSON result datatypes · e985d0b4

Vermaat authored 12 years ago

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/branches/spyne@577 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

e985d0b4

Move from rpclib to spyne · f942943b

Vermaat authored 12 years ago

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/branches/spyne@576 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

f942943b

Create spyne branch from trunk · a361697e

Vermaat authored 12 years ago

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/branches/spyne@575 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

a361697e

Add chromAccession.py to SOAP tools · 80db7b5b

Vermaat authored 12 years ago

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@574 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

80db7b5b

Jul 12, 2012

Support non-coding transcripts in position converter (#102) · 8300b90f

Vermaat authored 12 years ago

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@573 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

8300b90f

Support compound variants in position converter · 0875bfe0

Vermaat authored 12 years ago

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@572 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

0875bfe0

Add mappingInfo to SOAP tools · 6ac7b1b2

Vermaat authored 12 years ago

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@571 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

6ac7b1b2

Jul 11, 2012

Fix position converter for delins with explicit sequences · 5366cb35

Vermaat authored 12 years ago

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@570 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

5366cb35

Typo. · 4e48f80f

Laros authored 12 years ago

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@569 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

4e48f80f

Fix r563 to use * instead of counting · 5ac088a0

Vermaat authored 12 years ago

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@568 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

5ac088a0

Update unit tests for r563 · 6445361f

Vermaat authored 12 years ago

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@567 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

6445361f

Open development for 2.0.beta-21 · 4c2af46a

Vermaat authored 12 years ago

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@566 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

4c2af46a

Release 2.0.beta-20 · 4e915a2c

Vermaat authored 12 years ago

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@564 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

4e915a2c

Jul 10, 2012

Disabled the -u and +d convention in favour of the official HGVS · 8927d789

Laros authored 12 years ago

recommendations.



git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@563 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

8927d789

Fix rpclib installation · 68471fbf

Vermaat authored 12 years ago

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@562 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

68471fbf

Jun 21, 2012

Open development for 2.0.beta-20 · 663de152

Vermaat authored 12 years ago

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@561 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

663de152

Release 2.0.beta-19 · 05a9bc1e

Vermaat authored 12 years ago

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@559 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

05a9bc1e

Disable old mapping info in unit tests · e7af8a68

Vermaat authored 12 years ago

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@558 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

e7af8a68

Do not crash on inversions (introduced in r528) (fixes #99) · acfb2415

Vermaat authored 12 years ago

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@557 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

acfb2415

First download reference in GI unit tests · 061f3d34

Vermaat authored 12 years ago

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@556 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

061f3d34

Explicitely use MyISAM for now · 132e5b1c

Vermaat authored 12 years ago

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@555 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

132e5b1c