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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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Fixes #74.


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The old way of using the configuration file was by instantiating a Config
object which read the file. This instance was passed to every function and
object that might need it.

The new way is by simply calling config.get('name') to get the configuration
value for 'name'. This lazily reads the configuration file and the contents
are cached for future calls.


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This is a rebase of commit r202 to the current branch. Please not that this
is not a very clean implementation and still contains several Todo's. But
they don't affect functionality outside issue #38.

Please see the issue for more information.



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reference.



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- Warning can also be shown for a roll on the reverse strand.
- Only the roll warning about the selected strand is shown.
- Roll of insertion where the inserted sequence changes now has correct
  description on the reverse strand.



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Locations and python paths are correct with respect to the setup.py file.
For development, use
  svn up && python setup.py develop
and for deployment use
  svn up && sudo python setup.py install



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- Added error recovery to batch daemon.
- Added example init script for batch daemon.


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This merges the first part of exon-deletions-branch (the second part concerns
unknown exon offsets, denoted with the ? character). Except that we now keep
track of removed splice sites in the transcript, instead of in the Mutator
instance. I guess the latter was better, so we will probably revert to storing
this in the Mutator instance.

Issue #35.



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- Ditched use of web.session, just use web.cookies.
- Added detection of configuration file location.
- Removed ./var directory, everything is now in standard locations, but also
  configurable.
- Added more standard version management.



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This commmit brings in some bugs that take some time to fix. It will be
recommited in a new branch 'exon-deletions-branch' in a few moments.



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src/Modules/Mutator.py:
- Added method (add_removed_sites) to give splice sites that should be
  ignored. Now newSplice() does not process these splice sites.

src/Mutalyzer.py:
- Handle whole-exon deletions and exon-fusions by removing splice sites
  where we can. A notice is printed in this case. Otherwise, if splice
  sites are hit in some other way, no protein product is predicted. This
  fixes Trac issues #35 and #36.



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src/Mutalyzer.py:
- Output info message in case of a roll that was rolled back because it
  crossed exon boundaries.

src/Modules/Output.py:
- Fix: output messages from (and including) the level specified in the
  configuration.



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