• Laros's avatar
    Renewed the web interface. Worked on protein descriptions. Added more error · 2e170030
    Laros authored
    handling for incomplete and poorly annotated GenBank files.
    
    menu.html:
    - Template for all pages. Includes a menu and such.
    
    index.html:
    - The main page.
    
    base/:
    - Pictures, javascript, stylesheet, etc.
    
    interface.js:
    - Temporary script for gbupload.html.
    
    download.html:
    - Adjusted to work with the menu.html template.
    
    gbupload.html:
    - Adjusted to work with the menu.html template.
    
    check.html:
    - Extended the template to use more variables to increase flexibility.
    
    index.py:
    - Removed the capturing of the Mutalyzer output in the check() function,
      replaced it with retrieval of data from the Output object. 
    - Added a new index() function (see index.html).
    - Implemented the upload() function (see gbupload.html), currently it can only
      retrieve genes and chromosome slices from the NCBI.
    
    Web.py:
    - Enabled the parsing of the menu.html template in the tal() function.
    
    handler.py:
    - Modified to work with the new tal() function of Web.py.
    
    Output.py:
    - getMessages() now returns a list of messages, instead of printing it to 
      standard output.
    
    mail.txt:
    - Template message for finished batch jobs.
    
    Mutalyzer.py:
    - __bprint() now puts the visualisation of a protein in the Output object, 
      instead of printing it to standard output.
    - Made a new protein printing function that can highlight the changes, it is
      not used yet.
    - Added a __cdsLen() function that is used to see if a variant leads to a
      frameshift or not.
    - Added extention of a protein in the protein description function.
    - Added some error handling for `?' as a position.
    - Added error messages for invalid genes and transcript variants in the 
      input (suggesting possible options).
    - DNA / protein descriptions are now stored in the Output object.  
    - Added a legend.
    
    GenRecord.py:
    - Added functions listLoci() and listGenes() for suggestions when invalid 
      input is given.
    - Added a preprocessing step in the GenBank file parsing to deal with 
      missing locus tags (not functional yet).
    - Added some error handling for incomplete transcripts.
    
    
    
    git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@52 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1
    2e170030