descriptions, added a presentation about Mutalyzer.

Mutalyzer.py:
- Added a fix for a bug that was triggered when an expected frameshift leads to
  no change.

Parser.py:
- Added iupac codes as allowed nucleotides.



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

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



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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.



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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

Made some minor changes in the html templates.



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- 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).


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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.



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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.



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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.



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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.



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