Commits · 772d6c2f59fb3cf2070436fe5cd9d7b2c2fbdfcf · Mutalyzer / mutalyzer2

26 Jul, 2013 2 commits

Alisa Muraveva authored Jul 26, 2013

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/branches/mobile-2013@741 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

772d6c2f

The color of noncanonical amino acids was changed and the column was added to... · b1fe77c5

Alisa Muraveva authored Jul 26, 2013

The color of noncanonical amino acids was changed and the column was added to 'Translation exceptions for predicted protein' table 

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/branches/mobile-2013@740 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

b1fe77c5

25 Jul, 2013 1 commit

Some stupid mistakes were fixed · 2e1fe445

Alisa Muraveva authored Jul 25, 2013

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/branches/mobile-2013@739 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

2e1fe445

24 Jul, 2013 1 commit

Updated fix for features partially located on external reference · 244b7001

Vermaat authored Jul 24, 2013

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/branches/mobile-2013@738 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

244b7001

23 Jul, 2013 4 commits

It partially works with strange coordinates (with links to other reference) · 117487ad
Alisa Muraveva authored Jul 23, 2013
```
git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/branches/mobile-2013@737 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1
```
117487ad

Some grammar mistakes were fixed · d774c18f

Alisa Muraveva authored Jul 23, 2013

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/branches/mobile-2013@736 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

d774c18f

references were added in legend table · f6565c21

Alisa Muraveva authored Jul 23, 2013

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/branches/mobile-2013@735 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

f6565c21

some mistakes were fixed · 1b692ea1

Alisa Muraveva authored Jul 23, 2013

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/branches/mobile-2013@734 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

1b692ea1

22 Jul, 2013 3 commits

mRNA ID in LEGEND · 51aaa4d8

Alisa Muraveva authored Jul 22, 2013

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/branches/mobile-2013@733 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

51aaa4d8

Recognize Ensembl ID by ENS prefix · 9867966a

Vermaat authored Jul 22, 2013

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/branches/mobile-2013@732 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

9867966a

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