Commits · 818507eaf965f23f05793b29c41e08342567e4f6 · Mirrors / mutalyzer

Jan 13, 2012

Made a prototype of a module that generates a variant description from two · 818507ea

Laros authored 13 years ago

sequences.



git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@440 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

818507ea

Jan 08, 2012

Fix BED track for UCSC Genome Browser · 1f06518e

Vermaat authored 13 years ago

Previously, the 'color' field in the BED track we provide for the Genome
Browser was set to the empty string, but Gerard informed us that this is not
(always) handled correctly:

   Expecting number field 5 line 2 of https://mutalyzer.nl/bed?..., got +

We now explicitely set the 'color' field to '0'.


git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@439 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

1f06518e

Dec 14, 2011

Do not crash on EX positioning (fixes #79) · 2809d839

Vermaat authored 13 years ago

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@435 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

2809d839

Dec 07, 2011

Complete fix r431 and add a unit test · 1dae4cf5

Vermaat authored 13 years ago

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@433 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

1dae4cf5

Dec 02, 2011

Fixed a bug in genbank.py that was triggered while building a list of tags from · 1d0dbc36

Laros authored 13 years ago

the product list. Please check this fix.

Made some trivial changes in the rest of the files.

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@431 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

1d0dbc36

Nov 25, 2011

Open development for 2.0.beta-13 · b4baea9d

Vermaat authored 13 years ago

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@430 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

b4baea9d

Release 2.0.beta-12 · 92942c5f

Vermaat authored 13 years ago

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@428 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

92942c5f

Accept plasmid reference sequences · a6d7d62b

Vermaat authored 13 years ago

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@427 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

a6d7d62b

Nov 24, 2011

Fix typo · b1167e02

Vermaat authored 13 years ago

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@426 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

b1167e02

Merge browser-link-branch to trunk · c38fe12c

Vermaat authored 13 years ago

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@424 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

c38fe12c

Add strandedness to BED tracks · 325130bb

Vermaat authored 13 years ago

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/branches/browser-link-branch@423 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

325130bb

Some code cleanup and fixes · 7d0c55cd

Vermaat authored 13 years ago

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/branches/browser-link-branch@422 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

7d0c55cd

Merge r404-420 from trunk · 94251d65

Vermaat authored 13 years ago

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/branches/browser-link-branch@421 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

94251d65

Nov 23, 2011

Fix reverse complement of number parameter in position converter · d094cf4d
Vermaat authored 13 years ago
```
git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@420 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1
```
d094cf4d

Try being forgiving in dbSNP queries by retrying · ad0860e5

Vermaat authored 13 years ago

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@419 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

ad0860e5

Nov 14, 2011

Fix crash on variant without reference (thx Ivar) · 5fdc74c3

Vermaat authored 13 years ago

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@418 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

5fdc74c3

Nov 10, 2011

Add restriction site effects to batch output · 383b55f8

Vermaat authored 13 years ago

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@417 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

383b55f8

Fix bugs due to implicit config refactoring · 20cbda9e

Vermaat authored 13 years ago

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@416 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

20cbda9e

Nov 08, 2011

Merge implicit-config-branch to trunk · 1a6251c8

Vermaat authored 13 years ago

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@412 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

1a6251c8

Merge r407, r409, r410 from trunk to implicit-config-branch · 974e2a55

Vermaat authored 13 years ago

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/branches/implicit-config-branch@411 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

974e2a55

Retrieve full sequence for contig reference files · cff8ea36

Vermaat authored 13 years ago

Fixes #74.


git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@410 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

cff8ea36

Nov 04, 2011

Fix typo · b75860cb

Vermaat authored 13 years ago

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@409 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

b75860cb

Use implicit configuration object creation · ae2ae0c8

Vermaat authored 13 years ago

The old way of using the configuration file was by instantiating a Config
object which read the file. This instance was passed to every function and
object that might need it.

The new way is by simply calling config.get('name') to get the configuration
value for 'name'. This lazily reads the configuration file and the contents
are cached for future calls.

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/branches/implicit-config-branch@408 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

ae2ae0c8

Remove some old TODO items · 5b5160f9

Vermaat authored 13 years ago

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@407 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

5b5160f9

Create implicit-config-branch from trunk · d1e45249

Vermaat authored 13 years ago

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/branches/implicit-config-branch@406 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

d1e45249

Nov 01, 2011

Merge r402 from trunk to browser-link-branch · 56335113

Vermaat authored 13 years ago

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/branches/browser-link-branch@404 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

56335113

Convert genomic positions to any transcript · ca585e08

Vermaat authored 13 years ago

Add optional gene argument to the numberConvertion webservice method. If
present, it will convert genomic variants to any transcript of the given
gene, no matter how far away they are located (but on the same chromosome
of course). Fixes #70.

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@402 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

ca585e08

Oct 21, 2011

Fix url in BED track · df171de1

Vermaat authored 13 years ago

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/branches/browser-link-branch@396 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

df171de1

Fix positions in BED track on reverse strand · 892ae9b7

Vermaat authored 13 years ago

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/branches/browser-link-branch@395 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

892ae9b7

Oct 20, 2011

Implement BED tracks for Genome Browser · 8402dae3

Vermaat authored 13 years ago

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/branches/browser-link-branch@394 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

8402dae3

Oct 12, 2011

Properly implement link to variant region in Genome Browser · 3b048179

Vermaat authored 13 years ago

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/branches/browser-link-branch@393 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

3b048179

Merge r391 from trunk · 31527758

Vermaat authored 13 years ago

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/branches/browser-link-branch@392 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

31527758

Oct 11, 2011

Make install/upgrade scripts a bit more robust · 4e06a57c

Vermaat authored 13 years ago

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@391 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

4e06a57c

Fix Genome Browser link (issue #61) · 6b270da8

Vermaat authored 13 years ago

Link to UCSC Genome Browser now has a more proper implementation. Still todo
is error checking and such.

It uses the same infrastrucure as the position converter and is thus also
limited to variants on transcripts with c. notations.

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/branches/browser-link-branch@390 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

6b270da8

Merge r380-r388 from trunk to browser-link-branch · b58561a8

Vermaat authored 13 years ago

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/branches/browser-link-branch@389 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

b58561a8

Oct 10, 2011

Give an error on protein reference sequences · 18e228a6

Vermaat authored 13 years ago

Until protein reference sequences are supported, give an error with a message
instead of crashing. Fixes #62.

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@388 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

18e228a6

Accept IVS locations in Variant_info LOVD interface · 302ba055

Vermaat authored 13 years ago

The fix is a hack, basically copying the same functionality from the
namechecker. I think this should eventually be merged somehow.

Fixes #63


git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@387 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

302ba055

Update default Mutalyzer location in cache-sync cronjob · f4a60125

Vermaat authored 13 years ago

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@386 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

f4a60125

Oct 07, 2011

Copy user config from install as root (fixes #64) · cd447389

Vermaat authored 13 years ago

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@385 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

cd447389

Do apt-get update before installing in pre-install script · d0682e4b

Vermaat authored 13 years ago

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@384 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

d0682e4b