• Laros's avatar
    Rewrote the GBparser module to cope with multiple linking methods (to link · f299d5e6
    Laros authored
    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
    f299d5e6