Fabio [Mon, 26 Jan 2009 16:33:29 +0000 (17:33 +0100)]
+ changed check for intial setting of old_w. (matrix != None does not work in cvxopt)
Fabio [Thu, 23 Oct 2008 09:05:47 +0000 (11:05 +0200)]
+ update makefiles to fetch automatically valid Python includes and libs
Fabio [Wed, 22 Oct 2008 14:23:46 +0000 (16:23 +0200)]
+ changed parameter handling a bit (input files command line args and not inside conf file)
+ trainig data parser more flexible
Fabio [Wed, 22 Oct 2008 09:39:32 +0000 (11:39 +0200)]
+ fixed automatic Python path settings in Makefiles
Fabio [Tue, 21 Oct 2008 12:04:23 +0000 (14:04 +0200)]
+ set proper logging in optimizer code
+ cleaned up testcases a bit
+ minor modifications and cleanups
Fabio [Mon, 20 Oct 2008 14:07:16 +0000 (16:07 +0200)]
+ restructured test cases
+ added some checks and testcases for training
+ extended documentation to describe training data file format
Fabio [Wed, 15 Oct 2008 14:48:25 +0000 (16:48 +0200)]
+ fixed issue with negative strand in lookup table
Fabio [Wed, 15 Oct 2008 13:49:54 +0000 (15:49 +0200)]
+ extended manual to describe output file format
Fabio [Wed, 15 Oct 2008 13:03:04 +0000 (15:03 +0200)]
+ fixed alignment index calculation for negative strand
Fabio [Tue, 14 Oct 2008 16:38:29 +0000 (18:38 +0200)]
+ fixed minor bugs
Fabio [Tue, 14 Oct 2008 16:00:14 +0000 (18:00 +0200)]
+ extended test cases
+ fixed sequence fetching for 205: , -205: on negative strand
Fabio [Mon, 13 Oct 2008 15:39:44 +0000 (17:39 +0200)]
+ extended documentation
+ fixed index issues in sequence utils
+ added small example script for splice site score creation
Fabio [Mon, 13 Oct 2008 08:46:18 +0000 (10:46 +0200)]
+ fixed some issues with the splice site scores and ugly code fragments
Fabio [Fri, 10 Oct 2008 13:44:00 +0000 (15:44 +0200)]
+ extended docu
+ removed legacy code concerning run object
+ unified tests
+ added creation of artifical small dataset for faster debugging
Fabio [Wed, 8 Oct 2008 09:29:54 +0000 (11:29 +0200)]
+ got rid of some legacy code
+ added test code
+ fixed offsets in alignment file calculation
+ added license information to files with missing info
Fabio [Tue, 7 Oct 2008 09:55:20 +0000 (11:55 +0200)]
+ cleaned up directories
+ moved some files to the qpalma package
Fabio [Tue, 7 Oct 2008 09:40:25 +0000 (11:40 +0200)]
+ renamed dyn_prog directory
+ extended setup script and MANIFEST to work with C++ code
+ extended README
Fabio [Thu, 2 Oct 2008 16:55:23 +0000 (18:55 +0200)]
+ removed load_genomic dependency
Fabio [Thu, 2 Oct 2008 16:20:05 +0000 (18:20 +0200)]
+ added palma_utils file
+ added some license texts
Fabio [Thu, 2 Oct 2008 13:50:07 +0000 (15:50 +0200)]
+ added sample configuration file
+ minor modifications in the dataset utils
Fabio [Wed, 1 Oct 2008 13:47:07 +0000 (15:47 +0200)]
+ fixed minor inconsistencies in the code
+ first version where all 4 pipeline steps are running automated
Fabio [Tue, 30 Sep 2008 10:17:59 +0000 (12:17 +0200)]
+ combined two scripts that were responsible for generating the output format
Fabio [Mon, 29 Sep 2008 13:31:48 +0000 (15:31 +0200)]
+ extended pipeline code
+ refactoring last step of the prediction task
Fabio [Mon, 22 Sep 2008 11:01:56 +0000 (13:01 +0200)]
+ added some documentary text
+ some minor modifications
Fabio [Tue, 16 Sep 2008 20:28:26 +0000 (22:28 +0200)]
+ added some text and references to the documentation
+ added some logic to the last step in the pipeline
Fabio [Sun, 14 Sep 2008 03:41:15 +0000 (05:41 +0200)]
+ added module to convert pickled predictions to several output formats
Fabio [Sat, 13 Sep 2008 19:33:57 +0000 (21:33 +0200)]
fixed minor inconsistencies in the code (naming of new variables etc.)
Fabio [Sat, 13 Sep 2008 19:23:55 +0000 (21:23 +0200)]
+ moved file to module directory
Fabio [Sat, 13 Sep 2008 19:23:16 +0000 (21:23 +0200)]
+ added framework code for training modus
Fabio [Sat, 13 Sep 2008 02:16:56 +0000 (04:16 +0200)]
+ added paths for the dataset generation
+ checked dataset generation
Fabio [Thu, 11 Sep 2008 21:34:38 +0000 (23:34 +0200)]
+ added dataset generation function for training set
+ added result collection function for approximation step
Fabio [Wed, 10 Sep 2008 21:28:08 +0000 (23:28 +0200)]
+ changed dataset compilation to support new framework
Fabio [Wed, 10 Sep 2008 21:03:14 +0000 (23:03 +0200)]
+ got rid of minor bugs
+ ApproximationTask is running
Fabio [Wed, 10 Sep 2008 15:50:56 +0000 (17:50 +0200)]
+ changed module hierarchy a bit
Fabio [Wed, 10 Sep 2008 15:25:29 +0000 (17:25 +0200)]
+ added settings parser module
Fabio [Wed, 10 Sep 2008 15:09:28 +0000 (17:09 +0200)]
+ added settings parser module
Fabio [Wed, 10 Sep 2008 14:20:27 +0000 (16:20 +0200)]
+ added configuration file parsing and checking functions
Fabio [Tue, 9 Sep 2008 10:58:20 +0000 (12:58 +0200)]
+ added settings in the form of a global and a run specific part
+ settings are stored as dict. entries
Fabio [Fri, 5 Sep 2008 07:22:36 +0000 (09:22 +0200)]
+ added small parts to docu
Fabio [Tue, 2 Sep 2008 10:37:52 +0000 (12:37 +0200)]
+ added license text
+ changed parameter storage inside qpalma object
+ changed training code to use the new c++ interface
Fabio [Mon, 1 Sep 2008 16:37:15 +0000 (18:37 +0200)]
+ got rid of some unneccessary code
Fabio [Mon, 1 Sep 2008 15:11:28 +0000 (17:11 +0200)]
+ changed python and c code in order to perform easier parameter handling and
reduce wrapper code on the python layer
Fabio [Mon, 1 Sep 2008 14:14:24 +0000 (16:14 +0200)]
+ removed some obsolete dependencies
Fabio [Mon, 1 Sep 2008 14:02:45 +0000 (16:02 +0200)]
+ added some docu
+ changed interface for dynamic program
+ started refactoring of qpalma main code
Fabio [Mon, 1 Sep 2008 12:48:52 +0000 (14:48 +0200)]
+ added some flags to Makefile args
fabio [Mon, 1 Sep 2008 12:48:07 +0000 (12:48 +0000)]
+ added documentation
git-svn-id: http://svn.tuebingen.mpg.de/ag-raetsch/projects/QPalma@10492
e1793c9e-67f9-0310-80fc-
b846ff1f7b36
fabio [Mon, 1 Sep 2008 12:21:29 +0000 (12:21 +0000)]
+ minor changes in the paths
+ fixed some stuff in the approximation
+ freeze version for git checkout
git-svn-id: http://svn.tuebingen.mpg.de/ag-raetsch/projects/QPalma@10491
e1793c9e-67f9-0310-80fc-
b846ff1f7b36
fabio [Thu, 21 Aug 2008 12:56:52 +0000 (12:56 +0000)]
+ added raw framework of workflow
git-svn-id: http://svn.tuebingen.mpg.de/ag-raetsch/projects/QPalma@10392
e1793c9e-67f9-0310-80fc-
b846ff1f7b36
fabio [Thu, 21 Aug 2008 11:30:12 +0000 (11:30 +0000)]
+ fixed bug in reads stemming from negative strand
git-svn-id: http://svn.tuebingen.mpg.de/ag-raetsch/projects/QPalma@10391
e1793c9e-67f9-0310-80fc-
b846ff1f7b36
fabio [Thu, 14 Aug 2008 10:43:12 +0000 (10:43 +0000)]
+ added convenient script
git-svn-id: http://svn.tuebingen.mpg.de/ag-raetsch/projects/QPalma@10370
e1793c9e-67f9-0310-80fc-
b846ff1f7b36
fabio [Mon, 11 Aug 2008 07:34:50 +0000 (07:34 +0000)]
+ found negative strand bug
+ fix this version as a base for the distribution
git-svn-id: http://svn.tuebingen.mpg.de/ag-raetsch/projects/QPalma@10357
e1793c9e-67f9-0310-80fc-
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fabio [Thu, 7 Aug 2008 14:47:01 +0000 (14:47 +0000)]
+ fixed bug in position calculation for negative strand
git-svn-id: http://svn.tuebingen.mpg.de/ag-raetsch/projects/QPalma@10352
e1793c9e-67f9-0310-80fc-
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fabio [Wed, 6 Aug 2008 16:12:19 +0000 (16:12 +0000)]
+ minor mods in sequence_utils
+ addded alignment viz to Utils
git-svn-id: http://svn.tuebingen.mpg.de/ag-raetsch/projects/QPalma@10345
e1793c9e-67f9-0310-80fc-
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fabio [Wed, 6 Aug 2008 15:21:08 +0000 (15:21 +0000)]
+ added some testcases
git-svn-id: http://svn.tuebingen.mpg.de/ag-raetsch/projects/QPalma@10342
e1793c9e-67f9-0310-80fc-
b846ff1f7b36
fabio [Tue, 5 Aug 2008 10:25:32 +0000 (10:25 +0000)]
+ higher level cluster tasks interface for qpalma
git-svn-id: http://svn.tuebingen.mpg.de/ag-raetsch/projects/QPalma@10328
e1793c9e-67f9-0310-80fc-
b846ff1f7b36
fabio [Mon, 4 Aug 2008 14:34:00 +0000 (14:34 +0000)]
+ minor modifications for the prefetching the whole negative strand
git-svn-id: http://svn.tuebingen.mpg.de/ag-raetsch/projects/QPalma@10316
e1793c9e-67f9-0310-80fc-
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fabio [Mon, 4 Aug 2008 12:23:17 +0000 (12:23 +0000)]
+ minor fixes
git-svn-id: http://svn.tuebingen.mpg.de/ag-raetsch/projects/QPalma@10313
e1793c9e-67f9-0310-80fc-
b846ff1f7b36
fabio [Thu, 31 Jul 2008 21:15:48 +0000 (21:15 +0000)]
+ fixed quality conversion: According to new specs quality of prb is `ascii value - 64` _not_ 50 anymore !
git-svn-id: http://svn.tuebingen.mpg.de/ag-raetsch/projects/QPalma@10276
e1793c9e-67f9-0310-80fc-
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fabio [Thu, 31 Jul 2008 09:50:53 +0000 (09:50 +0000)]
+ modifications in order to use new data format / access methods
git-svn-id: http://svn.tuebingen.mpg.de/ag-raetsch/projects/QPalma@10268
e1793c9e-67f9-0310-80fc-
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fabio [Thu, 31 Jul 2008 09:22:34 +0000 (09:22 +0000)]
+ changed PipelinHeuristic to support new data access functions
+ fixed bug in the split_file utility function
+ minor changes in grid_ file
git-svn-id: http://svn.tuebingen.mpg.de/ag-raetsch/projects/QPalma@10267
e1793c9e-67f9-0310-80fc-
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fabio [Tue, 29 Jul 2008 17:36:12 +0000 (17:36 +0000)]
+ added some testcases for sequence_utils module
git-svn-id: http://svn.tuebingen.mpg.de/ag-raetsch/projects/QPalma@10220
e1793c9e-67f9-0310-80fc-
b846ff1f7b36
fabio [Tue, 29 Jul 2008 15:20:38 +0000 (15:20 +0000)]
+ adapted Lookup table to new data interface
git-svn-id: http://svn.tuebingen.mpg.de/ag-raetsch/projects/QPalma@10219
e1793c9e-67f9-0310-80fc-
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fabio [Tue, 29 Jul 2008 15:02:41 +0000 (15:02 +0000)]
+ changed sequence utils to support more general genomic/splice dirs and filenames
git-svn-id: http://svn.tuebingen.mpg.de/ag-raetsch/projects/QPalma@10218
e1793c9e-67f9-0310-80fc-
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fabio [Tue, 29 Jul 2008 10:44:03 +0000 (10:44 +0000)]
+ fix version before moving to new format
git-svn-id: http://svn.tuebingen.mpg.de/ag-raetsch/projects/QPalma@10216
e1793c9e-67f9-0310-80fc-
b846ff1f7b36
fabio [Thu, 10 Jul 2008 14:39:42 +0000 (14:39 +0000)]
+ Fixed issue with g being last element of a sequence (one donor score too much)
git-svn-id: http://svn.tuebingen.mpg.de/ag-raetsch/projects/QPalma@9991
e1793c9e-67f9-0310-80fc-
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fabio [Thu, 10 Jul 2008 09:24:52 +0000 (09:24 +0000)]
+ modified Lookup table to work with negative strands
+ added correct negative strand processing to the pipeline
git-svn-id: http://svn.tuebingen.mpg.de/ag-raetsch/projects/QPalma@9968
e1793c9e-67f9-0310-80fc-
b846ff1f7b36
fabio [Wed, 9 Jul 2008 17:16:25 +0000 (17:16 +0000)]
+ wrapped sequence and score functions in order to reduce function calls
git-svn-id: http://svn.tuebingen.mpg.de/ag-raetsch/projects/QPalma@9953
e1793c9e-67f9-0310-80fc-
b846ff1f7b36
fabio [Wed, 9 Jul 2008 14:39:16 +0000 (14:39 +0000)]
+ some bugfixes
git-svn-id: http://svn.tuebingen.mpg.de/ag-raetsch/projects/QPalma@9939
e1793c9e-67f9-0310-80fc-
b846ff1f7b36
fabio [Fri, 4 Jul 2008 14:12:59 +0000 (14:12 +0000)]
+ interesting version : it crashes but valgrind detects 0 errors
git-svn-id: http://svn.tuebingen.mpg.de/ag-raetsch/projects/QPalma@9878
e1793c9e-67f9-0310-80fc-
b846ff1f7b36
fabio [Fri, 4 Jul 2008 08:50:57 +0000 (08:50 +0000)]
+ recalculating exons boundaries fixed
git-svn-id: http://svn.tuebingen.mpg.de/ag-raetsch/projects/QPalma@9861
e1793c9e-67f9-0310-80fc-
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fabio [Fri, 4 Jul 2008 07:04:04 +0000 (07:04 +0000)]
+ added reverse complementation to filter reads function
git-svn-id: http://svn.tuebingen.mpg.de/ag-raetsch/projects/QPalma@9860
e1793c9e-67f9-0310-80fc-
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fabio [Thu, 3 Jul 2008 10:53:48 +0000 (10:53 +0000)]
+ moved tools from training dataset generation to their own folder
git-svn-id: http://svn.tuebingen.mpg.de/ag-raetsch/projects/QPalma@9854
e1793c9e-67f9-0310-80fc-
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fabio [Thu, 3 Jul 2008 10:52:59 +0000 (10:52 +0000)]
+ saving changes in the dataset generation
git-svn-id: http://svn.tuebingen.mpg.de/ag-raetsch/projects/QPalma@9853
e1793c9e-67f9-0310-80fc-
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fabio [Wed, 2 Jul 2008 17:34:10 +0000 (17:34 +0000)]
+ some optimization
git-svn-id: http://svn.tuebingen.mpg.de/ag-raetsch/projects/QPalma@9837
e1793c9e-67f9-0310-80fc-
b846ff1f7b36
fabio [Mon, 30 Jun 2008 15:16:48 +0000 (15:16 +0000)]
+ pruned a lot of import declarations
+ switched to new pythongrid version
+ renamed some ambiguous variables
+ cleaned up code base a bit
git-svn-id: http://svn.tuebingen.mpg.de/ag-raetsch/projects/QPalma@9800
e1793c9e-67f9-0310-80fc-
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fabio [Thu, 26 Jun 2008 09:32:24 +0000 (09:32 +0000)]
+ moved penalty lookup and compute_doncc to Plif module
+ added Param class to svn
git-svn-id: http://svn.tuebingen.mpg.de/ag-raetsch/projects/QPalma@9780
e1793c9e-67f9-0310-80fc-
b846ff1f7b36
fabio [Wed, 25 Jun 2008 12:15:21 +0000 (12:15 +0000)]
+ removed unnecessary file
+ changed configuration file usage
git-svn-id: http://svn.tuebingen.mpg.de/ag-raetsch/projects/QPalma@9773
e1793c9e-67f9-0310-80fc-
b846ff1f7b36
fabio [Wed, 25 Jun 2008 10:12:29 +0000 (10:12 +0000)]
+ cleaning up code base
git-svn-id: http://svn.tuebingen.mpg.de/ag-raetsch/projects/QPalma@9772
e1793c9e-67f9-0310-80fc-
b846ff1f7b36
fabio [Tue, 24 Jun 2008 13:01:14 +0000 (13:01 +0000)]
+ added small program for intron-position comparison
git-svn-id: http://svn.tuebingen.mpg.de/ag-raetsch/projects/QPalma@9736
e1793c9e-67f9-0310-80fc-
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fabio [Mon, 23 Jun 2008 08:43:31 +0000 (08:43 +0000)]
+ added proper treatment of reads overlapping into first/last 250 nucleotides of
a chromosome
git-svn-id: http://svn.tuebingen.mpg.de/ag-raetsch/projects/QPalma@9708
e1793c9e-67f9-0310-80fc-
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fabio [Fri, 20 Jun 2008 13:32:31 +0000 (13:32 +0000)]
+ added checks to see whether reads lie in the 250nuc are from the start/stop of a genomic
sequence as there are no splice scores present
git-svn-id: http://svn.tuebingen.mpg.de/ag-raetsch/projects/QPalma@9695
e1793c9e-67f9-0310-80fc-
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fabio [Fri, 20 Jun 2008 12:31:35 +0000 (12:31 +0000)]
+ optimized dataset generation/storage
+ added some assertions
git-svn-id: http://svn.tuebingen.mpg.de/ag-raetsch/projects/QPalma@9694
e1793c9e-67f9-0310-80fc-
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fabio [Wed, 18 Jun 2008 14:50:56 +0000 (14:50 +0000)]
+ cleaning up scripts directory
git-svn-id: http://svn.tuebingen.mpg.de/ag-raetsch/projects/QPalma@9657
e1793c9e-67f9-0310-80fc-
b846ff1f7b36
fabio [Wed, 18 Jun 2008 12:59:28 +0000 (12:59 +0000)]
+ added alignment reconstruction function
+ add script for est2gff processing
git-svn-id: http://svn.tuebingen.mpg.de/ag-raetsch/projects/QPalma@9653
e1793c9e-67f9-0310-80fc-
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fabio [Mon, 16 Jun 2008 14:48:38 +0000 (14:48 +0000)]
+ added two scripts for the psl2gff step
git-svn-id: http://svn.tuebingen.mpg.de/ag-raetsch/projects/QPalma@9622
e1793c9e-67f9-0310-80fc-
b846ff1f7b36
fabio [Sun, 15 Jun 2008 22:01:10 +0000 (22:01 +0000)]
+ saving alignment information now in array container (saves factor 8 memory
requirement)
TODO
+ check for all other places where it could be useful to use array.array instead
of [] (for example quality scores)
git-svn-id: http://svn.tuebingen.mpg.de/ag-raetsch/projects/QPalma@9613
e1793c9e-67f9-0310-80fc-
b846ff1f7b36
fabio [Thu, 12 Jun 2008 12:36:11 +0000 (12:36 +0000)]
+ added selection option for alignment format
+ added pythongrid script for alignment output
git-svn-id: http://svn.tuebingen.mpg.de/ag-raetsch/projects/QPalma@9579
e1793c9e-67f9-0310-80fc-
b846ff1f7b36
fabio [Wed, 11 Jun 2008 15:36:05 +0000 (15:36 +0000)]
+ changed output format of alignment file script to be compatible with est2gff
+ modified PipelineHeuristic to support faster parsers
git-svn-id: http://svn.tuebingen.mpg.de/ag-raetsch/projects/QPalma@9571
e1793c9e-67f9-0310-80fc-
b846ff1f7b36
fabio [Wed, 11 Jun 2008 10:30:14 +0000 (10:30 +0000)]
+ minor changes to support transcriptome data
git-svn-id: http://svn.tuebingen.mpg.de/ag-raetsch/projects/QPalma@9561
e1793c9e-67f9-0310-80fc-
b846ff1f7b36
fabio [Thu, 5 Jun 2008 15:24:51 +0000 (15:24 +0000)]
+ fixed some bugs in the negative strand lookup table
git-svn-id: http://svn.tuebingen.mpg.de/ag-raetsch/projects/QPalma@9406
e1793c9e-67f9-0310-80fc-
b846ff1f7b36
fabio [Wed, 4 Jun 2008 17:49:08 +0000 (17:49 +0000)]
+ extended Lookup object to support negative strand
git-svn-id: http://svn.tuebingen.mpg.de/ag-raetsch/projects/QPalma@9395
e1793c9e-67f9-0310-80fc-
b846ff1f7b36
fabio [Wed, 4 Jun 2008 14:30:17 +0000 (14:30 +0000)]
+ fixed other bug (missing n last entries of the acceptor scores)
git-svn-id: http://svn.tuebingen.mpg.de/ag-raetsch/projects/QPalma@9389
e1793c9e-67f9-0310-80fc-
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fabio [Wed, 4 Jun 2008 10:12:12 +0000 (10:12 +0000)]
+ fixed index error for negative stand queries of splice scores
git-svn-id: http://svn.tuebingen.mpg.de/ag-raetsch/projects/QPalma@9383
e1793c9e-67f9-0310-80fc-
b846ff1f7b36
fabio [Tue, 3 Jun 2008 15:59:42 +0000 (15:59 +0000)]
+ added code for negative strand processing
git-svn-id: http://svn.tuebingen.mpg.de/ag-raetsch/projects/QPalma@9374
e1793c9e-67f9-0310-80fc-
b846ff1f7b36
fabio [Tue, 3 Jun 2008 10:32:05 +0000 (10:32 +0000)]
+ added script to parallelize QPalma heuristic on the cluster
+ added datafile splitting and rejoining method to Utils
git-svn-id: http://svn.tuebingen.mpg.de/ag-raetsch/projects/QPalma@9360
e1793c9e-67f9-0310-80fc-
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fabio [Tue, 3 Jun 2008 08:18:14 +0000 (08:18 +0000)]
+ return value is a tuple now containing the original line as second element
git-svn-id: http://svn.tuebingen.mpg.de/ag-raetsch/projects/QPalma@9352
e1793c9e-67f9-0310-80fc-
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fabio [Mon, 2 Jun 2008 16:57:29 +0000 (16:57 +0000)]
+ added compatiblity to PipelineHeuristic parser
git-svn-id: http://svn.tuebingen.mpg.de/ag-raetsch/projects/QPalma@9342
e1793c9e-67f9-0310-80fc-
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fabio [Mon, 2 Jun 2008 15:34:46 +0000 (15:34 +0000)]
+ removed stupid temp file
git-svn-id: http://svn.tuebingen.mpg.de/ag-raetsch/projects/QPalma@9337
e1793c9e-67f9-0310-80fc-
b846ff1f7b36
fabio [Mon, 2 Jun 2008 15:24:36 +0000 (15:24 +0000)]
+ added VECTOR and MAP mode to ParaParser in order to handle entries with same
ids
git-svn-id: http://svn.tuebingen.mpg.de/ag-raetsch/projects/QPalma@9335
e1793c9e-67f9-0310-80fc-
b846ff1f7b36
fabio [Mon, 2 Jun 2008 14:15:03 +0000 (14:15 +0000)]
+ added some assertions
+ fixed bug for smaller format strings
git-svn-id: http://svn.tuebingen.mpg.de/ag-raetsch/projects/QPalma@9333
e1793c9e-67f9-0310-80fc-
b846ff1f7b36
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