git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/branches/refactor-mutalyzer-branch@280 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@279 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@112 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

distribution as it is under heavy development.

Most modules will have minor changes because of a difference in set up of both
the Db and Config module.

install.sh:
- Added functionality to enable the cron restart of the Batch Checker.
- Added the auto-generation of a .htaccess file.
- Added permission settings.

mutalyzer.conf:
- Added configuration options for the Scheduler, File and GenRecord modules.

Db.txt:
- Described how to make the new ChrName tables for hg18 and hg19.

errorcodes.txt:
- Added classifications to the messages.

doc:
- Made a set up for the documentation.
  TechnicalReference:
  - This will be a technical document that describes the internals of the
    project. It is only meant for developers.
  API:
  - This is a description of the API, it is auto generated by the mkapidoc.sh
    script. Also only meant for developers.

Mutalyzer.py:
- Added a new roll function that will always find both boundaries.
- Implemented a new protein naming scheme.
- Fixed the trimming of a delins.
- Rewrote the processing of a variant. 
  - Moved post processing of the GenBank record to the GenRecord module.
  - Moved the crossmapper instance to the GenBank module, to make one instance
    per transcript variant.
  - Moved the naming of a variant to the GenBank module, as is strongly
    interacts with the crossmapper instance.
- Moved the constructCDS function to the GenRecord module.

handler.py:
- Added functionality for the batch checker (retrieve results).
- Added functionality for the genbank uploader (retrieve GenBank files).

webservice.py:
- Modified to work with the new Db module.

UCSC_update.py:
- Modified to work with the new Db module.

GenRecord.py:
- Replaced the dictionary structure with a nested list structure to make
  iteration more convenient.
- Added names to the Locus and Gene objects.
- Added all information needed to do a crossmapping in the Locus object.
- Wrote functions to find Loci and Genes.
- Wrote a function that expands a description of a variant (coupled to a Locus).

Mutator.py:
- Added documentation.

Parser.py:
- Added documentation.

Web.py:
- Added documentation.
- Added a function that checks whether a string is an e-mail address.

Scheduler.py:
- Implemented a batch scheduler that uses a MySQL database for queueing.

File.py:
- Implemented a CSV, XLS and ODS parser for use in the Scheduler module.

Output.py:
- Added documentation.

Mapper.py:
- Modified the complex object initialisation.

Config.py:
- Made subclasses to configure the separate modules.

Db.py:
- Added documentation.
- Split the Db modules into different classes, according to functionality, they
  all inherit the query function from the Db base class.
- Added chromosome accession number to name conversion functions and vice versa.
- Added functionality for the batch checker.

Crossmap.py:
- Added documentation.

Retriever.py:
- Added documentation.
- Added fall back functionality when searching for a gene.

index.py:
- Added a batch submit interface.

batch.html:
- The layout of the batch submit interface.



git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@30 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1