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  1. Jan 17, 2011
  3. Jan 14, 2011
  5. Jan 12, 2011
    • Laros's avatar
      Updated the release date and version number. · 3ee551ba
      Laros authored 
      
git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@134 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1
      3ee551ba
    • 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
  7. Jan 07, 2011
  9. Jan 06, 2011
  11. Jan 05, 2011
  13. Jan 03, 2011
  15. Dec 29, 2010
  17. Dec 28, 2010
  19. Dec 20, 2010
  21. Dec 10, 2010
    • Laros's avatar
      Fixed a bug in the __locationList2posList() function. · 94bb67e1
      Laros authored 
      
git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@110 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1
      94bb67e1
    • Laros's avatar
      Updated the version and release date. · f2777d29
      Laros authored 
      
git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@109 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1
      f2777d29
    • Laros's avatar
      Added presentations, fixed a bug in the numberConversion() webservice function · c6c7c522
      Laros authored 
      and added a couple of functions to the webservice.

doc:
- Added all presentations given on Mutalyzer.

doc/TechnicalReference/bnf.tex:
- Updated the documentation of the BNF.

Mutalyzer.py:
- Added a check for a valid start position in the __rv() function. If it is not
  set, the parser has accepted the variant description, but did not do anything
  more (unimplemented variant types for example). An ``unknown error'' is
  returned for now.
- Added the following to the output object in the __ppp() function, needed by
  the runMutalyzer() function of the webservice:
  - Original genomic reference sequence.
  - Mutated genomic reference sequence.
  - Original RNA sequence.
  - Mutated RNA sequence.
  - Original CDS sequence.
  - Mutated CDS sequence.
  - Original Protein sequence.
  - Mutated Protein sequence.
  - Alternative Protein sequence.

webservice.py:
- Added a function getTranscriptsByGeneName() that returns a list of
  transcripts, given a gene name.
- Fixed the getTranscriptsRange() function (see Mapper.py).
- Added the sequences described above in the Mutalyzer.py section to the output
  of the runMutalyzer() function.
- Added the summary of the output messages to the return object of the
  runMutalyzer() function.
- Added a getGeneAndTranscipt() function, that given a genomic reference
  sequence and a transcript accession number (NM_...) returns the gene name and
  transcript variant. 

Serializers.py:
- Modified the MutalyzerOutput class to contain the values described in the
  Mutalyzer.py and webservice.py section.

Scheduler.py:
- Modified a call to chrom2c(), (see Mapper.py).

Mapper.py:
- Added an extra check on the start location (also see Mutalyzer.py, first
  point).
- Modified the chrom2c() function to use an additional argument to control the
  return type. It can now either return a list or a dictionary.

Db.py:
- Added a function get_TranscriptsByGeneName(), for the
  getTranscriptsByGeneName() function of the webservice.

VarInfo.py:
- Added (commented out) debug code.

index.py:
- Modified a call to chrom2c(), (see Mapper.py).

sp.py:
- Added examples for (some of) the new functions of the webservice.



git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@108 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1
      c6c7c522
  23. Nov 16, 2010