Commits · 220f9806a2a0aa8fc185407503c6487fb1ca1f44 · Mutalyzer / mutalyzer2

22 Jul, 2013 1 commit

Warnings about ignored sequences, geneNames in EMBL format · 220f9806

Alisa Muraveva authored Jul 22, 2013

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/branches/mobile-2013@731 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

220f9806

19 Jul, 2013 1 commit

Some mistakes are fixed · d9ca56b0

Alisa Muraveva authored Jul 19, 2013

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/branches/mobile-2013@730 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

d9ca56b0

17 Jul, 2013 2 commits

stars were got back in the ends of proteins, the transl_exception table are... · 1d940e80

Alisa Muraveva authored Jul 17, 2013

stars were got back in the ends of proteins, the transl_exception table are visible only if it does not empty.

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/branches/mobile-2013@729 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

1d940e80

Correctly parse CDS on reverse strand from EMBL · 6236a00c

Vermaat authored Jul 17, 2013

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/branches/mobile-2013@728 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

6236a00c

16 Jul, 2013 2 commits

Look only ENS***... genes (but not ENSEST...). And file in *.embl format · 0148a9fc
Alisa Muraveva authored Jul 16, 2013
```
git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/branches/mobile-2013@727 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1
```
0148a9fc

Nothing works =(((( · 6a8df824

Alisa Muraveva authored Jul 16, 2013

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/branches/mobile-2013@726 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

6a8df824

15 Jul, 2013 5 commits

Recognize Ensembl id by leading _ (temporary) · 82b9f8df

Vermaat authored Jul 15, 2013

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/branches/mobile-2013@725 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

82b9f8df

We also added the exceptions table in terminal output · f94c0398

Alisa Muraveva authored Jul 15, 2013

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/branches/mobile-2013@724 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

f94c0398

highliting letters works in website toosudo /etc/init.d/apache2 restart! =) · 5c88331d
Alisa Muraveva authored Jul 15, 2013
```
git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/branches/mobile-2013@723 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1
```
5c88331d

highliting letters works only in terminal · 7a755959

Alisa Muraveva authored Jul 15, 2013

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/branches/mobile-2013@722 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

7a755959

new embl parser does not work=_( · 621e5ba8

Alisa Muraveva authored Jul 15, 2013

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/branches/mobile-2013@721 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

621e5ba8

11 Jul, 2013 4 commits

exceptions for predicted protein were added · 2431455e

Alisa Muraveva authored Jul 11, 2013

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/branches/mobile-2013@720 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

2431455e

exceptions table for original_protein was added · 9da75638

Alisa Muraveva authored Jul 11, 2013

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/branches/mobile-2013@719 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

9da75638

Start codon always Met. Warning changing · cb1436f0

Alisa Muraveva authored Jul 11, 2013

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/branches/mobile-2013@718 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

cb1436f0

Some math errors were fixed · 4b5c0b2c

Alisa Muraveva authored Jul 11, 2013

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/branches/mobile-2013@717 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

4b5c0b2c

10 Jul, 2013 4 commits

Differences in lrg.py (making transl_except) · 612428a6

Alisa Muraveva authored Jul 10, 2013

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/branches/mobile-2013@716 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

612428a6

At last, we added Warning Messages! · ead5d896

Alisa Muraveva authored Jul 10, 2013

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/branches/mobile-2013@715 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

ead5d896

Now we can find and substitute new uncanonical acids in protein_variant :) · 1cf22acb
Alisa Muraveva authored Jul 10, 2013
```
git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/branches/mobile-2013@714 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1
```
1cf22acb
Now we can find and substitute new uncanonical acids in protein_variant :) · f1471f47
Alisa Muraveva authored Jul 10, 2013
```
git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/branches/mobile-2013@713 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1
```
f1471f47

09 Jul, 2013 3 commits

delete end position of transl_excepy in variantchecker.pyand genbank.py · 8f5373dc
Alisa Muraveva authored Jul 09, 2013
```
git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/branches/mobile-2013@712 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1
```
8f5373dc

protein spliting after * in variantchecker.py · aecdbfd8

Alisa Muraveva authored Jul 09, 2013

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/branches/mobile-2013@711 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

aecdbfd8

* substitution in variantchecker.py · ee360d37

Alisa Muraveva authored Jul 09, 2013

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/branches/mobile-2013@710 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

ee360d37

08 Jul, 2013 2 commits

some documentation added in variantchecker.py · c4baab90

Alisa Muraveva authored Jul 08, 2013

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/branches/mobile-2013@709 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

c4baab90

Two functions to change txTables were added in variantchecker.py · 5414f36b

Alisa Muraveva authored Jul 08, 2013

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/branches/mobile-2013@708 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

5414f36b

05 Jul, 2013 1 commit

create_exception was added in genbank.py file in right places · 127dca16

Alisa Muraveva authored Jul 05, 2013

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/branches/mobile-2013@707 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

127dca16

04 Jul, 2013 4 commits

create_exception function was added to genbank.py file · bf5b0efc

Alisa Muraveva authored Jul 04, 2013

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/branches/mobile-2013@706 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

bf5b0efc

Fix order in post-install script · 94c9e8b0

Alisa Muraveva authored Jul 04, 2013

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/branches/mobile-2013@705 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

94c9e8b0

Merge trunk r702-703 · ea7c7ea5

Vermaat authored Jul 04, 2013

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/branches/mobile-2013@704 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

ea7c7ea5

Fix missing fields in example config · e1aeaa14

Vermaat authored Jul 04, 2013

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@703 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

e1aeaa14

03 Jul, 2013 1 commit

Start branch for Mobile 2013 summer project · 9765e855

Vermaat authored Jul 03, 2013


git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/branches/mobile-2013@702 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

9765e855

18 Jun, 2013 2 commits

Open development for 2.0.beta-28 · 0bc53d34

Vermaat authored Jun 18, 2013

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@701 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

0bc53d34

Release 2.0.beta-27 · 5d42d883

Vermaat authored Jun 18, 2013

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@699 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

5d42d883

12 Jun, 2013 1 commit

Limited cache lifetime for mrna-protein links · 5c5f8dea

Vermaat authored Jun 12, 2013

Rework the caching of transcript<->protein accession number links. If no
link is reported by the NCBI, this is now also cached. For these type of
negative links and the normal links, separate cache lifetimes can be
defined.

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@698 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

5c5f8dea

21 May, 2013 1 commit

Paper: exon deletions and fuzzy offsets · 4762914d

Vermaat authored May 21, 2013

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@697 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

4762914d

09 Apr, 2013 5 commits

No weird instance attribute names starting with double underscore · 206c51d9
Vermaat authored Apr 09, 2013
```
git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@694 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1
```
206c51d9

Switch order of migrations 011 and 012 · 6a2299a3

Vermaat authored Apr 09, 2013

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@693 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

6a2299a3

Open development for 2.0.beta-27 · fe567b67

Vermaat authored Apr 09, 2013

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@692 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

fe567b67

Release 2.0.beta-26 · 3076481a

Vermaat authored Apr 09, 2013

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@690 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

3076481a

Add help link for each module in the web interface · 304a8ab5

Vermaat authored Apr 09, 2013

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@689 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

304a8ab5

08 Apr, 2013 1 commit

Proposal for student project: MoBiLe 2013 · 945a659b

Vermaat authored Apr 08, 2013

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@688 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

945a659b