1. 22 Jul, 2013 1 commit
  2. 16 Jul, 2013 1 commit
  3. 15 Jul, 2013 1 commit
  4. 29 Oct, 2012 1 commit
  5. 24 Sep, 2012 1 commit
  6. 11 Jul, 2012 1 commit
  7. 21 Jun, 2012 1 commit
  8. 12 Mar, 2012 2 commits
  9. 20 Feb, 2012 1 commit
  10. 18 Feb, 2012 1 commit
    • Laros's avatar
      Added the Variant Description Extractor as a web interface. · b8640a1f
      Laros authored
      describe.py:
      - Module that provides the Variant Description Extractor functions.
      
      __init__.py:
      - Added an automated copyright year update.
      
      website.py:
      - Added the Variant Description Extractor web interface.
      
      templates/descriptionExtract.html:
      -  Template page for the Variant Description Extractor.
      
      templates/snp.html:
      templates/menu.html:
      templates/converter.html:
      templates/index.html:
      templates/parse.html:
      - Cosmetic changes.
      
      Added a presentation.
      
      
      
      git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@479 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1
      b8640a1f
  11. 16 Feb, 2012 1 commit
  12. 31 Jan, 2012 1 commit
  13. 26 Jan, 2012 2 commits
  14. 25 Jan, 2012 1 commit
  15. 23 Nov, 2011 1 commit
  16. 08 Nov, 2011 2 commits
  17. 04 Nov, 2011 2 commits
  18. 10 Oct, 2011 1 commit
  19. 20 Sep, 2011 1 commit
  20. 06 Sep, 2011 1 commit
  21. 05 Sep, 2011 1 commit
  22. 08 Apr, 2011 1 commit
  23. 31 Mar, 2011 1 commit
  24. 25 Mar, 2011 1 commit
  25. 23 Mar, 2011 4 commits
  26. 17 Mar, 2011 2 commits
  27. 31 Jan, 2011 1 commit
  28. 17 Jan, 2011 1 commit
  29. 20 Dec, 2010 1 commit
  30. 16 Nov, 2010 1 commit
    • Laros's avatar
      Fixed a bug in simplifying a delins and a minor bug in the translation of an · abf9721d
      Laros authored
      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
      abf9721d
  31. 31 Aug, 2010 1 commit
  32. 04 Aug, 2010 1 commit
    • Laros's avatar
      Started on the TRM, therefore the separate files Db.txt and errorcodes.txt have · 0aa697dd
      Laros authored
      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
      0aa697dd