1. 22 Jul, 2013 2 commits
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  16. 07 Dec, 2011 1 commit
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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, ...
      
      mutalyzer.sql:
      - Definitions of the mutalyzer database (to be merged with documentation).
      
      Install.txt:
      - Added the definition of the map table.
      
      batch.html:
      - Modified the help text to reflect the internal functionality.
      
      Mutalyzer.py:
      - Added the function __overSplice() that checks whether a splice site is 
        destroyed.
      - Added a check for splice site destruction by calling aforementioned function.
      
      webservice.py:
      - Removed a typo (getGeneAndTranscipt() -> getGeneAndTranscript()).
      
      Mutator.py:
      - 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.
      
      GBparser.py:
      - Fixed a bug that was triggered if the input is a minimally annotated one-exon
        gene.
      
      
      
      git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@133 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1
      bae57923
  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.
      
      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
      518b5e14
  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
        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).
      
      
      git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@87 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1
      407fbe2b
  34. 31 Aug, 2010 1 commit