It now shuts down gracefully, completing the current job item. General
daemon handling code is now also better, including PID file handling.



git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/branches/refactor-mutalyzer-branch@238 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/branches/refactor-mutalyzer-branch@237 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

This implements the revert mentioned in the previous commit and now this
branch fully merged the first part of exon-deletions-branch. The second
part of that branch is about unknown offsets, but that implementation is
not yet fit to be merged.



git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/branches/refactor-mutalyzer-branch@234 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

This merges the first part of exon-deletions-branch (the second part concerns
unknown exon offsets, denoted with the ? character). Except that we now keep
track of removed splice sites in the transcript, instead of in the Mutator
instance. I guess the latter was better, so we will probably revert to storing
this in the Mutator instance.

Issue #35.



git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/branches/refactor-mutalyzer-branch@233 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/branches/refactor-mutalyzer-branch@232 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/branches/refactor-mutalyzer-branch@231 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/branches/refactor-mutalyzer-branch@230 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/branches/refactor-mutalyzer-branch@229 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/branches/refactor-mutalyzer-branch@228 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

Static transcript information should now also be shown if there were errors
with the variant.



git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/branches/refactor-mutalyzer-branch@227 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/branches/refactor-mutalyzer-branch@226 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/branches/refactor-mutalyzer-branch@225 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/branches/refactor-mutalyzer-branch@224 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

Mostly this was adding documentation, cleaning code, and adding exception
paths.



git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/branches/refactor-mutalyzer-branch@223 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

- Ditched use of web.session, just use web.cookies.
- Added detection of configuration file location.
- Removed ./var directory, everything is now in standard locations, but also
  configurable.
- Added more standard version management.



git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/branches/refactor-mutalyzer-branch@222 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

- Moved mail.txt to templates/batch-mail.txt.
- Moved Obsoleted.txt and TODO into a README.
- Move mutalyzer.sql into INSTALL.



git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/branches/refactor-mutalyzer-branch@221 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/branches/refactor-mutalyzer-branch@220 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/branches/refactor-mutalyzer-branch@219 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/branches/refactor-mutalyzer-branch@218 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

* Updated output.Message class to include __repr__ and __str__ methods.
* The output.Output.getMessages() method now returns Message instances
  instead of strings.
* New styling of messages in web interface.



git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/branches/refactor-mutalyzer-branch@217 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

Mostly variant checker, now using exceptions on some places.



git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/branches/refactor-mutalyzer-branch@216 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/branches/refactor-mutalyzer-branch@215 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/branches/refactor-mutalyzer-branch@214 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/branches/refactor-mutalyzer-branch@213 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/branches/refactor-mutalyzer-branch@212 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/branches/refactor-mutalyzer-branch@211 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

A lot of the old Mutalyzer.py functionality is now split up. Part of it ended
up in util.py, part of it in check.py (command line interface), and part of
it in variant_checker.py.



git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/branches/refactor-mutalyzer-branch@210 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/branches/refactor-mutalyzer-branch@209 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

bottom, no real restructuring yet.



git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/branches/refactor-mutalyzer-branch@208 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/branches/refactor-mutalyzer-branch@207 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@206 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@205 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/branches/refactor-mutalyzer-branch@204 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

This will contain some refactoring of src/Mutalyzer.py, separate from trunk.



git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/branches/refactor-mutalyzer-branch@203 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

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