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

bnf.tex, Parser.py:
- Updated documentaion of the BNF.

webservice.py:
- Added logging to the getGeneAndTranscipt() function.



git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@111 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@110 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@109 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

and added a couple of functions to the webservice.

doc:
- Added all presentations given on Mutalyzer.

doc/TechnicalReference/bnf.tex:
- Updated the documentation of the BNF.

Mutalyzer.py:
- Added a check for a valid start position in the __rv() function. If it is not
  set, the parser has accepted the variant description, but did not do anything
  more (unimplemented variant types for example). An ``unknown error'' is
  returned for now.
- Added the following to the output object in the __ppp() function, needed by
  the runMutalyzer() function of the webservice:
  - Original genomic reference sequence.
  - Mutated genomic reference sequence.
  - Original RNA sequence.
  - Mutated RNA sequence.
  - Original CDS sequence.
  - Mutated CDS sequence.
  - Original Protein sequence.
  - Mutated Protein sequence.
  - Alternative Protein sequence.

webservice.py:
- Added a function getTranscriptsByGeneName() that returns a list of
  transcripts, given a gene name.
- Fixed the getTranscriptsRange() function (see Mapper.py).
- Added the sequences described above in the Mutalyzer.py section to the output
  of the runMutalyzer() function.
- Added the summary of the output messages to the return object of the
  runMutalyzer() function.
- Added a getGeneAndTranscipt() function, that given a genomic reference
  sequence and a transcript accession number (NM_...) returns the gene name and
  transcript variant. 

Serializers.py:
- Modified the MutalyzerOutput class to contain the values described in the
  Mutalyzer.py and webservice.py section.

Scheduler.py:
- Modified a call to chrom2c(), (see Mapper.py).

Mapper.py:
- Added an extra check on the start location (also see Mutalyzer.py, first
  point).
- Modified the chrom2c() function to use an additional argument to control the
  return type. It can now either return a list or a dictionary.

Db.py:
- Added a function get_TranscriptsByGeneName(), for the
  getTranscriptsByGeneName() function of the webservice.

VarInfo.py:
- Added (commented out) debug code.

index.py:
- Modified a call to chrom2c(), (see Mapper.py).

sp.py:
- Added examples for (some of) the new functions of the webservice.



git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@108 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@105 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

EST. Made the runMutalyzer() function in the webservices more robust and added
some better error messages in the Retriever module.

Mutalyzer.py:
- A deletion in the first 3 nucleotides on an EST resulted in a crash, this is
  fixed.
- A delins with a deletion and an insertion with either a common prefix or
  suffix was handled incorrectly.

webservice.py:
- Made the retrieval of information in the runMutalyzer() function more robust
  by using the getIndexedOutput() function of the Output object.

Retriever.py:
- Added a more sensible error when a record could not be retrieved.

menu.html:
- Fixed some capitalisation for more consistency in the web pages.



git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@104 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

- Fixed a bug that was triggered when a wrong range was given, now an error is
  returned.

Web.py:
- Modified the release date.

menu.html:
- Updated the link to Mutalyzer 1.0.4.



git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@103 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

- Added misc_RNA, ncRNA, rRNA, tRNA and tmRNA as valid RNA fields.

GenRecord.py:
- Enabled the transcription of non-coding RNA.

Web.py:
- Increased the version number and release date.



git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@102 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

fixed a bug that was triggered when a range is used in combination with a
genomic notation.

webservice.py:
- Added a function runMutalyzer(), full programmatic access to Mutalyzer (to 
  be expanded).

Serializers.py:
- Added the class MutalyzerOutput() which will contain any data needed by the
  webservice. For now it only contains the original and mutated DNA sequence.

sp.py:
- Added the new runMutalyzer() function to the examples.

GenRecord.py:
- Activated the transcription of non-coding RNA.

GBparser.py:
- Added the gathering of non-coding RNA data from an NR reference sequence.

Mutalyzer.py:
- Fixed a bug that was triggered when a range is used in combination with a 
  genomic notation.
- Added the full original and mutated string to the output object for use in
  webservices.

Parser.py:
- Corrected some comment.

bnf.tex:
- Synchronised the BNF with the functionality of the parser.

help.html:
- Corrected some text.



git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@99 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

is in fact a duplication. The duplicated region was reported incorrectly.


git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@96 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

reference to it. This script was not executed because of this.



git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@92 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@91 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

Made some minor changes in the html templates.



git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@90 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

mutalyzer.conf:
- Increased the UpdateInterval window to three weeks (apparently 7 was too
  small since we sometimes miss an update).

handler.py:
- Added mimetype guessing for all files in base/ (to make images cacheable and
  to reduce browser errors).

UCSC_update.py:
- Fixed a bug that made the update program crash.

GenRecord.py:
- Added a function __checkExonList() that checks whether CDS start and CDS stop
  are in the list of gathered exons.
- Added error handling for incomplete exon lists.

Web.py:
- Updated the release date.

menu.html:
- Fixed a syntax bug.

style.css:
- Fixed a syntax bug.



git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@89 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@88 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

- Made the ``multiple transcripts found'' message more descriptive.
- Made the ``in frame stop codon'' check work for all organisms (and
  organelles).

GBparser.py:
- Added mitochondrial DNA to the list of possible molecular types to be
  checked, it will be treated like genomic DNA.
- Allowed genes without CDS list or mRNA list (only a CDS location) as a
  genomic description only if there are no other CDS's for that gene. 

GenRecord.py:
- Fixed a bug in the naming of the link method (it should also apply when mRNA
  is constructed from a CDS location only).


git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@87 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@86 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

Lots of comments





git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@85 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

offset in the intron notation.


git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@84 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@83 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

- The `*' (after STOP codon) was not interpreted in one case.

Fixed a bug that was introduced while adding the intron (and upstream and
downstream) notation check:
- Checks were not working for transcripts on the minus strand.



git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@82 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@81 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

Mutator.py:
- In the newSplice() function, The call to shiftpos() is changed back to the
  original one. This version (shiftpos(i + 1) - 1) was done to make an
  insertion at the end of an exon possible. So this functionality is not
  available right now.


git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@80 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

Wrote documentation:
- Removed the bibliography database and replaced it with a (generated) bbl
  file.
- Wrote a number of new sections in the TRM.
- Modified the Makefile for the new bibliography method.

Mutalyzer.py:
- Added documentation.
- Reinstated the ``alternative protein'' (alternative start codon).
- Added the molType to the output object, this is needed in the check.html
  template.

Scheduler.py:
- Fixed a bug that made any position conversion batch job crash.

File.py:
- Fixed a bug that made every batch job with no errors in the input crash.

index.py:
- Added a variable genomicDNA to the arguments in the check() function.
- Fixed a bug in the syntaxCheck() function, that made the syntax checker
  crash.

check.html:
- Added a ``clear field'' button.
- Added different headers for genomic DNA and mRNA.
- Modified the ``alternative protein'' visualisation.

snp.html:
- Added a ``clear field'' button.

menu.html:
- Fixed a bug in the background image.
- Removed the link to HGVS_nomenclature_extension_proposal.pdf and made it an
  external link.
- Added a link to Mutalyzer 1.0.4.

menu.js:
- Added a clearForm() function that clears one element in a form.

converter.html:
- Added a ``clear field'' button.

parse.html:
- Added a ``clear field'' button.



git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@79 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

Added help and about pages.

Extended the TRM.

Mutalyzer.py:
- Added a __checkDNA() funtion for input checking.
- Added a warning message for ``rolled'' insertions that are not duplications.
- Added a warning for unsupported RNA descriptions.

Web.py:
- Added a release date variable.
- Increased version numbers.

index.py:
- Added functions for the new pages (help.html and about.html)
- Fixed a cosmetic bug that occurred when using html tags in the input.

menu.html:
- Made the top and bottom links compatible with Internet Explorer.
- Added a link to the about page.
- Added a link to the name generator page.
- Removed some comment, altered some layout.

index.html:
- Moved some technical data to the about page.



git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@78 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

=====
src/Modules/Mapper.py
    * LOVDERR fixed
	Correct return string when the Variant-info requests a reference
	that could not be found in the database

ADDED FEATURES
==============
Name Generator

src/index.py
    * Added the Name Generator reference

templates/menu.html
    * Updated the Menu to include the Name Generator

templates/generator.html
    * Main HTML file for the name generator

templates/base/js/generator.js
    * Main JS file for the name generator

TODO
====
Name Generator
    Add Protein description, allel and exotic names





git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@77 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

src/
    Mutalyzer.py
	Batch Jobs omit additional mutalyzer results when an error occures

    LRGParser.py
	Added the locus tag, transcriptProduct and proteinProduct
    
    GenRecord.py
	Removed transLongName & protLongName.
	Substituted by transcriptProduct and proteinProduct

    File.py
	Empty lines in batch files are preserved
	A better summary of errors is displayed
	A threshold of 5% is set which omits erroreneous entries
	Added the skip flag ~! for entries to be skipped at all
	    Used for empty lines and lines that do not follow
	    the formatting of either the new of old style
	
    Db.py
	Added the option to set a flag when inserting an entry

templates/
    batch.html
	Moved the error below the input form


TODO:
    File.py
	Add threshold to config file
	


git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@76 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

vanished. Fixed a large number of bugs.

Db.txt, errorcodes.txt:
- Renamed and converted to LaTeX.

bibliography.bib:
- Added references for the TRM.

TechnicalReference.tex:
- Documented a large part of the modules.

Mutalyzer.py:
- Added a __formatRange() function for better output of a range.
- Added a __checkIntronPosition() function that checks the validity of an 
  intronic notation.
- Fixed a bug that made a change in the first 9 nucleotides result in an
  unknown protein description.
- Modified the error- and warning messages for large strings (see Mutator.py)
  and ranges.
- Added a filter for indexing by protein isoform.

Mutator.py:
- Replaced the calculation of restriction sites using sets with code that does
  so using multisets. This allows the deletion of a site while an other site
  with the same name remains to be detected. Restriction sites are also
  reported in a more compact way.
- Extracted the part of the visualisation where large strings are represented
  by their pre- and suffix and a number of omitted nucleotides. This is now
  available as a function visualiseLargeString().

Parser.py:
- Separated the visualisation of a parse error from the error message. The 
  visualisation is now put in the output object as "parseError".

Output.py:
- Added documentation.

GBparser.py:
- Moved the reverse-complement logic for the __findMismatch() function to the
  function itself.
- Added an extra check for retrieving slicing information.
- Added a filter for poorly annotated exons.
- Added documentation.

Retriever.py:
- Added file type information (for lrg and gb files).
- Added sanity checks for the snpConvert() function.
- Added documentation.

GenRecord.py:
- Added a new type "construction" to the linking methods, meaning that the
  mRNA is generated from the CDS.

Web.py:
- Added an email variable for output to the website.

index.py:
- Added error information, to hide parts of the output.
- Added file type information (see Retriever.py) to make download links more
  sensible.
- Modified the syntax checker to work with the new parser output (see
  Parser.py).
- Fixed a bug (selecting the human build) in the position converter.
- Renamed download() to webservices().
- Renamed ConversionChecker to PositionConverter.

disclaimer.html:
- Added.

check.html:
- Modified the template to work with the new restriction site format and the
  new parse error format.
- Made lots of things conditional.

skel.html:
- Added.

snp.html:
- Added an example.

menu.html:
- Modified the layout, added some links, etc.

Other templates:
- Mainly edited the layout and indentation.



git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@75 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

Mutalyzer.py
    * Typo

handler.py
    * Reverted the download of sp.py to the original version -r25

VarInfo.py
    * Fixed a return bug of the mainMapping

index.py
    * dropped redirect function

#######Modules#######

LRGParser.py
    * added a few checks for existing XML tags

GBparser.py
    * __tagLocus product tag fixed if not existing

Mapper.py
    * _FieldsFromDb fixed if versions is ""

#######Templates######
sp.py
    * reverted to version 25


    


git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@74 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

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

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@72 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

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@68 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

notation. Implemented the detection of the addition or removal of restriction 
sites. Added additional information about the transcript under scrutiny (if
any), like the g. and c. positions of the exons, as well as the CDS start
and stop.

install.sh:
- Added a rewrite rule to link to the bug tracker.

Db.txt:
- Updated the definition of the GBInfo table.

errorcodes.txt:
- Added a new error (EPOS).

templates/base/images:
- Made new images for the template (temporary).

style.css:
- Added a new class to make a form button look like a clickable link (used in
  check.html).
- Added a new <td> class for right aligned text.

check.html:
- Made a lot of output conditional, depending on what Mutalyzer returns.
- Made the submit forms conditional, depending on the method of retrieval:
  - GET ->  No forms.
  - POST -> Full output.
- Added exon and CDS information.
- Added restriction site information, coupled to the `raw variants'.
- Added a download link for the reference sequence.
- Made the affected transcripts clickable (post to Mutalyzer).
- Added highlighting of changed amino acids for the protein changes.

gbupload.html:
- Added a conditional output section for uploaded sequences.

menu.html:
- Changed the logos.
- Added a link to the bug tracker.

index.html:
- Cleaned up the layout (indenting).
- Added link to Gen2Phen.

Mutator.py:
- Implemented the detection of the addition or removal of restriction sites.
  - Of each raw variant and its flanking sequences, two sets of restriction
    sites is constructed. One for the original subsequence and one for the
    mutated subsequence.
  - Additions and deletions can be detected by using the minus operator for
    sets.
- Changed the `visualisation' output list from a bare list to a list of 
  triples.
- Added verbose output to all raw variants.

Parser.py:
- Added productions for the EX and IVS position notations.

Output.py:
- Added a function that returns the data at the index in a list. Neither the
  list, nor the index need to be present, in which case None will be returned.
  This is convenient in index.py.

GBparser.py:
- Added a version variable to the record class (not used yet).
- Fixed a bug in matching transcripts and CDS by using a locus tag.

Retriever.py:
- Added return values for downloadrecord() and uploadrecord(), so they can be
  used in index.py.

GenRecord.py:
- Added translate and transcribe variables to the Locus class, to be used to
  skip translation of non coding transcripts and to skip the processing of 
  incomplete transcripts as a whole.

Web.py:
- Revived the old tal parser to return a more basic html page (used when GET
  instead of POST is used in index.py). Mainly for LOVD.

Scheduler.py:
- Testing.

Crossmap.py:
- Updated comment.
- Added:
  - getSpliceSite(), get the g. position of a splice site.
  - numberOfIntrons(), get the number of introns in a transcript.
  - numberOfExons(), get the number of exons in a transcript.

index.py:
- check():
  - Removed checks by using the getIndexedOutput() function.
  - Added a call to the `old' tal parser in case of a GET request.
  - Added more output (exon/CDS info, restriction sites, ...).
- upload():
  - Implemented calls to the uploadrecord() and downloadrecord() functions of
    the Retriever module.

Mutalyzer.py:
- Implemented a new protein visualisation function that highlights the changes.
- Used __toProtDescr() (and therefore the findInFrameDescription() and 
  findFrameShift() functions) to return the extent of the change, as well as a
  description of it. The extent is coded as a triple: (from, original end,
  variant end). This is used for the new visualisation.
- Added a check for an inversion of length 1 (actually a substitution).
- Added translation from EX and IVS positions (and ranges) to standard HGVS 
  positions.
- Added a check for out of boundary positions (outside the reference sequence).
- Added exon and CDS information to the output.
- Made the translation of a CDS depend on the translate member variable of the
  Locus class.



git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@66 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/branches/lrg@65 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/branches/lrg@63 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@61 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

    - Schedular.py
	addJob calls Popen and returns immediatly this kills the spawned process
	and leaves an unjoined child. This must be fixed with e.g. multiprocessing
    - 

CHANGES:
    - templates
	* menu.html	- include navigation to new features
	* check.html	- <pre>mutalyzer output</pre>
	* batch.html	- change Name Checker Batch Output
    - Modules
	* Db.py		- addJob  function attributes include jobType
			  getJobs function returns JobID & JobType
	* Schedular.py  - process function now support different jobtypes
			  addJob  function new attribute jobType
					   disabled BatchChecker -> TODO
	* LRGparser.py  - removed the names of transcript in the updatable
			    section
    - /
	* index.py	- batchCheck fn cleaned up and implemented
	* Mutalyzer.py  - added _batchOutput function to generate a batch output
			  entry in the output object, which is used in the batch
			  version of the NameChecker


NOTES:
    - Modules
	* Schedular.py	- __sendMail doesn't handle mail errors.
			  addJob doesn't start the batchchecker
    - /
	* index.py	- batchConvert fn in the middle of development, cleaning
			  up previous version: batchConversion
			- checkingSyntax function needs to be moved to
			  another section and be reused in the batchSyntaxCheck



git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/branches/lrg@60 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1