Commits · 6ead8b65a08509600a06edf67064a1daecdebc91 · Mirrors / mutalyzer

Jan 31, 2012

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

Jan 22, 2012

Added rolling for insertions and deletions. Needs checking. · bfc3f7cb

Laros authored 13 years ago


git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@442 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

bfc3f7cb

Jan 15, 2012

- Modified the LongestCommonSubstring() function to give the end locations and · 7ecc60eb

Laros authored 13 years ago

  the length of the longest common substring in two sequences.
- Changed the splitting on the longest common substring for direct slicing
  based on the new return values of LongestCommonSubstring().
- Added the removal of the lcs from the leftVariant and the lcp from the
  rightVariant in the inversion part of the DNA_description() function.


git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@441 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

7ecc60eb

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