can be sent to this object, which sends errors and explicit logging messages
to a log (defined in mutalyzer.conf) and warning messages to standard output.
Behaviour of this object may change in the future, adding severity and logging
above a certain severity level is one option that would increase debugging 
possibilities.
- NiceName() returns a short description of the calling program (we can not 
  use the default __name__ here.
- ErrorMsg() Print the nice name of the calling module, an error message and 
  log it. Also increase an error counter.
- WarningMsg() Print the nice name of the calling module and an error message.
  Also increase a warning counter.
- LogMsg() Only log the message (nice name of the calling module and the 
  message itself).
- Summary() Give the number of errors and warnings.
- A unit test is also defined (it does not do much at this moment).

Added index.py: The web interface to mutalyzer, it is dependent on mod-python,
we chose for this interface to eliminate the need for php. Also apache is now
added to the list of dependencies. The configuration of mod-python is described
in Install.txt.

GenRecord.py: 
- Moved the splice() function to Main.py. 
- Added an exon list to the Plist class. This list can be used as a fallback
  in case the mRNA tag is missing from a GenBank file.
- Added an empty unit test.

Mutator.py:
- Added a standard alignment for visualisation. This will probably be replaced
  in newer versions.

Parser.py:
- Added functionality for the new output module.
- Made the parser gracefully return, instead of exit on a parse error. This is
  needed for the web interface.

Variant_info.py:
- Added functionality for the new output module. Note that output generated by
  this program should go to a different log, something for a future version.
- Fixed a bug that occurred when a CDS start or stop was on an exon boundary.

Main.py (heavily under development, names of functions are not very descriptive
  yet):
- Added functionality for the new output module.
- Fixed a bug in the roll() function, it returned a wrong value for forward
  genes.
- Added the function bprint(), it formats a large string to be printed in an
  insightful way (like GenBank does it), it also prints the offsets at the
  beginning of each line.
- Obsoleted the ErrorMsg() and WarningMsg() functions.
- Added constructCDS(), a function that is able to construct a CDS from an
  mRNA list, CDS start and CDS stop. In the future we would like to work 
  without a CDS list, so this function will be obsoleted.
- Added the splice() function (from GenRecord.py).
- Made a function rv() that is able to process a RawVar. This function is
  seperated from the ppp() function to be able to work with an allele 
  description.
- Added splicing.
- Added translation to a protein.
- Added a function rrr() which is to be called from Main.py itself or from 
  index.py.

Config.py:
- Added a log variable for Output.py.

Crossmap.py:
- Fixed a bug concerning genes where the entire CDS is in one exon.
- Added more uncertainty handling.

Retriever.py:
- Added functionality for the new output module.
- Added handling of accession numbers with no version. It downloads the latest
  version, and gives a warning.



git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@10 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1