Commits · 1376c5249e40533837cd19805587439a1d044a36 · Mirrors / mutalyzer

Mar 01, 2012

Fix CDS start and stop in mapping database · 1376c524

Vermaat authored 13 years ago

During import of the NCBI transcript mappings, CDS start or stop positions
were not picked up for some transcripts (where these are on exon boundaries).

Bug reported by S Venkata Suresh Kumar.

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@490 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

1376c524

Feb 29, 2012

Typo · 160b3a06

Vermaat authored 13 years ago

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@489 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

160b3a06

Feb 21, 2012

Fix del with deleted sequence length as argument · 1b7c9c03

Vermaat authored 13 years ago

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@488 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

1b7c9c03

Feb 20, 2012

Open development for 2.0.beta-16 · 78bab4ad

Vermaat authored 13 years ago

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@487 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

78bab4ad

Release 2.0.beta-15 · 45a34156

Vermaat authored 13 years ago

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@485 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

45a34156

Added disclaimer and documentation. · 0e68e078

Laros authored 13 years ago

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@484 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

0e68e078

Unit tests for describe module · f143415d

Vermaat authored 13 years ago

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@483 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

f143415d

Implement copyright years as package constant · 0b8d5c14

Vermaat authored 13 years ago

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@482 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

0b8d5c14

Fix for EFetch Version 2.0 release · 7f26e9e0

Vermaat authored 13 years ago

Fetching genbank files was broken due to new default parameter values in the
efetch service. See http://www.ncbi.nlm.nih.gov/mailman/pipermail/utilities-announce/2012-February/000085.html

Also fix dbSNP converter web interface by properly logging IP address.

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@481 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

7f26e9e0

Feb 18, 2012

Added a standardised description length to the describe module. · 15f74803

Laros authored 13 years ago

Added simple error handling for the description extractor.



git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@480 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

15f74803

Added the Variant Description Extractor as a web interface. · b8640a1f

Laros authored 13 years ago

describe.py:
- Module that provides the Variant Description Extractor functions.

__init__.py:
- Added an automated copyright year update.

website.py:
- Added the Variant Description Extractor web interface.

templates/descriptionExtract.html:
-  Template page for the Variant Description Extractor.

templates/snp.html:
templates/menu.html:
templates/converter.html:
templates/index.html:
templates/parse.html:
- Cosmetic changes.

Added a presentation.



git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@479 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

b8640a1f

Feb 16, 2012

Entrez dbSNP api suddenly returns other XML structure · 5f840e3f

Vermaat authored 13 years ago

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@478 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

5f840e3f

Feb 15, 2012

First version of an abstract for the ESHG 2012. · 2a2ccf76

Laros authored 13 years ago

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@477 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

2a2ccf76

Feb 01, 2012

Add chromosomal positions to getTranscriptsAndInfo webservice (#86) · 7957573b
Vermaat authored 13 years ago
```
git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@476 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1
```
7957573b

Added a new method for rolling a substring. · fbd397a5

Laros authored 13 years ago


git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@475 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

fbd397a5

Fix chromosome slicing on reverse complement · 4d27a0bd

Vermaat authored 13 years ago

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@474 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

4d27a0bd

Jan 31, 2012

Fix bug introduced with r471 · 7a5dfd01

Vermaat authored 13 years ago

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@473 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

7a5dfd01

Describe NOP variants with = (#88) · 0c5f32ea

Vermaat authored 13 years ago

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@472 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

0c5f32ea

Reference sequence info in runMutalyzer response (#87) · 7d39cbf0

Vermaat authored 13 years ago

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@471 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

7d39cbf0

Unit tests for GI references · 6ead8b65

Vermaat authored 13 years ago

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@470 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

6ead8b65

Jan 30, 2012

Finished the HGVS DNA description prototype. · 14bb6c53

Laros authored 13 years ago

- Fixed the bug in the insertions / duplications code.
- Added documentation and pointers on how to integrate this as a module.
- Added a wrapper for the recursive function.



git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@469 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

14bb6c53

Add checkSyntax to SOAP tools · c031d6c7

Vermaat authored 13 years ago

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@468 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

c031d6c7

Fix mapping info for genes mapped to more than one chromosome · 5896fe3b

Vermaat authored 13 years ago

Some genes (e.g. in the PAR) are mapped on both the X and Y chromosomes, but
are (apart from the chromosome names) indistinguishable from transcripts that
are mapped using different contigs. Transcripts of the latter type should be
merged, those of the former type should not be merged.

Our fix consists of only including exons where positions are consistent with
the transcript mapping and allowing transcripts to be mapped more than once,
but only to two different chromosomes.

This fixes #82.

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@467 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

5896fe3b

Jan 29, 2012

- Made a member function of RawVar() called description() that gives the HGVS · c57f8b86

Laros authored 13 years ago

  description of the stored raw variant.
- Made a function that returns an allele description given a list of raw
  variants.
- Removed the hgvs member variable from RawVar().
- Removed the HGVS description generation from DNA_description().
- Started refacoring the DNA_description() function.

TODO: rolling for insertions and duplications is not working properly.



git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@466 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

c57f8b86

Finished generating the allele description. · f7108427

Laros authored 13 years ago


git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@465 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

f7108427

Jan 28, 2012

Found a good criterium for the recursion, started adding an allele description · 70b4ff98

Laros authored 13 years ago

as a list of objects.


git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@464 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

70b4ff98

Jan 27, 2012

Use more descriptive error messages in position converter (#85) · 1cd31294
Vermaat authored 13 years ago
```
git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@463 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1
```
1cd31294

Add logging to all website entry points (#84) · eb151384

Vermaat authored 13 years ago

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@462 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

eb151384

Jan 26, 2012

Also check for httplib.HTTPException in Entrez API call · 08c162fc

Vermaat authored 13 years ago

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@461 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

08c162fc

Fix bug in Entrez API call retry logic · 8d4fdfe5

Vermaat authored 13 years ago

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@460 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

8d4fdfe5

Open development for 2.0.beta-15 · 0ca4e27e

Vermaat authored 13 years ago

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@459 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

0ca4e27e

Release 2.0.beta-14 · 47c11c10

Vermaat authored 13 years ago

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@457 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

47c11c10

Fix unit test for commit -r449 · 8bdac8dd

Vermaat authored 13 years ago

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@456 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

8bdac8dd

Do not crash on non-numeric locus tag end, fixes #81 · 38f90d91

Vermaat authored 13 years ago


git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@452 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

38f90d91

Add getTranscriptsMapping webservice method · dba5b193

Vermaat authored 13 years ago

For use by LOVD (NGS variants import, Jerry Hoogenboom), implement the SOAP
webservice method getTranscriptsMapping. The calling signature is the same as
for the existing getTranscriptsRange method, but the new method returns more
than just the transcript names.

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@451 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

dba5b193

Add rCRS NC_012920.1 as chrM for hg19 · 6ed18b73

Vermaat authored 13 years ago

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@450 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

6ed18b73

Jan 25, 2012

Add note and fix spacing in TAL template · 1f849c97

Vermaat authored 13 years ago

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@449 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

1f849c97

Open development for 2.0.beta-14 · 90134b66

Vermaat authored 13 years ago

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@448 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

90134b66

Release 2.0.beta-13 · 8fea80ff

Vermaat authored 13 years ago

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@446 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

8fea80ff

Fix LRG reference sequences · 5f77ecaf

Vermaat authored 13 years ago

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@445 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

5f77ecaf