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    • 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
  57. 20 Dec, 2010 1 commit
  59. 10 Dec, 2010 1 commit
  61. 11 Nov, 2010 1 commit
  63. 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
  65. 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
  67. 31 Aug, 2010 1 commit
  69. 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.

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