qpalma.git
10 years ago+ changed check for intial setting of old_w. (matrix != None does not work in cvxopt) master
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)

11 years ago+ update makefiles to fetch automatically valid Python includes and libs
Fabio [Thu, 23 Oct 2008 09:05:47 +0000 (11:05 +0200)]
+ update makefiles to fetch automatically valid Python includes and libs

11 years ago+ changed parameter handling a bit (input files command line args and not inside...
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

11 years ago+ fixed automatic Python path settings in Makefiles
Fabio [Wed, 22 Oct 2008 09:39:32 +0000 (11:39 +0200)]
+ fixed automatic Python path settings in Makefiles

11 years ago+ set proper logging in optimizer code
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

11 years ago+ restructured test cases
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

11 years ago+ fixed issue with negative strand in lookup table
Fabio [Wed, 15 Oct 2008 14:48:25 +0000 (16:48 +0200)]
+ fixed issue with negative strand in lookup table

11 years ago+ extended manual to describe output file format
Fabio [Wed, 15 Oct 2008 13:49:54 +0000 (15:49 +0200)]
+ extended manual to describe output file format

11 years ago+ fixed alignment index calculation for negative strand
Fabio [Wed, 15 Oct 2008 13:03:04 +0000 (15:03 +0200)]
+ fixed alignment index calculation for negative strand

11 years ago+ fixed minor bugs
Fabio [Tue, 14 Oct 2008 16:38:29 +0000 (18:38 +0200)]
+ fixed minor bugs

11 years ago+ extended test cases
Fabio [Tue, 14 Oct 2008 16:00:14 +0000 (18:00 +0200)]
+ extended test cases
+ fixed sequence fetching for 205: , -205: on negative strand

11 years ago+ extended documentation
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

11 years ago+ fixed some issues with the splice site scores and ugly code fragments
Fabio [Mon, 13 Oct 2008 08:46:18 +0000 (10:46 +0200)]
+ fixed some issues with the splice site scores and ugly code fragments

11 years ago+ extended docu
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

11 years ago+ got rid of some legacy code
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

11 years ago+ cleaned up directories
Fabio [Tue, 7 Oct 2008 09:55:20 +0000 (11:55 +0200)]
+ cleaned up directories
+ moved some files to the qpalma package

11 years ago+ renamed dyn_prog directory
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

11 years ago+ removed load_genomic dependency
Fabio [Thu, 2 Oct 2008 16:55:23 +0000 (18:55 +0200)]
+ removed load_genomic dependency

11 years ago+ added palma_utils file
Fabio [Thu, 2 Oct 2008 16:20:05 +0000 (18:20 +0200)]
+ added palma_utils file
+ added some license texts

11 years ago+ added sample configuration file
Fabio [Thu, 2 Oct 2008 13:50:07 +0000 (15:50 +0200)]
+ added sample configuration file
+ minor modifications in the dataset utils

11 years ago+ fixed minor inconsistencies in the code
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

11 years ago+ combined two scripts that were responsible for generating the output format
Fabio [Tue, 30 Sep 2008 10:17:59 +0000 (12:17 +0200)]
+ combined two scripts that were responsible for generating the output format

11 years ago+ extended pipeline code
Fabio [Mon, 29 Sep 2008 13:31:48 +0000 (15:31 +0200)]
+ extended pipeline code
+ refactoring last step of the prediction task

11 years ago+ added some documentary text
Fabio [Mon, 22 Sep 2008 11:01:56 +0000 (13:01 +0200)]
+ added some documentary text
+ some minor modifications

11 years ago+ added some text and references to the documentation
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

11 years ago+ added module to convert pickled predictions to several output formats
Fabio [Sun, 14 Sep 2008 03:41:15 +0000 (05:41 +0200)]
+ added module to convert pickled predictions to several output formats

11 years agofixed minor inconsistencies in the code (naming of new variables etc.)
Fabio [Sat, 13 Sep 2008 19:33:57 +0000 (21:33 +0200)]
fixed minor inconsistencies in the code (naming of new variables etc.)

11 years ago+ moved file to module directory
Fabio [Sat, 13 Sep 2008 19:23:55 +0000 (21:23 +0200)]
+ moved file to module directory

11 years ago+ added framework code for training modus
Fabio [Sat, 13 Sep 2008 19:23:16 +0000 (21:23 +0200)]
+ added framework code for training modus

11 years ago+ added paths for the dataset generation
Fabio [Sat, 13 Sep 2008 02:16:56 +0000 (04:16 +0200)]
+ added paths for the dataset generation
+ checked dataset generation

11 years ago+ added dataset generation function for training set
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

11 years ago+ changed dataset compilation to support new framework
Fabio [Wed, 10 Sep 2008 21:28:08 +0000 (23:28 +0200)]
+ changed dataset compilation to support new framework

11 years ago+ got rid of minor bugs
Fabio [Wed, 10 Sep 2008 21:03:14 +0000 (23:03 +0200)]
+ got rid of minor bugs
+ ApproximationTask is running

11 years ago+ changed module hierarchy a bit
Fabio [Wed, 10 Sep 2008 15:50:56 +0000 (17:50 +0200)]
+ changed module hierarchy a bit

11 years ago+ added settings parser module
Fabio [Wed, 10 Sep 2008 15:25:29 +0000 (17:25 +0200)]
+ added settings parser module

11 years ago+ added settings parser module
Fabio [Wed, 10 Sep 2008 15:09:28 +0000 (17:09 +0200)]
+ added settings parser module

11 years ago+ added configuration file parsing and checking functions
Fabio [Wed, 10 Sep 2008 14:20:27 +0000 (16:20 +0200)]
+ added configuration file parsing and checking functions

11 years ago+ added settings in the form of a global and a run specific part
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

11 years ago+ added small parts to docu
Fabio [Fri, 5 Sep 2008 07:22:36 +0000 (09:22 +0200)]
+ added small parts to docu

11 years ago+ added license text
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

11 years ago+ got rid of some unneccessary code
Fabio [Mon, 1 Sep 2008 16:37:15 +0000 (18:37 +0200)]
+ got rid of some unneccessary code

11 years ago+ changed python and c code in order to perform easier parameter handling and
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

11 years ago+ removed some obsolete dependencies
Fabio [Mon, 1 Sep 2008 14:14:24 +0000 (16:14 +0200)]
+ removed some obsolete dependencies

11 years ago+ added some docu
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

11 years ago+ added some flags to Makefile args
Fabio [Mon, 1 Sep 2008 12:48:52 +0000 (14:48 +0200)]
+ added some flags to Makefile args

11 years ago+ added documentation
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

11 years ago+ minor changes in the paths
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

11 years ago+ added raw framework of workflow
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

11 years ago+ fixed bug in reads stemming from negative strand
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

11 years ago+ added convenient script
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

11 years ago+ found negative strand bug
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-b846ff1f7b36

11 years ago+ fixed bug in position calculation for negative strand
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-b846ff1f7b36

11 years ago+ minor mods in sequence_utils
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-b846ff1f7b36

11 years ago+ added some testcases
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

11 years ago+ higher level cluster tasks interface for qpalma
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

11 years ago+ minor modifications for the prefetching the whole negative strand
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-b846ff1f7b36

11 years ago+ minor fixes
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

11 years ago+ fixed quality conversion: According to new specs quality of prb is `ascii value...
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-b846ff1f7b36

11 years ago+ modifications in order to use new data format / access methods
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-b846ff1f7b36

11 years ago+ changed PipelinHeuristic to support new data access functions
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-b846ff1f7b36

11 years ago+ added some testcases for sequence_utils module
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

11 years ago+ adapted Lookup table to new data interface
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-b846ff1f7b36

11 years ago+ changed sequence utils to support more general genomic/splice dirs and filenames
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-b846ff1f7b36

11 years ago+ fix version before moving to new format
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

11 years ago+ Fixed issue with g being last element of a sequence (one donor score too much)
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-b846ff1f7b36

11 years ago+ modified Lookup table to work with negative strands
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

11 years ago+ wrapped sequence and score functions in order to reduce function calls
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

11 years ago+ some bugfixes
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

11 years ago+ interesting version : it crashes but valgrind detects 0 errors
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

11 years ago+ recalculating exons boundaries fixed
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-b846ff1f7b36

11 years ago+ added reverse complementation to filter reads function
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-b846ff1f7b36

11 years ago+ moved tools from training dataset generation to their own folder
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-b846ff1f7b36

11 years ago+ saving changes in the dataset generation
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-b846ff1f7b36

11 years ago+ some optimization
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

11 years ago+ pruned a lot of import declarations
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-b846ff1f7b36

11 years ago+ moved penalty lookup and compute_doncc to Plif module
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

11 years ago+ removed unnecessary file
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

11 years ago+ cleaning up code base
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

11 years ago+ added small program for intron-position comparison
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-b846ff1f7b36

11 years ago+ added proper treatment of reads overlapping into first/last 250 nucleotides of
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-b846ff1f7b36

11 years ago+ added checks to see whether reads lie in the 250nuc are from the start/stop of...
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-b846ff1f7b36

11 years ago+ optimized dataset generation/storage
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-b846ff1f7b36

11 years ago+ cleaning up scripts directory
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

11 years ago+ added alignment reconstruction function
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-b846ff1f7b36

11 years ago+ added two scripts for the psl2gff step
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

11 years ago+ saving alignment information now in array container (saves factor 8 memory
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

11 years ago+ added selection option for alignment format
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

11 years ago+ changed output format of alignment file script to be compatible with est2gff
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

11 years ago+ minor changes to support transcriptome data
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

11 years ago+ fixed some bugs in the negative strand lookup table
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

11 years ago+ extended Lookup object to support negative strand
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

11 years ago+ fixed other bug (missing n last entries of the acceptor scores)
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-b846ff1f7b36

11 years ago+ fixed index error for negative stand queries of splice scores
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

11 years ago+ added code for negative strand processing
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

11 years ago+ added script to parallelize QPalma heuristic on the cluster
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-b846ff1f7b36

11 years ago+ return value is a tuple now containing the original line as second element
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-b846ff1f7b36

11 years ago+ added compatiblity to PipelineHeuristic parser
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-b846ff1f7b36

11 years ago+ removed stupid temp file
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

11 years ago+ added VECTOR and MAP mode to ParaParser in order to handle entries with same
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

11 years ago+ added some assertions
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