mRNA and CDS fields). Added a SNP converter. Implemented a first check for
variants that hit splice sites. Added a chromosomal position for NC slices.
Added a check for the use of intronic positions in a transcript reference 
sequence.

mutalyzer.conf:
- Added variables for splice site mutation detection.

Mutator.py:
- Merged the restriction sites (added, deleted) in one object.

Output.py:
- Changed the return type of getIndexedOutput() and getOutput() from None to
  an empty list for convenience.

Config.py:
- Added variables for splice site mutation detection.

GBparser.py:
- Completely rewrote this module.
  - Will now collect all CDS, mRNA and exon information.
  - Tries to match a CDS and mRNA based upon the range.
    - When this succeeds, try to match on protein, locus tag or product name.
    - If all fails and there is only one option left, link it.
  - Will remove genes that are not fully annotated (half outside the record
    for example).

Retriever.py:
- Added a snpConvert() function.
- Added a check for uploaded records or slices that have no sequence in them
  (a complete contig for example).

GenRecord.py:
- Added variables to cope with chromosomal coordinates.
- Added a toChromPos() function to convert a g. notation to a g. on a
  chromosome.
- Added a addToChromDescription() function to generate a chromosomal
  description of a variant.
- Modified some warnings concerning missing mRNA or missing CDS.
- Added a checkIntron() function that gives a warning when a variant hits a
  splice site.

Web.py:
- Added a nomenclature version variable.
- Added a urlEncode() function to generate valid links.

File.py:
- Made the getMimeType() function public.

Mutalyzer.py:
- Added a __intronicPosition() function that checks whether the user used an
  intronic position.
- Added checks for illegal use of intronic positions.
- Fixed a bug in the __toProtDescr() function.
- Added more checks for the translation and transcription of transcripts.
- Added a better CDS start site mutation detection.
- Added a chromosomal description if available.
- Added more information to the legend (product and linking method).
- Merged the restriction sites (added, deleted) in one object.

handler.py:
- Added guessing of mime types for downloadable files (it used to default to
  text/plain).

index.py:
- Added a snp() function to interface with the snp() function of the Retriever.
- Added a checkForward() function to accommodate for HTTP GET links.
- Removed the `version' variable from all functions, it is now moved to the
  menu.

check.html:
- Modified to cope with the new functionality.

gbupload.html:
- Restructured the layout.

snp.html:
- New page for the SNP converter.

menu.html:
- Modified to cope with the new functionality.

style.css:
- Modified to make some better tables and helper boxes.

index.html:
- Completely rewritten it.

parse.html:
- Restructured the layout to make it uniform with the name checker.



git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@73 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

Mutalyzer.py
    * Updated the batch output generator

handler.py
    * Make result file downloadable

webservice.py
    * Make webservice compatible with the new Mapper module

VarInfo.py
    * Updated functions to reflect new Mapper module

index.py
    * Added a redirect option to move get messages to the check form
    * Updated check to use the Session from redirect
    * implented __checkInt to catch user errors in upload
    * Added a progress option to get updates about batch progress
    * updated batch to show batch progress after submit

#Templates
interface.js
    * Added the AJAX request to get a batch progress counter
    * Started the linkify to change all Mutalyzer instances to clickable links

batch.html
    * Added a hidden form to support the batch progress

gbupload.html
    * Display Errors 



#Modules
Output.py
    * Added the getMessagesWithErrorCode

LRGParser.py
    * Made the seq a BioSequence for the restriction function

Retriever.py
    * Added BatchFlags support to prevent jobs to hang at the same problem
    * Updated some returnvalues to reflect errors

Scheduler.py
    * Implemented the Flags to skip or alter other batch entries
    * Cleaned up the nameCheckerbatch significantly
    * Added a try/except clause around the namechecker to prevent batchhangs
    * Changed output fileextension to txt

Mapper.py
    * Cleaned up Module
    * mainTranscript function updated to reflect webservice needs
    * Correct errors when retrieving fields from DB in _FieldsFromDb

Db.py
    * Impemented entriesLeftForJob to get info about how a job is doing
    * Added updateBatchDb and skipBatchDb to skip/alter batch entries




git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@71 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

		- update errorcodes.txt
		- rewrite some webservice.py functions
		- File.py ods files are not read in correctly. Temp file deleted before it
			can be used

    
CHANGES:
		- mutalyzer.conf
				Added pidfile reference
				Added Output Headers for the Batch Jobs

		- Db.txt
				Updated the Db.txt file so that it reflects the database changes
					* BatchJob now contains an Arg1 attribute, which is used by the
						Conversion Batch to store the build version. This could be
						changed to use the Filter Field.
					* Dropped the Var table
					* BatchQueue -> AccNo, Gene, Variant are dropped and replaced by
						single column input. This fields contains a single full
						mutalyzer variant description.

		- Install.txt
				Added the python-daemon dependency

		- handler.py
				Added a downloads handler for the old and new batch files
				Other handlers are changed so the filter for extensions now matches the
				trailing characters

		- webservice.py
				Made the functions compatible with the new Mapper.Converter class
				*** This webservice.py can use a bit more structure ***

		- index.py
				Moved a lot of logic from the index file to the Mapper.py module
				Implemented the batch handler, which has multiple entry points
				positionConverter now uses the Mapper.Converter class

		- BatchChecker.py
				Fixed the multiprocessing bugs. Now uses python-daemon to spawn a
				process and uses the var/batch.pid as a lockfile for the process

		---- Modules

		- Ouput.py
				Added getSoapMessages, which returns Soap compatible Messages for over
				the wire
				Added getBatchMessages, which returns messages above %level and filters
				the ParseError to one line
		
		- LRGparser.py
				Included the usage of transcription.translate and transcribe for the
				main transcript

		- Config.py
				Added the Batch Headers to the configfile
				Added a Batch Config object for the PID file

		- Scheduler.py
				Added the SyntaxCheck Batch
				Added the Conversion Batch
				Have the BatchProcesser read the Argument from the Batch
				Changed outputfile format to csv

		- File.py
				Changed the csv sniffer to drop the ":" delimiter in batch entries
				Updated some Job logic to detect all lines with basic errors

		- Mapper.py
				Practically a complete refactor of the module
				Added the Converter class for chromosome to c and back conversions
				Added a SoapMessage class which instances can be send over the wire
				Updated the Mapper.Mapping class to use SoapMessage messages
				Basically create correct mappings between c 2 chrom 2 c [tested]
				Reduced the number of Database calls needed significantly

		- Db.py
				Implemented getAllFields to retrieve complete dataset of Fields of
				intereset, this reduced the number of database calls
				Updated the Db logic to encompass the new Batch Job logic:
						Input entries are 1 field
						Jobs have a type
						Jobs can have arguments (1 at the moment, use BITFLAGS)


		---- Templates

		REMOVED 
				- batchCheck.html				-> All Batch jobs are united in batch.html
				- batch_convert.html		->  								"
				- convert.html					-> Replaced by converter.html

		CHANGED
				- batch.html
						Included big file type help
						Made template compatible with the three different batchTypes

				- gbupload.html & menu.html
						Fixed an onload javascript bug which caused a stream of javascript
						errors on pages other than gbupload
		
				- interface.js
						Added the changeBatch and toggle_visibility functions

		ADDED
				- downloads
						Added example download files for old & new batchfiles


NOTES:
		- change permission on var/batch.pid to have apache read/write it
		- 



git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/branches/lrg@67 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

list with priorities, and all output is stored in a dictionary. This dictionary
can be read at a later time.
The Retriever module is changed to accommodate for uploaded GenBank files and
slices of a chromosome.
A Scheduler was added for batch checking.

mutalyzer.conf:
- Added variables for the Retriever module:
  - maxDldSize, minDldSize ; Maximum and minimum sizes for slices and uploaded 
    GenBank files.
- Added variables for the Output module:
  - loglevel, outputlevel ; Specify default verbosity levels for logging and 
    output.
- Added variables for the Scheduler module:
  - processName ; Name of the running scheduler.

Db.txt:
- Added information on how to create the newly used tables GbInfo, BatchQueue
  and BatchJob.

errorcodes.txt:
- Short description of the error codes used in the Output module.

webservice.py:
- Added a Complex class to test more complicated return types (see the web_dev
  branch).
- Modified the code to work with the new Output module.

index.py:
- Made a first upload page.

Mutalyzer.py:
- Modified the code to work with the new Output module.

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

Variant_info.py:
- Modified the code to work with the new Output module.

GenRecord.py:
- Added documentation.

Mutator.py:
- Modified the code to work with the new Output module.

Misc.py:
- New file, used for generating unique IDs.

Parser.py:
- Made a change to the definition of an UD accession number.
- Modified the code to work with the new Output module.

Scheduler.py:
- Made a batch checker scheduler.
  - isDaemonRunning() ; See if we need to be started.
  - process() ; Start the batch checker.
  - addJob() ; Add jobs to a queue in the database.

Output.py:
- Added a Message class to store all debug, info, warning, error and fatal
  messages.
  - If a message is given that exceeds the configured log level, it will be
    logged immediately.
- A function is added to the Output class to read all messages that exceed a 
  certain verbosity level.
- A function is added to create a named list as an output node.
- With the getOutput function the content of this list can be retrieved.

Config.py:
- Several sub-classes were added for each configurable module.

Db.py:
- Added documentation.
- Added functionality that is used by the Retriever module.
- Added functionality that is used by the Scheduler module.

Retriever.py:
- Added functionality to be able to use custom GenBank files and chromosome
  slices.
  - Information on these created files are stored in a database to be able to
    re-create them when the cache is cleaned.
  - The hash of each file is stored for error detection.

BatchChecker.py:
- A wrapper that is called either from the addJob() function from the Scheduler
  module, or from cron. It dispatches a background process that processes the
  batch jobs.

gbupload.html:
- Test template for uploading files (copied from Mutalyzer 1.0.4).

sp.py:
- Some test with a complex return type.

download.html:
- Did some first tests with a METAL template.



git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@26 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/branches/web_dev@24 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

The classes Mutator, Output and Db are now derived classes of Config. The
class Retriever is a derived class of Output. This reduces the amount of
code and variable passing significantly.

mutalyzer.conf:
- Converted the dbName variable to a dbName list, to accommodate for more than
  one database.
- Added variables flanksize, maxvissize and flankclipsize for the visualisation
  in Mutator.py (instead of the previous alignment).

Mutalyzer.py:
- Resolved the range-swap issues.
- Resolved the reverse-complement (cosmetic) issues.
- Fixed a cosmetic bug in the __bprint() function.
- Added a new function __nsplice(), to accommodate for a CDS extension.
- Added a function __toProtDescr(), that gives a protein description in case
  of a simple substitution.
- Added functionality for n. m. and EST notations.
- Added functionality for other species (translation tables).
- Corrected the roll-rule for insertions.
- Added fallbacks for missing CDS and mRNA lists and positions (for an EST for
  example).
- Added an input check for wrong gene symbols.
- Added a temporary exception for in frame stop codons.

webservice.py:
- Added the private functions __checkBuild(), __checkChrom() and __checkPos()
  that do routine checks in a number of services.
- Added a 'build' variable to getTranscripts(), getTranscriptsRange() and
  getGeneName()
- Added exceptions that raise a Fault() object to make the client receive a
  SOAP exception.

UCSC_update.py:
- Added functionality for more than one database.

Variant_info.py:
- Added functionality for more than one database.
- Added functionality to deal with non-coding transcripts.

Genrecord.py:
- Made a RecordObj() object that consists of the old 'genelist' dictionary, 
  combined with 'mol_type' and 'organelle' variables. Also, a fake gene named
  'source' is included to accommodate for sequences that do not contain any
  annotated genes (an EST for example).
- The Locus object is extended with a 'txTable' variable to accommodate for
  different organelles (mitochondria) and other species.

Mutator.py:
- Replaced the alignment visualisation by a home-made one. Also see the
  variables that were added to the configuration file to alter the behaviour of
  this visualisation.
- Modified the shiftpos() function when inserting something on a splice site
  boundary (now it extends the exon).

Output.py:
- Minor modifications for the new inheritance scheme.

Config.py:
- Minor modifications for the new inheritance scheme.

Db.py:
- Minor modifications for the new inheritance scheme.
- Added functionality to handle multiple databases.
- Added an isChrom() function, used by the webservices check functions.

Crossmap.py:
- Made a change in the usage of the '__STOP' variable. It is set to
  transcription stop if there is no stop codon present. This makes conversion
  to an n. notation trivial.

Retriever.py:
- Minor modifications for the new inheritance scheme.
- Added a check for invalid accession numbers (or versions).
- Added a check for erroneous genbank files that can occur when the NCBI is
  overloaded. The erroneous file is purged and the user can try again.

templates/sp.py
- Modified the sample code to accommodate for the new 'build' variable.



git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@20 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

wrote documentation.

Made an accumulative mapping info table, this requires regular polling of new
data from the UCSC:
- Added:
  - install.sh: A preliminary installation script. Now only used for cron 
    entries.
  - Db.txt: Some loose documentation on how to make the new mapping table, to 
    be incorporated with an installation script.
  - src/UCSC_update.py: The update program, to be called from cron each day.
- Modified:
  - mutalyzer.conf: Added variables needed for the remote database of the UCSC.
  - Db.py: Rewritten nearly every SQL query to work with the new mapping table
    and to be able to download and import updates from the UCSC.
  - Config.py: Modifications to work with the new configuration variables.

Added:
- templates/sp.py: A webservice client template script.
- templates/download.html: The download page for developers.

Modified:
- Install.txt: Added more depenencies.

Switched to soaplib for the generation of a WSDL file. Webservices are now
published by adding functions to the MutalyzerService class in webservice.py,
each function should have a soapmethod decorator to specify the types.

Modified:
- handler.py: To work with soaplib.
- webservice.py: 
  - Put everything in a class to make soaplib able to generate a WSDL file.
  - Added the varInfo() webservice (calls the Variant_info script).
- index.py: Added documentation.
- Mutator.py: Added documentation.
- Web.py: Added documentation.
- Mutalyzer.py: Added generation of a new description in g. and c. notation.
- Db.py: Modified the get_Transcripts function to be able to work with
  overlapping and non-overlapping ranges.



git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@16 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

Added:
- Web.py: A module with some general functions used by the interfaces.
  - A version (this is deliberately kept out of the config file).
  - A run() wrapper that returns standard output of any function as a string.
  - A tal() function that parses a TAL template.
  - A read() function that returns the input of a file.

Modified:
- Install.txt: In the apache config, a PythonPath must be set now (dynamically
  setting it did not give consistent output).
- handler.py : Cleaned the source by using the Web class.
- webservice.py : Cleaned the source by using the Web class.
- index.py : Cleaned the source by using the Web class.



git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@15 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

The main structure is as follows:

/                     ; Root of the installation.
  - Install.txt
  - Todo.txt
  - Obsoleted.txt
  - mutalyzer.conf
  - var/              ; Variable data.
      - cache/
      - mutalyzer.log
  - templates/        ; HTML, XML, JavaScript, etc.
  - src/
    - Mutalyzer.py
    - Variant_info.py
    - Services/       ; Webservices.
    - Clients/        ; Example clients for webservices.
    - Modules/        ; The core modules.
    - Interfaces/     ; Interfaces to mod_python.

Apart from changes that were needed to deal with this new structure, no changes
in the code were made.


git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@14 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

- Todo.txt.
- handler.py: A general handler for mod_python. This handler dispatches
  SOAP services and a normal HTML publisher. Furthermore, it is able to handle
  raw requests to dump HTML or XML files. This handler is TAL enabled.
- webservice.py: A publisher for webservices. When a new webservice is
  added, this is the entrypoint for the server side (just like index.py, add
  a function).
- getTranscripts.py: A webservice that reports all transcripts that overlap 
  with a certain genomic position (chomosome, position). 
- getGeneName.py: A webservice that finds the gene name of a given transcript.
- service.wsdl: This is the definition of the interface for webservices.
  A client must download this file and parse it to obtain a programming 
  interface, then the client can use this interface just like any local 
  function.
- Obsoleted.txt: A list of things that will be deleted in the future (but are
  still functional for backwards compatibility).
- client/sp.py: A test client for the two webservices.

Renamed Main.py to Mutalyzer.py.

Modified:
- mutalyzer.conf: Added a configurable date prefix for logging.
- Install.txt: 
  - To reflect the difference in configuration of apache to work with the new 
    handler (requires less configuration).
  - Added TAL as a new dependency.
- html/check.html: Made it a full TAL template. Title, version and output are
  now separated from the HTML design.
- Mutator.py: Made the shiftpos() function public, this is needed for insertion
  checking.
- Parser.py: Updated the comments.
- Variant_info: Made all internal functions private.
- Output.py: Updated the comments.
- Config.py: Modified to reflect the changes in mutalyzer.conf.
- Db.py:
  - We now keep the handle to the database open until the object is deleted.
  - Added a destructor that closes the handle to the database.
  - Added getTranscripts(): Get a list of transcripts, given a chromosome and a
    position on that chromosome.
  - Added get_GeneName(): Get the gene name of a given transcript.
- Retriever.py: Updated the comments.
- Crossmap.py:
  - Made a patch that handles a CDS start on the first position of the 
    transcript.
  - Added more unit tests.
- index.py: 
  - Added a switch for older versions of LOVD, to generate the expected output 
    in Variant_info.
  - Made this publisher compatible with TAL.
- Mutalyzer.py: Made all internal functions private.



git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@13 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

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

put it in a new module named Config. This is done because an other new module
named Db also needs the configuration file.

De file Db.py is new and contains a function that interfaces to a MySQL 
database. This database is used for the mapping of NM to NP accession numbers.

The file mutalyzer.conf now has two more options: a MySQL user name and a 
database name. 

Started the documentation of a fresh installation, see Install.txt for more
details.

In Mutator.py: Added a function that calculates the positions of splice sites
after mutatations.

In Scheduler.py: Added some code (still in comment) that can parallelise jobs
by using treads and detecting the number of processors present on the host.



git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@5 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

- Crossmap.py does the conversions g. -> c. or n. and vice versa.
- Retriever.py fetches a record from the NCBI or the cache.
- Main.py contains a couple of functions to test Crossmap.py and Retriever.py.
- clean.sh is a script that removes cache/* and src/*.pyc.
- mutalyzer.conf contains configuration variables.

Make sure to call all functions from . (not ./src), otherwise relative paths
can no longer be used (now used in Retriever.py and mutalyzer.conf).


git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@2 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1