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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. 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
  3. Jan 30, 2014
  5. May 21, 2013
  7. Apr 08, 2013
  9. Jan 03, 2013
  11. Dec 06, 2012
  13. Oct 20, 2012
  15. Sep 28, 2012
  17. Sep 26, 2012
  19. Sep 25, 2012
  21. Apr 23, 2012
  23. Apr 19, 2012
  25. Apr 18, 2012
  27. Apr 16, 2012
  29. 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
  31. Feb 15, 2012
  33. May 23, 2011
  35. May 20, 2011
  37. May 16, 2011
  39. May 13, 2011
  41. Apr 18, 2011
  43. Apr 13, 2011
  45. Apr 12, 2011
  47. Mar 31, 2011
  49. Feb 25, 2011
  51. Jan 17, 2011
  53. Dec 20, 2010
  55. 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
  57. 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
  59. Sep 22, 2010
  61. Sep 03, 2010
    • 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
  63. Aug 16, 2010
    • Laros's avatar
      Beta-2 release. · 1755a402
      Laros authored 
      Wrote documentation:
- Removed the bibliography database and replaced it with a (generated) bbl
  file.
- Wrote a number of new sections in the TRM.
- Modified the Makefile for the new bibliography method.

Mutalyzer.py:
- Added documentation.
- Reinstated the ``alternative protein'' (alternative start codon).
- Added the molType to the output object, this is needed in the check.html
  template.

Scheduler.py:
- Fixed a bug that made any position conversion batch job crash.

File.py:
- Fixed a bug that made every batch job with no errors in the input crash.

index.py:
- Added a variable genomicDNA to the arguments in the check() function.
- Fixed a bug in the syntaxCheck() function, that made the syntax checker
  crash.

check.html:
- Added a ``clear field'' button.
- Added different headers for genomic DNA and mRNA.
- Modified the ``alternative protein'' visualisation.

snp.html:
- Added a ``clear field'' button.

menu.html:
- Fixed a bug in the background image.
- Removed the link to HGVS_nomenclature_extension_proposal.pdf and made it an
  external link.
- Added a link to Mutalyzer 1.0.4.

menu.js:
- Added a clearForm() function that clears one element in a form.

converter.html:
- Added a ``clear field'' button.

parse.html:
- Added a ``clear field'' button.



git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@79 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1
      1755a402
  65. Aug 09, 2010
    • Laros's avatar
      First Beta release. · e0024265
      Laros authored 
      Added help and about pages.

Extended the TRM.

Mutalyzer.py:
- Added a __checkDNA() funtion for input checking.
- Added a warning message for ``rolled'' insertions that are not duplications.
- Added a warning for unsupported RNA descriptions.

Web.py:
- Added a release date variable.
- Increased version numbers.

index.py:
- Added functions for the new pages (help.html and about.html)
- Fixed a cosmetic bug that occurred when using html tags in the input.

menu.html:
- Made the top and bottom links compatible with Internet Explorer.
- Added a link to the about page.
- Added a link to the name generator page.
- Removed some comment, altered some layout.

index.html:
- Moved some technical data to the about page.



git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@78 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1
      e0024265
  67. Aug 04, 2010
    • 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