git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/branches/refactor-mutalyzer-branch@337 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/branches/refactor-mutalyzer-branch@335 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/branches/refactor-mutalyzer-branch@309 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/branches/refactor-mutalyzer-branch@293 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/branches/refactor-mutalyzer-branch@287 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/branches/refactor-mutalyzer-branch@285 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

fabfile.py:
- Automatic deployment to remote servers using Fabric.

extras/pre-install.sh:
extras/post-install.sh:
extras/post-upgrade.sh:
INSTALL:
- Refactoring of deployment.
- Better handling of installation vs upgrade.
- Install crontab.
- Install init script links.
- Restart Apache and Mutalyzer batch daemon.

bin/mutalyzer-webservice.wsgi:
bin/mutalyzer-website.wsgi:
- Moved WSGI interfaces from mutalyzer package to bin directory.
- Fixed use of built-in webserver.

extras/apache/mutalyzer.conf:
- Use /var/www/mutalyzer/base symlink for static files.



git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/branches/refactor-mutalyzer-branch@284 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/branches/refactor-mutalyzer-branch@265 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/branches/refactor-mutalyzer-branch@259 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/branches/refactor-mutalyzer-branch@258 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/branches/refactor-mutalyzer-branch@256 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/branches/refactor-mutalyzer-branch@255 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/branches/refactor-mutalyzer-branch@240 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/branches/refactor-mutalyzer-branch@224 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

- Moved mail.txt to templates/batch-mail.txt.
- Moved Obsoleted.txt and TODO into a README.
- Move mutalyzer.sql into INSTALL.



git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/branches/refactor-mutalyzer-branch@221 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

Mostly variant checker, now using exceptions on some places.



git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/branches/refactor-mutalyzer-branch@216 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

Install.txt:
- Added a dependency.

wsgi.py:
- Updated the release date and version number.

webservice.py:
- Added the function sliceChromosomeByGene(), which is used to get a reference 
  sequence, given a gene name, organism and a length of flanking sequences.
- Added templates for other GenBank upload functions:
  - upLoadGenBankLocalFile()
  - upLoadGenBankRemoteFile()
  - sliceChromosome()

wsdl-viewer.xsl:
- Modified the template to use stable internal links, instead of randomly
  generated ones. This is only an example, more links should be treated like
  this.



git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@162 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/branches/wsgi-branch@150 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

andfixed a bug in the GenBank parser.

version 2.0 bugs.txt, beta-feedback.pdf, suggestions.txt, beta-feedback.txt:
- Suggestions, bugs, todo lists, ...

mutalyzer.sql:
- Definitions of the mutalyzer database (to be merged with documentation).

Install.txt:
- Added the definition of the map table.

batch.html:
- Modified the help text to reflect the internal functionality.

Mutalyzer.py:
- Added the function __overSplice() that checks whether a splice site is 
  destroyed.
- Added a check for splice site destruction by calling aforementioned function.

webservice.py:
- Removed a typo (getGeneAndTranscipt() -> getGeneAndTranscript()).

Mutator.py:
- Reinstated the insertion of sequences on splice junctions to be added to the
  exon instead of the intron.
- Fixed a bug in the shiftpos() function.

GBparser.py:
- Fixed a bug that was triggered if the input is a minimally annotated one-exon
  gene.



git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@133 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

record. Added a legend for transcripts and proteins.

Install.txt:
- Added dependency information.

Mutalyzer.py:
- Rewrote the roll function to roll both ways at the same time.
- Rewrote the trim function (fixed a lcs bug).
- Moved the semantic checking of raw variants to separate functions.
- Removed lots of conversion code. We now convert to g. first and check this
  to all transcripts.
- Added protein descriptions for all transcripts.

GenRecord.py:
- Added more gathering information (locus tags, transcript- and protein 
  identifiers, etc.)
- Made a separate function that checks the gathered information after 
  retrieval. This can be used later on by the LRG parser.
- Modified the name() function to give better descriptions.

Parser.py:
- Added code to distinguish between GenBank records and LRG records.



git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@41 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

	python-soaplib   >= 0.8.1
which had been forgotten

Added to webservice.py:
	from Variant_info import Complex
because you use the Complex object in the SOAP decorator
	@soapmethod(String, String, String, String, _returns = Complex)
Changed some stuff in the documentation
Replaced the return type in the SOAP decorator of varInfo()
	@soapmethod(String, String, String, String, _returns = Complex)
The whole definition of varInfo() was added:
	+        import Variant_info
	+        from Modules import Web
	+        from Modules import Config
	+        from Modules import Db
	+        from Modules import Output
	+    
	+        C = Config.Config()
	+        D = Db.Db(C, "local")
	+        L = Output.Output(C, __file__)
	+    
	+        L.LogMsg(__file__, "Reveived request varInfo(%s %s %s %s)" % (
	+                 v1, v2, v3, v4))
	+
	+        W = Web.Web()
	+        result = Variant_info.main(v1, v2, v3, v4)
	+        del W
	+
	+        L.LogMsg(__file__, "Finished processing varInfo(%s %s %s %s)" % (
	+                 v1, v2, v3, v4))
	+
	+        del L
	+        del D
	+        del C
	+#        return str(result.split("\n")[:-1])
	+        return result
Added to webservic.py:
	+    @soapmethod(String, String, String, String, _returns = Complex)
	+    def mapInfo(self, v1, v2, v3, v4) :
	and so on
because varInfo() now lacks the ability to deal with the possibility that
the variant (v4) is not provided, this functionality has been transferred to
varMap() in Variant_map.py

Variant_info.py has also been copied to /src/Services
Variant_map.py has also been copied to /src/Services

In Variant_info.py a new Python object was defined:
	+class Complex(ClassSerializer) :
	and further
to return an object holding the information about a variant, and not a string
as was previously done, and which had to be parsed.
This also includes the type code definition with TC.struct:
	+Complex.typecode = TC.Struct(Complex, [ TC.Integer('startmain'),
	+                                        TC.Integer('startoffset'),
	+                                        TC.Integer('endmain'),
	+                                        TC.Integer('endoffset'),
	+                                        TC.Integer('start_g'),
	+                                        TC.Integer('end_g'),
	+                                        TC.String('mutationType') ], 'Complex')
	+
	+
Improved the following error messages:
	if not db_version :
	if db_version != version :
Added an error message:
	if not var :
because this functionality moved to Variant_map.py
Changed the return type from string to the Complex object V
And changed the main part to:
	-    __process(LOVD_ver, build, acc, var, Conf, O)
	+    result = __process(LOVD_ver, build, acc, var, Conf, O)
	+    return result
Changed the following stuff in Config.py:
	+        # Figure out where this program is located and go two levels up.
	+        import os
	+        myPath = os.path.dirname(__file__) + "/../.."
	+        os.chdir(myPath)
which is necessary for finding the mutalyzer.conf file



git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/branches/web_dev@22 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

html includes, a server directive has to be altered (described in Install.txt).
- check.html: The main page for mutation checks (used to be a large string in 
  index.py).

Output.py:
- Added an instance variable, this is the name of the module that created the
  Output object. This variable is used for more verbose logging.

Variant_info.py:
- Modifications for the new Output.py.
- Added error handling for parse errors.

Main.py:
- Modifications for the new Output.py.
- Renamed function rrr() to main().

index.py:
- Removed the large html string, it is now loaded from file with the 
  __readhtml() function.
- Made a __run() function, that wraps any function, executes it and returns
  standard output of this function as a string.



git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@12 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

- src/c2g.py
  - This program returns the genomic coordinates of a position in c. notation,
    it depends on the Config, Db Crossmap and Parser modules.
  - The input consists of the following variables:
    - LOVD_ver      ; The version of LOVD, ignored for now.
    - build         ; The build of the human genome, assumed to be hg19 for now.
    - accno.version ; The accession number and version on which the c. 
                      positions are defined.
    - var           ; The variation (without an accession number).
  - If the accession number and version are present in the database, it returns
    all positions (one or two) in g. notation relative to the chromosome.
- c2g.php 
  - This is a web interface for c2g.py, it is called in the following way:
    c2g.php?LOVD_ver=a&build=b&acc=c.d&var=e where a, b, c, d and e are 
    described above (note that the variation (e) should be HTML encoded).

Altered (with respect to c2g.py):
- Install.txt
  - Documented how to set up the c2g program.
- Db.py
  - Added two new query functions:
    - get_NM_info    ; Get exonStarts, exonEnds, cdsStart, cdsEnd and strand
                       information, given an NM accession number.
    - get_NM_version ; Get the NM version, given an NM accession number.
  - Made a general query function, that is called by the specific query 
    functions.
- Crossmap.py
  - Added helper functions for the output of c2g.
    - c2str ; Returns a string given mainsgn, main, offsgn and offset.
    - c2g   ; Returns a genomic position given mainsgn, main, offsgn and offset.

Altered (for Mutalyzer itself):
- GenRecord.py
  - Added default locus tag handling.
- Mutator.py
  - Added a duplication function.
- Parser.py
  - Added argument passing:
    - Substitutions: Arg1, Arg2 (Arg1>Arg2 for example).
    - Deletions: Arg1 (delArg1).
    - Ins: Arg1 (insArg1).
- Retriever.py
  - Added code to make the cache directory if it does not exist. This 
    eliminates the need for the clean.sh script.
- Main.py (most of the new functions have to be migrated elsewhere)
  - Altered the roll function to be able to roll in both directions.
  - Made a palindrome snoop function that finds the smallest string that is 
    not invariant under reverse complement, this function is also used to 
    detect perfect palindromes.
  - Made PtLoc2main and PtLoc2offset; get integers from the locations returned
    by the nomenclature parser.
  - Made Error and Warning message wrapper functions.
  - Made a function that tests if a string is an integer.
  - Made the parsing less verbose.
  - Extracted the positions from raw variations.
  - Wrote code to deal with reversed ranges.
  - Added error handling and warning messages for:
    - Substitutions.
    - Deletions.
    - Duplications.
    - Inversions.
    - Insertions.

Removed:
  - clean.sh
    - It is no longer needed, since all temporary files and directories are no
      longer in subversion.


git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@7 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