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  • Laros Laros j.f.j.laros
  • Mihai Lefter Mihai Lefter mlefter
  • git mirror git mirror gitmirror
  • wgallard wgallard wgallard
4 authors
  1. May 13, 2014
  3. Apr 30, 2014
  5. Apr 25, 2014
  7. Apr 23, 2014
    • Vermaat's avatar
      Move to Sphinx for developer documentation · 2f33e62c
      Vermaat authored 
      This is quite a large commit, touching many things related to developer
documentation. It is all focussed on getting as much of this as possible
into the new Sphinx-based documentation.

Some highlights:

- Start Sphinx-based developer documentation, including fairly complete
  instructions for installation and configuration.
- Remove epydoc API docs.
- Rework some docstrings to conform to reStructuredText, so they can be
  used in the API docs generated by Sphinx.
- Move all of the top-level text files to reStructuredText so they can
  linked from the Sphinx-based docs and for consistency.
- Remove many obsolete things from the extras/ directory, including old
  installation scripts and migrations.

Many of the installation related documentation and scripts are removed
or adapted in light of the new automated deployment using Ansible.
      2f33e62c
  9. Jan 30, 2014
  11. May 21, 2013
  13. Apr 08, 2013
  15. Jan 03, 2013
  17. Dec 06, 2012
  19. Oct 20, 2012
  21. Sep 28, 2012
  23. Sep 26, 2012
  25. Sep 25, 2012
  27. Apr 23, 2012
  29. Apr 19, 2012
  31. Apr 18, 2012
  33. Apr 16, 2012
  35. Feb 18, 2012
    • 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
  37. Feb 15, 2012
  39. May 23, 2011
  41. May 20, 2011
  43. May 16, 2011
  45. May 13, 2011
  47. Apr 18, 2011
  49. Apr 13, 2011
  51. Apr 12, 2011
  53. Mar 31, 2011
  55. Feb 25, 2011
  57. Jan 17, 2011
  59. Dec 20, 2010
  61. Dec 10, 2010
    • 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
  63. Nov 08, 2010
    • 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
  65. Sep 22, 2010