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.



git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@197 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@196 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

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.



git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@194 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@193 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

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.



git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@192 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

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



git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@191 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

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.



git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@190 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

- genomic description
- transcript descriptions
- protein descriptions



git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@189 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

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.



git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@188 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@187 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@186 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

mutation region.



git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@185 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

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.



git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@184 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

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



git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@183 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

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



git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@182 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

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



git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@181 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

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.



git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@180 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@179 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@178 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@177 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

inside an other gene description.



git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@176 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@175 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@174 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

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

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@173 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

available at the NCBI when using the GenBank uploader.



git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@172 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

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.



git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@171 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

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.



git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@170 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

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



git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@169 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

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.



git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@168 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

checker input files (5MB).

mutalyzer.conf:
src/Modules/Config.py:
- Add maximum size for batch checker input files.

src/wsgi.py:
templates/batch.html:
- Fixed maximum size for uploaded genbank files. Added maximum size for
  batch checker input files (5MB).

tests/test_wsgi.py:
- Added test for a too big batch input file.



git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@167 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

- Link to bugtracker is now absolute.
- Header for external links is no longer a link.

src/Modules/File.py:
- Bugfix for previous commit (transparent support for different types of
  line endings in batch input files).

src/tests/test_wsgi.py:
- Added batch tests with big input files. Added batch tests for different
  types of line endings in input files.



git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@166 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

Transparently support different line ending styles in batch checker input files (Unix, Mac, and Windows styles).

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@165 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

documentation page for webservices. Modified the getGeneAndTranscript()
webservice function to return both the name of the transcript and the
description of the product.

Todo.txt:
version 2.0 bugs.txt:
beta-feedback.pdf:
suggestions.txt:
beta-feedback.txt:
- Removed these files and added them to the bugtracking system.

wsgi.py:
- Added a page webservdoc (just a test, don't use).

webservdoc.html:
- Template for webservice documentation (just a test, don't use).

wsdl-viewer.xsl:
- Disabled the extensive footer.
- Removed borders.
- Removed the title.

webservice.py:
- Modified the getGeneAndTranscript() webservice function to return both the
  name of the transcript and the description of the product in a container.

Serializers.py:
- Added the container used by getGeneAndTranscript() (see webservice.py).



git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@164 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

src/wsgi.py:
- Updated batch routing to include SNP converter.

mutalyzer.conf:
src/Modules/Config.py:
- Added result file header line for batch SNP converter.

src/Modules/Scheduler.py:
- Added batch SNP converter.

src/Modules/File.py:
- Updated batch CSV input file parsing. Default is now standard Excel format
  and only if the CSV sniffer can find another dialect using a predefined set
  of delimiter characters without error we use that one.

templates/menu.html:
- Added link for batch SNP converter.


git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@163 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

Install.txt:
- Added a dependency.

wsgi.py:
- Updated the release date and version number.

webservice.py:
- Added the function sliceChromosomeByGene(), which is used to get a reference 
  sequence, given a gene name, organism and a length of flanking sequences.
- Added templates for other GenBank upload functions:
  - upLoadGenBankLocalFile()
  - upLoadGenBankRemoteFile()
  - sliceChromosome()

wsdl-viewer.xsl:
- Modified the template to use stable internal links, instead of randomly
  generated ones. This is only an example, more links should be treated like
  this.



git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@162 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@161 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

Renamed SOAP webservice from MutalyzerService to Mutalyzer.
Updated copyright years in HTML template.
Added test checking availability of WSDL file.



git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@160 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@159 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

Set web.py debugging mode. Refactored rendering of static pages into one handler class (Static). In the generated webservice documentation, get the WSDL directly from the webservice module instead of through a HTTP request. Also fixed this generated webservice documentation to have a text/html content type.

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@158 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1