git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@498 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@497 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@496 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

For UD slices we also generate g. descriptions on the chromosome reference. We
now also apply the roll rule there and use correct ranges and sequences on the
reverse strand. Fixes #75.


git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@495 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@494 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@493 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@491 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

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

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

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

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

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

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

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

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

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

Added simple error handling for the description extractor.



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

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

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

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

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@476 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

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

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

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

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

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

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

- 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

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

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

  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

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

as a list of objects.


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

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@463 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

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

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

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

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

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

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