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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.


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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.


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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.


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Added simple error handling for the description extractor.



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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.



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- 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.



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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.


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  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.



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as a list of objects.


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