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Swapped names (Jeroen <-> Martijn) in NBIC presentation. Fixed text positioning in transcript picture.

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log file.


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can happen when the reference sequence contains IUPAC codes.


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This commmit brings in some bugs that take some time to fix. It will be
recommited in a new branch 'exon-deletions-branch' in a few moments.



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src/Modules/Mutator.py:
- Added method (add_removed_sites) to give splice sites that should be
  ignored. Now newSplice() does not process these splice sites.

src/Mutalyzer.py:
- Handle whole-exon deletions and exon-fusions by removing splice sites
  where we can. A notice is printed in this case. Otherwise, if splice
  sites are hit in some other way, no protein product is predicted. This
  fixes Trac issues #35 and #36.



git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@195 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

src/Mutalyzer.py:
- Output info message in case of a roll that was rolled back because it
  crossed exon boundaries.

src/Modules/Output.py:
- Fix: output messages from (and including) the level specified in the
  configuration.



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descriptions, added a presentation about Mutalyzer.

Mutalyzer.py:
- Added a fix for a bug that was triggered when an expected frameshift leads to
  no change.

Parser.py:
- Added iupac codes as allowed nucleotides.



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This was already implemented, but I added a few comments to the code. This
fixes issue #37.



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src/Modules/Mutator.py:
- The newSplice() method no longer includes insertions in exons for the
  first and last sites in the given list of splice sites. The result is
  that this inclusion in exons does not apply to translation start/end
  and CDS start/end. This fixes issue #39.



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- genomic description
- transcript descriptions
- protein descriptions



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src/Modules/Mutator.py:
- For deletions, position shifts are now active from the first position
  following the deletion. Previous behaviour was from (but not including)
  the first position of the deletion itself.
- Added method to check if the resulting shift gets smaller at some
  specific position: Mutator.shift_minus_at(position).
- The positions in the shift list are now interpreted as a shift from
  (and including) the listed position. Previous behaviour was following
  (and not including) the listed position.
- The Mutator.newSplice(sites) method has some additional logic. This
  fixes some bugs, including Trac bug #30.

src/tests/test_mutator.py:
- Written a lot of unit tests for the changes in Mutator.py.



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mutation region.



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The SOAP runMutalyzer method now also returns a list of raw variants, where
each raw variant consists of (1) a textual description and (2) a visualisation
in ASCII-art suitable for printing with a monospaced font.



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src/webservice.py:
src/test_webservice.py:
- Added optional geneName argument to getTranscriptsAndInfo SOAP method to
  restrict returned transcripts to some gene.



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A query to getGS should show results in non-interactive mode, that is without
site menu and form.



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The methods upLoadGenBankLocalFile and upLoadGenBankRemoteFile are not yet
implemented and as such now throw an exception with this message.



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LOVD insists (incorrectly) on uploading a genbank file urlencoded while we
ask for multipart/form-data. We now also accept urlencoded requests to be
done with it.



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inside an other gene description.



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Method descriptions in generated WSDL documentation are now properly indented and typeset in monospace.

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available at the NCBI when using the GenBank uploader.



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transcripts and exon positions for a gene.

Fix: redirect stdout to stderror.

src/wsgi.py:
src/webservice.py:
- Redirect stdout to stderror since WSGI does not allow any output to stdout
  and Mutalyzer tends to print some debug info here and there.

src/webservice.py:
src/Modules/Serializers.py:
- New getTranscriptsAndInfo webservice method.



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runMutalyzer() function and added a new example script.


webservice.py:
- Added sliceChromosome(), which returns an UD number given a chromosome
  accession number, a start and end and an orientation.
- Modified the runMutalyzer() function to also return a description on the
  chromosome.
Serializers.py:
- Added chromDescription to the MutalyzerOutput class (see webservice.py).

webservices.html, textmining.py, textmining_sample.txt:
- Added a small textmining example.



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webservice.py. This makes the output more reliable and serves as a template for
a new function (getTranscriptsAndInfo()).



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src/wsgi.py:
- Now use Python string formatting instead of TAL in Download.

src/webservice.py:
src/Modules/Serializers.py:
- Don't use our List type, but standard Array for SOAP.
- Add messages field in output of checkSyntax and runMutalyzer.

templates/client-php.php:
- Added PHP example SOAP client.

templates/client-mono.cs:
templates/client-soappy.py:
templates/client-suds.py:
- Updated example SOAP clients to all do the same thing.



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