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  25. 23 Mar, 2011 3 commits
  26. 25 Feb, 2011 1 commit
  27. 31 Jan, 2011 1 commit
  28. 12 Jan, 2011 1 commit
    • Laros's avatar
      Added feedback and todo information, added splice site destruction detection · bae57923
      Laros authored
      andfixed a bug in the GenBank parser.
      version 2.0 bugs.txt, beta-feedback.pdf, suggestions.txt, beta-feedback.txt:
      - Suggestions, bugs, todo lists, ...
      - Definitions of the mutalyzer database (to be merged with documentation).
      - Added the definition of the map table.
      - Modified the help text to reflect the internal functionality.
      - Added the function __overSplice() that checks whether a splice site is 
      - Added a check for splice site destruction by calling aforementioned function.
      - Removed a typo (getGeneAndTranscipt() -> getGeneAndTranscript()).
      - Reinstated the insertion of sequences on splice junctions to be added to the
        exon instead of the intron.
      - Fixed a bug in the shiftpos() function.
      - Fixed a bug that was triggered if the input is a minimally annotated one-exon
      git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@133 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1
  29. 20 Dec, 2010 1 commit
  30. 10 Dec, 2010 1 commit
  31. 11 Nov, 2010 1 commit
  32. 08 Nov, 2010 1 commit
    • Laros's avatar
      Added a new function to the webservice, enabled analysis of non-coding RNA and · 518b5e14
      Laros authored
      fixed a bug that was triggered when a range is used in combination with a
      genomic notation.
      - Added a function runMutalyzer(), full programmatic access to Mutalyzer (to 
        be expanded).
      - Added the class MutalyzerOutput() which will contain any data needed by the
        webservice. For now it only contains the original and mutated DNA sequence.
      - Added the new runMutalyzer() function to the examples.
      - Activated the transcription of non-coding RNA.
      - Added the gathering of non-coding RNA data from an NR reference sequence.
      - 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
      - Corrected some comment.
      - Synchronised the BNF with the functionality of the parser.
      - Corrected some text.
      git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@99 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1
  33. 03 Sep, 2010 1 commit
    • Laros's avatar
      Mutalyzer.py: · 407fbe2b
      Laros authored
      - Made the ``multiple transcripts found'' message more descriptive.
      - Made the ``in frame stop codon'' check work for all organisms (and
      - 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. 
      - 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
  34. 31 Aug, 2010 1 commit
  35. 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.
      - Added references for the TRM.
      - Documented a large part of the modules.
      - 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.
      - 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().
      - Separated the visualisation of a parse error from the error message. The 
        visualisation is now put in the output object as "parseError".
      - Added documentation.
      - 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.
      - Added file type information (for lrg and gb files).
      - Added sanity checks for the snpConvert() function.
      - Added documentation.
      - Added a new type "construction" to the linking methods, meaning that the
        mRNA is generated from the CDS.
      - Added an email variable for output to the website.
      - Added error information, to hide parts of the output.
      - Added file type information (see Retriever.py) to make download links more
      - Modified the syntax checker to work with the new parser output (see
      - Fixed a bug (selecting the human build) in the position converter.
      - Renamed download() to webservices().
      - Renamed ConversionChecker to PositionConverter.
      - Added.
      - Modified the template to work with the new restriction site format and the
        new parse error format.
      - Made lots of things conditional.
      - Added.
      - Added an example.
      - 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