qpalma.git
12 years agogit-svn-id: http://svn.tuebingen.mpg.de/ag-raetsch/projects/QPalma@8599 e1793c9e...
raetsch [Thu, 17 Apr 2008 19:34:52 +0000 (19:34 +0000)]
git-svn-id: svn.tuebingen.mpg.de/ag-raetsch/projects/QPalma@8599 e1793c9e-67f9-0310-80fc-b846ff1f7b36

12 years agogit-svn-id: http://svn.tuebingen.mpg.de/ag-raetsch/projects/QPalma@8598 e1793c9e...
raetsch [Thu, 17 Apr 2008 19:27:34 +0000 (19:27 +0000)]
git-svn-id: svn.tuebingen.mpg.de/ag-raetsch/projects/QPalma@8598 e1793c9e-67f9-0310-80fc-b846ff1f7b36

12 years agogit-svn-id: http://svn.tuebingen.mpg.de/ag-raetsch/projects/QPalma@8597 e1793c9e...
raetsch [Thu, 17 Apr 2008 19:26:10 +0000 (19:26 +0000)]
git-svn-id: svn.tuebingen.mpg.de/ag-raetsch/projects/QPalma@8597 e1793c9e-67f9-0310-80fc-b846ff1f7b36

12 years agogit-svn-id: http://svn.tuebingen.mpg.de/ag-raetsch/projects/QPalma@8596 e1793c9e...
raetsch [Thu, 17 Apr 2008 19:25:04 +0000 (19:25 +0000)]
git-svn-id: svn.tuebingen.mpg.de/ag-raetsch/projects/QPalma@8596 e1793c9e-67f9-0310-80fc-b846ff1f7b36

12 years agogit-svn-id: http://svn.tuebingen.mpg.de/ag-raetsch/projects/QPalma@8595 e1793c9e...
raetsch [Thu, 17 Apr 2008 19:23:55 +0000 (19:23 +0000)]
git-svn-id: svn.tuebingen.mpg.de/ag-raetsch/projects/QPalma@8595 e1793c9e-67f9-0310-80fc-b846ff1f7b36

12 years agogit-svn-id: http://svn.tuebingen.mpg.de/ag-raetsch/projects/QPalma@8594 e1793c9e...
raetsch [Thu, 17 Apr 2008 19:22:59 +0000 (19:22 +0000)]
git-svn-id: svn.tuebingen.mpg.de/ag-raetsch/projects/QPalma@8594 e1793c9e-67f9-0310-80fc-b846ff1f7b36

12 years agogit-svn-id: http://svn.tuebingen.mpg.de/ag-raetsch/projects/QPalma@8593 e1793c9e...
raetsch [Thu, 17 Apr 2008 19:22:29 +0000 (19:22 +0000)]
git-svn-id: svn.tuebingen.mpg.de/ag-raetsch/projects/QPalma@8593 e1793c9e-67f9-0310-80fc-b846ff1f7b36

12 years agogit-svn-id: http://svn.tuebingen.mpg.de/ag-raetsch/projects/QPalma@8592 e1793c9e...
raetsch [Thu, 17 Apr 2008 19:21:49 +0000 (19:21 +0000)]
git-svn-id: svn.tuebingen.mpg.de/ag-raetsch/projects/QPalma@8592 e1793c9e-67f9-0310-80fc-b846ff1f7b36

12 years agogit-svn-id: http://svn.tuebingen.mpg.de/ag-raetsch/projects/QPalma@8591 e1793c9e...
raetsch [Thu, 17 Apr 2008 19:18:56 +0000 (19:18 +0000)]
git-svn-id: svn.tuebingen.mpg.de/ag-raetsch/projects/QPalma@8591 e1793c9e-67f9-0310-80fc-b846ff1f7b36

12 years agogit-svn-id: http://svn.tuebingen.mpg.de/ag-raetsch/projects/QPalma@8590 e1793c9e...
raetsch [Thu, 17 Apr 2008 19:16:29 +0000 (19:16 +0000)]
git-svn-id: svn.tuebingen.mpg.de/ag-raetsch/projects/QPalma@8590 e1793c9e-67f9-0310-80fc-b846ff1f7b36

12 years agogit-svn-id: http://svn.tuebingen.mpg.de/ag-raetsch/projects/QPalma@8589 e1793c9e...
raetsch [Thu, 17 Apr 2008 19:14:47 +0000 (19:14 +0000)]
git-svn-id: svn.tuebingen.mpg.de/ag-raetsch/projects/QPalma@8589 e1793c9e-67f9-0310-80fc-b846ff1f7b36

12 years agofirst version of faster heuristic
raetsch [Thu, 17 Apr 2008 19:10:14 +0000 (19:10 +0000)]
first version of faster heuristic

git-svn-id: http://svn.tuebingen.mpg.de/ag-raetsch/projects/QPalma@8588 e1793c9e-67f9-0310-80fc-b846ff1f7b36

12 years ago+ updated filtering
fabio [Thu, 17 Apr 2008 18:34:18 +0000 (18:34 +0000)]
+ updated filtering
+ some minor changes in parsers and data processing

git-svn-id: http://svn.tuebingen.mpg.de/ag-raetsch/projects/QPalma@8587 e1793c9e-67f9-0310-80fc-b846ff1f7b36

12 years ago+ changes
fabio [Thu, 17 Apr 2008 18:33:36 +0000 (18:33 +0000)]
+ changes

git-svn-id: http://svn.tuebingen.mpg.de/ag-raetsch/projects/QPalma@8586 e1793c9e-67f9-0310-80fc-b846ff1f7b36

12 years ago+ added small script for the evaluation of the first vmatch round
fabio [Thu, 17 Apr 2008 14:26:06 +0000 (14:26 +0000)]
+ added small script for the evaluation of the first vmatch round

git-svn-id: http://svn.tuebingen.mpg.de/ag-raetsch/projects/QPalma@8573 e1793c9e-67f9-0310-80fc-b846ff1f7b36

12 years ago+ changed alignment output format to be more blat-like
fabio [Thu, 17 Apr 2008 09:54:19 +0000 (09:54 +0000)]
+ changed alignment output format to be more blat-like
+ performed prediction to see whether changes are correct

git-svn-id: http://svn.tuebingen.mpg.de/ag-raetsch/projects/QPalma@8561 e1793c9e-67f9-0310-80fc-b846ff1f7b36

12 years ago+ extended alignment script
fabio [Thu, 17 Apr 2008 08:28:42 +0000 (08:28 +0000)]
+ extended alignment script
+ modified evalutation script in order to produce error_vs_pos table

git-svn-id: http://svn.tuebingen.mpg.de/ag-raetsch/projects/QPalma@8558 e1793c9e-67f9-0310-80fc-b846ff1f7b36

12 years ago+ minor modifications to allow for parallel prediction of large datasets
fabio [Wed, 16 Apr 2008 22:31:23 +0000 (22:31 +0000)]
+ minor modifications to allow for parallel prediction of large datasets

git-svn-id: http://svn.tuebingen.mpg.de/ag-raetsch/projects/QPalma@8556 e1793c9e-67f9-0310-80fc-b846ff1f7b36

12 years ago+ added new format for QPalma alignment output
fabio [Wed, 16 Apr 2008 15:27:47 +0000 (15:27 +0000)]
+ added new format for QPalma alignment output
+ still experimenting with the heuristic parameters

git-svn-id: http://svn.tuebingen.mpg.de/ag-raetsch/projects/QPalma@8554 e1793c9e-67f9-0310-80fc-b846ff1f7b36

12 years ago+ added field to prediction dict
fabio [Wed, 16 Apr 2008 13:08:38 +0000 (13:08 +0000)]
+ added field to prediction dict
+ extended pipeline heuristic
+ added small script to create alignment file out of alignment objects

git-svn-id: http://svn.tuebingen.mpg.de/ag-raetsch/projects/QPalma@8549 e1793c9e-67f9-0310-80fc-b846ff1f7b36

12 years ago+ refined creation of alternative alignments
fabio [Mon, 14 Apr 2008 14:41:32 +0000 (14:41 +0000)]
+ refined creation of alternative alignments

git-svn-id: http://svn.tuebingen.mpg.de/ag-raetsch/projects/QPalma@8519 e1793c9e-67f9-0310-80fc-b846ff1f7b36

12 years ago+ finished first running version of the spliced/unspliced heuristic
fabio [Mon, 14 Apr 2008 12:28:38 +0000 (12:28 +0000)]
+ finished first running version of the spliced/unspliced heuristic
+ removed dead code from the data generation script
TODO
- generation of alternative alignments in the heuristic may not be optimal

git-svn-id: http://svn.tuebingen.mpg.de/ag-raetsch/projects/QPalma@8516 e1793c9e-67f9-0310-80fc-b846ff1f7b36

12 years ago+ added information on cut positions of spliced reads
fabio [Mon, 14 Apr 2008 07:43:24 +0000 (07:43 +0000)]
+ added information on cut positions of spliced reads

git-svn-id: http://svn.tuebingen.mpg.de/ag-raetsch/projects/QPalma@8511 e1793c9e-67f9-0310-80fc-b846ff1f7b36

12 years ago+ added first version of the heuristic for the mapping pipeline.
fabio [Wed, 9 Apr 2008 13:39:43 +0000 (13:39 +0000)]
+ added first version of the heuristic for the mapping pipeline.

git-svn-id: http://svn.tuebingen.mpg.de/ag-raetsch/projects/QPalma@8426 e1793c9e-67f9-0310-80fc-b846ff1f7b36

12 years agominor changes in the dataset compilation and the evaluation scripts
fabio [Mon, 7 Apr 2008 09:07:09 +0000 (09:07 +0000)]
minor changes in the dataset compilation and the evaluation scripts

git-svn-id: http://svn.tuebingen.mpg.de/ag-raetsch/projects/QPalma@8396 e1793c9e-67f9-0310-80fc-b846ff1f7b36

12 years ago+ minor changes in qpalma_main to take into accout that jobs may be rescheduled
fabio [Thu, 20 Mar 2008 21:37:04 +0000 (21:37 +0000)]
+ minor changes in qpalma_main to take into accout that jobs may be rescheduled
via exit(99)
+ added switch to run objects to disable support point for disabled intron
length model runs
+ minor changes to the evaluation function

git-svn-id: http://svn.tuebingen.mpg.de/ag-raetsch/projects/QPalma@8224 e1793c9e-67f9-0310-80fc-b846ff1f7b36

12 years ago+ changes in the main configuration -> no pickled init vector necessary anymore
fabio [Thu, 20 Mar 2008 21:31:28 +0000 (21:31 +0000)]
+ changes in the main configuration -> no pickled init vector necessary anymore
+ added switch inside solver to disable optimization for intron length model
   (set corresponding values to 0.0)

git-svn-id: http://svn.tuebingen.mpg.de/ag-raetsch/projects/QPalma@8223 e1793c9e-67f9-0310-80fc-b846ff1f7b36

12 years ago+ added function to create tex table from results
fabio [Thu, 20 Mar 2008 10:52:04 +0000 (10:52 +0000)]
+ added function to create tex table from results

git-svn-id: http://svn.tuebingen.mpg.de/ag-raetsch/projects/QPalma@8221 e1793c9e-67f9-0310-80fc-b846ff1f7b36

12 years ago+ minor changes in Evaluation an soap remapping wrapper
fabio [Thu, 20 Mar 2008 01:17:42 +0000 (01:17 +0000)]
+ minor changes in Evaluation an soap remapping wrapper

git-svn-id: http://svn.tuebingen.mpg.de/ag-raetsch/projects/QPalma@8219 e1793c9e-67f9-0310-80fc-b846ff1f7b36

12 years ago+ added script to automatically perform alignment using SOAP 1.07
fabio [Wed, 19 Mar 2008 17:02:17 +0000 (17:02 +0000)]
+ added script to automatically perform alignment using SOAP 1.07
+ added parser for the SOAP 1.07 result format

git-svn-id: http://svn.tuebingen.mpg.de/ag-raetsch/projects/QPalma@8213 e1793c9e-67f9-0310-80fc-b846ff1f7b36

12 years ago+ added splice site score exception to training/prediction
fabio [Tue, 18 Mar 2008 14:37:07 +0000 (14:37 +0000)]
+ added splice site score exception to training/prediction
+ refactored evaluation script count the number of score comparisons correctly

git-svn-id: http://svn.tuebingen.mpg.de/ag-raetsch/projects/QPalma@8197 e1793c9e-67f9-0310-80fc-b846ff1f7b36

12 years ago+ removed duplicated code
fabio [Mon, 17 Mar 2008 13:08:41 +0000 (13:08 +0000)]
+ removed duplicated code
+ found bug in the evaluation -> wrong position calculation for chr 6 and 7

git-svn-id: http://svn.tuebingen.mpg.de/ag-raetsch/projects/QPalma@8172 e1793c9e-67f9-0310-80fc-b846ff1f7b36

12 years ago+ training works,
fabio [Fri, 14 Mar 2008 17:29:26 +0000 (17:29 +0000)]
+ training works,
+ prediction however has still some issues with the correct dna sequence

git-svn-id: http://svn.tuebingen.mpg.de/ag-raetsch/projects/QPalma@8160 e1793c9e-67f9-0310-80fc-b846ff1f7b36

12 years ago+ fixed mentioned index bugs of the SpliceAlign of the ground truth
fabio [Wed, 12 Mar 2008 14:28:24 +0000 (14:28 +0000)]
+ fixed mentioned index bugs of the SpliceAlign of the ground truth

git-svn-id: http://svn.tuebingen.mpg.de/ag-raetsch/projects/QPalma@8134 e1793c9e-67f9-0310-80fc-b846ff1f7b36

12 years ago+ fixed nasty index bugs in the when creating the label of the ground truth
fabio [Wed, 12 Mar 2008 14:27:48 +0000 (14:27 +0000)]
+ fixed nasty index bugs in the when creating the label of the ground truth
+ computeWeights is now happy -> follow the convention acceptor scores are
located at the 'g' of 'ag'

git-svn-id: http://svn.tuebingen.mpg.de/ag-raetsch/projects/QPalma@8133 e1793c9e-67f9-0310-80fc-b846ff1f7b36

12 years ago+ now using the new interval query interface
fabio [Tue, 11 Mar 2008 14:18:53 +0000 (14:18 +0000)]
+ now using the new interval query interface
+ checked code up to splice scores
+ code runs with splice scores disabled

git-svn-id: http://svn.tuebingen.mpg.de/ag-raetsch/projects/QPalma@8126 e1793c9e-67f9-0310-80fc-b846ff1f7b36

12 years ago+ fixed bug in the index calculation of donor/acceptor scores
fabio [Mon, 10 Mar 2008 16:02:55 +0000 (16:02 +0000)]
+ fixed bug in the index calculation of donor/acceptor scores
+ extended check script

git-svn-id: http://svn.tuebingen.mpg.de/ag-raetsch/projects/QPalma@8111 e1793c9e-67f9-0310-80fc-b846ff1f7b36

12 years ago+ changed training method to work with new dataset format
fabio [Fri, 7 Mar 2008 17:47:42 +0000 (17:47 +0000)]
+ changed training method to work with new dataset format
+ minor changes

git-svn-id: http://svn.tuebingen.mpg.de/ag-raetsch/projects/QPalma@8103 e1793c9e-67f9-0310-80fc-b846ff1f7b36

12 years ago+ refactored compile dataset -> removed remaining redundancies in dataset object
fabio [Thu, 6 Mar 2008 17:34:53 +0000 (17:34 +0000)]
+ refactored compile dataset -> removed remaining redundancies in dataset object
+ added sanity check for data

git-svn-id: http://svn.tuebingen.mpg.de/ag-raetsch/projects/QPalma@8085 e1793c9e-67f9-0310-80fc-b846ff1f7b36

12 years ago+ fixed index of reads in filterReads
fabio [Thu, 6 Mar 2008 17:00:55 +0000 (17:00 +0000)]
+ fixed index of reads in filterReads
+ added script to check for valid splice sites defined by gff files

git-svn-id: http://svn.tuebingen.mpg.de/ag-raetsch/projects/QPalma@8083 e1793c9e-67f9-0310-80fc-b846ff1f7b36

12 years ago+ removed some obsolete variables
fabio [Wed, 5 Mar 2008 16:10:31 +0000 (16:10 +0000)]
+ removed some obsolete variables

git-svn-id: http://svn.tuebingen.mpg.de/ag-raetsch/projects/QPalma@8042 e1793c9e-67f9-0310-80fc-b846ff1f7b36

12 years ago+ refactored code further
fabio [Wed, 5 Mar 2008 16:09:21 +0000 (16:09 +0000)]
+ refactored code further
+ evaluation script and job submission works now
TODO
+ check indices for those sites found by vmatch which are arbitrary off the
original ones

git-svn-id: http://svn.tuebingen.mpg.de/ag-raetsch/projects/QPalma@8041 e1793c9e-67f9-0310-80fc-b846ff1f7b36

12 years ago+ added small app to ease profiling
fabio [Wed, 5 Mar 2008 13:16:59 +0000 (13:16 +0000)]
+ added small app to ease profiling

git-svn-id: http://svn.tuebingen.mpg.de/ag-raetsch/projects/QPalma@8036 e1793c9e-67f9-0310-80fc-b846ff1f7b36

12 years ago+ extended scripts
fabio [Thu, 28 Feb 2008 13:18:32 +0000 (13:18 +0000)]
+ extended scripts
+ added function to parse map.vm files from vmatch

git-svn-id: http://svn.tuebingen.mpg.de/ag-raetsch/projects/QPalma@7976 e1793c9e-67f9-0310-80fc-b846ff1f7b36

12 years ago+ minor changes
fabio [Wed, 27 Feb 2008 14:59:55 +0000 (14:59 +0000)]
+ minor changes

git-svn-id: http://svn.tuebingen.mpg.de/ag-raetsch/projects/QPalma@7970 e1793c9e-67f9-0310-80fc-b846ff1f7b36

12 years agogit-svn-id: http://svn.tuebingen.mpg.de/ag-raetsch/projects/QPalma@7959 e1793c9e...
raetsch [Tue, 26 Feb 2008 20:56:30 +0000 (20:56 +0000)]
git-svn-id: svn.tuebingen.mpg.de/ag-raetsch/projects/QPalma@7959 e1793c9e-67f9-0310-80fc-b846ff1f7b36

12 years ago+ first running version of Evaluation script
fabio [Tue, 26 Feb 2008 11:28:16 +0000 (11:28 +0000)]
+ first running version of Evaluation script
+ fixed some missing/delocated imports

git-svn-id: http://svn.tuebingen.mpg.de/ag-raetsch/projects/QPalma@7957 e1793c9e-67f9-0310-80fc-b846ff1f7b36

12 years ago+ performed some further refactoring
fabio [Mon, 25 Feb 2008 14:56:47 +0000 (14:56 +0000)]
+ performed some further refactoring
+ added Utils module

git-svn-id: http://svn.tuebingen.mpg.de/ag-raetsch/projects/QPalma@7950 e1793c9e-67f9-0310-80fc-b846ff1f7b36

12 years ago+ did some refactoring to reduce duplicated code
fabio [Mon, 25 Feb 2008 13:47:53 +0000 (13:47 +0000)]
+ did some refactoring to reduce duplicated code

git-svn-id: http://svn.tuebingen.mpg.de/ag-raetsch/projects/QPalma@7949 e1793c9e-67f9-0310-80fc-b846ff1f7b36

12 years ago+ dataset size is smaller now (just storing indices).
fabio [Mon, 25 Feb 2008 11:01:20 +0000 (11:01 +0000)]
+ dataset size is smaller now (just storing indices).
+ started refactoring mainloop

git-svn-id: http://svn.tuebingen.mpg.de/ag-raetsch/projects/QPalma@7948 e1793c9e-67f9-0310-80fc-b846ff1f7b36

12 years ago+ added use of all remapped possibilities of a given read
fabio [Thu, 21 Feb 2008 15:21:40 +0000 (15:21 +0000)]
+ added use of all remapped possibilities of a given read

git-svn-id: http://svn.tuebingen.mpg.de/ag-raetsch/projects/QPalma@7932 e1793c9e-67f9-0310-80fc-b846ff1f7b36

12 years ago+ fixed bug in the check for aligned dna fragments -> now we only have <= 0.1%
fabio [Thu, 21 Feb 2008 13:01:01 +0000 (13:01 +0000)]
+ fixed bug in the check for aligned dna fragments -> now we only have <= 0.1%
of unaligned sequences

git-svn-id: http://svn.tuebingen.mpg.de/ag-raetsch/projects/QPalma@7927 e1793c9e-67f9-0310-80fc-b846ff1f7b36

12 years ago+ refactored code of dataset generation method
fabio [Thu, 21 Feb 2008 11:33:07 +0000 (11:33 +0000)]
+ refactored code of dataset generation method
TODO
+ check boundaries

git-svn-id: http://svn.tuebingen.mpg.de/ag-raetsch/projects/QPalma@7926 e1793c9e-67f9-0310-80fc-b846ff1f7b36

12 years ago+ added code to allow for configuration
fabio [Mon, 18 Feb 2008 10:53:34 +0000 (10:53 +0000)]
+ added code to allow for configuration

git-svn-id: http://svn.tuebingen.mpg.de/ag-raetsch/projects/QPalma@7906 e1793c9e-67f9-0310-80fc-b846ff1f7b36

12 years ago+ small script for plotting fraction of wrong reads for each possible overlap
fabio [Tue, 12 Feb 2008 06:58:51 +0000 (06:58 +0000)]
+ small script for plotting fraction of wrong reads for each possible overlap

git-svn-id: http://svn.tuebingen.mpg.de/ag-raetsch/projects/QPalma@7815 e1793c9e-67f9-0310-80fc-b846ff1f7b36

12 years ago+ model selection scripts are ready
fabio [Mon, 11 Feb 2008 16:01:37 +0000 (16:01 +0000)]
+ model selection scripts are ready

git-svn-id: http://svn.tuebingen.mpg.de/ag-raetsch/projects/QPalma@7783 e1793c9e-67f9-0310-80fc-b846ff1f7b36

12 years ago+ added minor functionality pprinting ...
fabio [Mon, 11 Feb 2008 14:23:12 +0000 (14:23 +0000)]
+ added minor functionality pprinting ...

git-svn-id: http://svn.tuebingen.mpg.de/ag-raetsch/projects/QPalma@7782 e1793c9e-67f9-0310-80fc-b846ff1f7b36

12 years ago+ added basic scripts to generate runs for an experiment
fabio [Mon, 11 Feb 2008 14:06:10 +0000 (14:06 +0000)]
+ added basic scripts to generate runs for an experiment

git-svn-id: http://svn.tuebingen.mpg.de/ag-raetsch/projects/QPalma@7781 e1793c9e-67f9-0310-80fc-b846ff1f7b36

12 years ago+ added scripts for model selection on the cluster
fabio [Mon, 11 Feb 2008 12:01:27 +0000 (12:01 +0000)]
+ added scripts for model selection on the cluster
+ added option for variable number of constraints to be generated
between solver calls (per "round")

git-svn-id: http://svn.tuebingen.mpg.de/ag-raetsch/projects/QPalma@7780 e1793c9e-67f9-0310-80fc-b846ff1f7b36

12 years ago+ changed filter behavior (tendency towards smaller read fragments)
fabio [Sun, 10 Feb 2008 22:38:55 +0000 (22:38 +0000)]
+ changed filter behavior (tendency towards smaller read fragments)
+ removed monotonicity assertion for objective

git-svn-id: http://svn.tuebingen.mpg.de/ag-raetsch/projects/QPalma@7777 e1793c9e-67f9-0310-80fc-b846ff1f7b36

12 years ago+ fixed a bug in the filtering (forgot to disable remove_ambiguities)
fabio [Sun, 10 Feb 2008 15:45:49 +0000 (15:45 +0000)]
+ fixed a bug in the filtering (forgot to disable remove_ambiguities)
+ added assertions in the compile dataset

git-svn-id: http://svn.tuebingen.mpg.de/ag-raetsch/projects/QPalma@7773 e1793c9e-67f9-0310-80fc-b846ff1f7b36

12 years ago+ fixed bug in the combination of reads with deletions
fabio [Sat, 9 Feb 2008 19:24:54 +0000 (19:24 +0000)]
+ fixed bug in the combination of reads with deletions

git-svn-id: http://svn.tuebingen.mpg.de/ag-raetsch/projects/QPalma@7759 e1793c9e-67f9-0310-80fc-b846ff1f7b36

12 years ago+ modified dataset generation in order to recalculate exons boundaries
fabio [Sat, 9 Feb 2008 14:53:16 +0000 (14:53 +0000)]
+ modified dataset generation in order to recalculate exons boundaries

git-svn-id: http://svn.tuebingen.mpg.de/ag-raetsch/projects/QPalma@7754 e1793c9e-67f9-0310-80fc-b846ff1f7b36

12 years ago+ fixed bug in the filtering function (if read offset overlapped into [AC]
fabio [Sat, 9 Feb 2008 14:42:05 +0000 (14:42 +0000)]
+ fixed bug in the filtering function (if read offset overlapped into [AC]
position then we got single brackets)

git-svn-id: http://svn.tuebingen.mpg.de/ag-raetsch/projects/QPalma@7753 e1793c9e-67f9-0310-80fc-b846ff1f7b36

12 years ago+ extended filtering to take indels [A-] resp. [-A] into account
fabio [Sat, 9 Feb 2008 12:14:26 +0000 (12:14 +0000)]
+ extended filtering to take indels [A-] resp. [-A] into account

git-svn-id: http://svn.tuebingen.mpg.de/ag-raetsch/projects/QPalma@7729 e1793c9e-67f9-0310-80fc-b846ff1f7b36

12 years ago+ fixed bug in the computeSpliceAlign... function
fabio [Fri, 8 Feb 2008 20:33:39 +0000 (20:33 +0000)]
+ fixed bug in the computeSpliceAlign... function
+ added some more assertions and log messages

git-svn-id: http://svn.tuebingen.mpg.de/ag-raetsch/projects/QPalma@7728 e1793c9e-67f9-0310-80fc-b846ff1f7b36

12 years ago+ minor changes to filterReads
fabio [Fri, 8 Feb 2008 16:40:22 +0000 (16:40 +0000)]
+ minor changes to filterReads
+ added some assertions to computeSpliceAlign...
+ removed a bug in the feature calculation of the label

git-svn-id: http://svn.tuebingen.mpg.de/ag-raetsch/projects/QPalma@7726 e1793c9e-67f9-0310-80fc-b846ff1f7b36

12 years ago+ fixed uninitialised values
fabio [Thu, 7 Feb 2008 13:55:18 +0000 (13:55 +0000)]
+ fixed uninitialised values

git-svn-id: http://svn.tuebingen.mpg.de/ag-raetsch/projects/QPalma@7703 e1793c9e-67f9-0310-80fc-b846ff1f7b36

12 years ago+ new version of the filterReads program
fabio [Thu, 7 Feb 2008 11:47:17 +0000 (11:47 +0000)]
+ new version of the filterReads program

git-svn-id: http://svn.tuebingen.mpg.de/ag-raetsch/projects/QPalma@7701 e1793c9e-67f9-0310-80fc-b846ff1f7b36

12 years ago+ some fixes of the filterReads and parser functions
fabio [Thu, 7 Feb 2008 00:12:36 +0000 (00:12 +0000)]
+ some fixes of the filterReads and parser functions

git-svn-id: http://svn.tuebingen.mpg.de/ag-raetsch/projects/QPalma@7698 e1793c9e-67f9-0310-80fc-b846ff1f7b36

12 years ago+ resolved an issue with the memory mapping in filterReads
fabio [Wed, 6 Feb 2008 22:04:30 +0000 (22:04 +0000)]
+ resolved an issue with the memory mapping in filterReads
+ added more checks in filterReads

git-svn-id: http://svn.tuebingen.mpg.de/ag-raetsch/projects/QPalma@7697 e1793c9e-67f9-0310-80fc-b846ff1f7b36

12 years ago+ rearranged code
fabio [Wed, 6 Feb 2008 14:47:29 +0000 (14:47 +0000)]
+ rearranged code
+ added capability produce "pretty-print" alignment output using palma scripts

git-svn-id: http://svn.tuebingen.mpg.de/ag-raetsch/projects/QPalma@7694 e1793c9e-67f9-0310-80fc-b846ff1f7b36

12 years ago+ extended dataset compilation function
fabio [Tue, 5 Feb 2008 21:56:44 +0000 (21:56 +0000)]
+ extended dataset compilation function
+ added regularization parameters
+ fixed a bug in the regularizer (off-diagonal terms)
+ decreased number of support points

git-svn-id: http://svn.tuebingen.mpg.de/ag-raetsch/projects/QPalma@7688 e1793c9e-67f9-0310-80fc-b846ff1f7b36

12 years ago+ minor bugfixes in the compile_dataset script
fabio [Tue, 5 Feb 2008 11:10:45 +0000 (11:10 +0000)]
+ minor bugfixes in the compile_dataset script
+ added parameters to Configuration script
+ changed representation of entries in the parser

git-svn-id: http://svn.tuebingen.mpg.de/ag-raetsch/projects/QPalma@7683 e1793c9e-67f9-0310-80fc-b846ff1f7b36

12 years ago+ minor changes
fabio [Mon, 4 Feb 2008 15:51:54 +0000 (15:51 +0000)]
+ minor changes
+ restored some dataset creation functionality
+ stored random but fixed init values in a pickle file

git-svn-id: http://svn.tuebingen.mpg.de/ag-raetsch/projects/QPalma@7681 e1793c9e-67f9-0310-80fc-b846ff1f7b36

12 years ago+ modified filtering of reads
fabio [Mon, 4 Feb 2008 10:11:34 +0000 (10:11 +0000)]
+ modified filtering of reads
+ extended dataset generation script
+ rearranged loading functions for qpalma training

git-svn-id: http://svn.tuebingen.mpg.de/ag-raetsch/projects/QPalma@7678 e1793c9e-67f9-0310-80fc-b846ff1f7b36

12 years ago+ added script to generate datasets
fabio [Sat, 2 Feb 2008 15:06:08 +0000 (15:06 +0000)]
+ added script to generate datasets
+ added parsers for the solexa reads

git-svn-id: http://svn.tuebingen.mpg.de/ag-raetsch/projects/QPalma@7668 e1793c9e-67f9-0310-80fc-b846ff1f7b36

12 years ago+ added read structure for new parser
fabio [Sat, 2 Feb 2008 14:03:56 +0000 (14:03 +0000)]
+ added read structure for new parser
+ added missing strand check
+ changin map parser to read remapped reads

git-svn-id: http://svn.tuebingen.mpg.de/ag-raetsch/projects/QPalma@7667 e1793c9e-67f9-0310-80fc-b846ff1f7b36

12 years ago+ extended evaluation function to return positionwise deviations
fabio [Thu, 31 Jan 2008 16:32:41 +0000 (16:32 +0000)]
+ extended evaluation function to return positionwise deviations
+ changed data loading to use load_genomic for sequences fetching
+ added more assertions
+ changed weights in the regularizer to account for different number of features

git-svn-id: http://svn.tuebingen.mpg.de/ag-raetsch/projects/QPalma@7654 e1793c9e-67f9-0310-80fc-b846ff1f7b36

12 years ago+ removed duplicated code
fabio [Mon, 28 Jan 2008 12:07:15 +0000 (12:07 +0000)]
+ removed duplicated code
+ added regularization of quality plifs

git-svn-id: http://svn.tuebingen.mpg.de/ag-raetsch/projects/QPalma@7600 e1793c9e-67f9-0310-80fc-b846ff1f7b36

12 years ago+ renamed files
fabio [Fri, 25 Jan 2008 17:40:33 +0000 (17:40 +0000)]
+ renamed files

git-svn-id: http://svn.tuebingen.mpg.de/ag-raetsch/projects/QPalma@7588 e1793c9e-67f9-0310-80fc-b846ff1f7b36

12 years ago+ fix
fabio [Fri, 25 Jan 2008 17:09:36 +0000 (17:09 +0000)]
+ fix

git-svn-id: http://svn.tuebingen.mpg.de/ag-raetsch/projects/QPalma@7587 e1793c9e-67f9-0310-80fc-b846ff1f7b36

12 years ago+ renaming business
fabio [Fri, 25 Jan 2008 16:49:48 +0000 (16:49 +0000)]
+ renaming business

git-svn-id: http://svn.tuebingen.mpg.de/ag-raetsch/projects/QPalma@7585 e1793c9e-67f9-0310-80fc-b846ff1f7b36

12 years agomerged training/prediction scripts
fabio [Fri, 25 Jan 2008 16:48:54 +0000 (16:48 +0000)]
merged training/prediction scripts

git-svn-id: http://svn.tuebingen.mpg.de/ag-raetsch/projects/QPalma@7584 e1793c9e-67f9-0310-80fc-b846ff1f7b36

12 years ago+ fix development stage before doing some refactoring
fabio [Fri, 25 Jan 2008 16:08:29 +0000 (16:08 +0000)]
+ fix development stage before doing some refactoring

git-svn-id: http://svn.tuebingen.mpg.de/ag-raetsch/projects/QPalma@7582 e1793c9e-67f9-0310-80fc-b846ff1f7b36

12 years ago+ added exons read boundary output to filterReads output
fabio [Fri, 25 Jan 2008 14:33:07 +0000 (14:33 +0000)]
+ added exons read boundary output to filterReads output
+ minor modifications of data processing tools to allow for train/predict mode

git-svn-id: http://svn.tuebingen.mpg.de/ag-raetsch/projects/QPalma@7580 e1793c9e-67f9-0310-80fc-b846ff1f7b36

12 years ago+ minor fixes
fabio [Thu, 24 Jan 2008 17:48:37 +0000 (17:48 +0000)]
+ minor fixes
+ some checks

git-svn-id: http://svn.tuebingen.mpg.de/ag-raetsch/projects/QPalma@7571 e1793c9e-67f9-0310-80fc-b846ff1f7b36

12 years ago+ resolved some index bugs concerning the intron boundaries resp. splicesite
fabio [Thu, 24 Jan 2008 14:23:12 +0000 (14:23 +0000)]
+ resolved some index bugs concerning the intron boundaries resp. splicesite
scores

git-svn-id: http://svn.tuebingen.mpg.de/ag-raetsch/projects/QPalma@7559 e1793c9e-67f9-0310-80fc-b846ff1f7b36

12 years ago+ added splicesite scores to training
fabio [Wed, 23 Jan 2008 16:55:02 +0000 (16:55 +0000)]
+ added splicesite scores to training
+ moved splicesite stuff to tools dir of the qpalma module
TODO
+ find index +1 bug in the decoded SpliceAlign vectors

git-svn-id: http://svn.tuebingen.mpg.de/ag-raetsch/projects/QPalma@7546 e1793c9e-67f9-0310-80fc-b846ff1f7b36

12 years ago+ minor mods
fabio [Wed, 23 Jan 2008 15:13:40 +0000 (15:13 +0000)]
+ minor mods

git-svn-id: http://svn.tuebingen.mpg.de/ag-raetsch/projects/QPalma@7545 e1793c9e-67f9-0310-80fc-b846ff1f7b36

12 years ago+ changed output in the filterReads
fabio [Wed, 23 Jan 2008 12:01:24 +0000 (12:01 +0000)]
+ changed output in the filterReads
+ changed data parser to correct exons start/stop positions

git-svn-id: http://svn.tuebingen.mpg.de/ag-raetsch/projects/QPalma@7544 e1793c9e-67f9-0310-80fc-b846ff1f7b36

12 years ago+ restored functionality
fabio [Wed, 23 Jan 2008 11:39:31 +0000 (11:39 +0000)]
+ restored functionality
+ exon_idx bug repaired (+1 offset for all was incorrect)
+ rearranged python code

git-svn-id: http://svn.tuebingen.mpg.de/ag-raetsch/projects/QPalma@7543 e1793c9e-67f9-0310-80fc-b846ff1f7b36

12 years ago+ svn file moving
fabio [Wed, 23 Jan 2008 11:17:17 +0000 (11:17 +0000)]
+ svn file moving

git-svn-id: http://svn.tuebingen.mpg.de/ag-raetsch/projects/QPalma@7540 e1793c9e-67f9-0310-80fc-b846ff1f7b36

12 years agoannoying svn business
fabio [Wed, 23 Jan 2008 11:11:43 +0000 (11:11 +0000)]
annoying svn business

git-svn-id: http://svn.tuebingen.mpg.de/ag-raetsch/projects/QPalma@7539 e1793c9e-67f9-0310-80fc-b846ff1f7b36

12 years ago+ some changes concerning filter params
fabio [Wed, 23 Jan 2008 11:10:09 +0000 (11:10 +0000)]
+ some changes concerning filter params
+ some rearrangement of the code
+ extension of the solexa parser to take exon_indices into account

git-svn-id: http://svn.tuebingen.mpg.de/ag-raetsch/projects/QPalma@7538 e1793c9e-67f9-0310-80fc-b846ff1f7b36

12 years ago+ renamed main dir in order to create python module hierarchy
fabio [Wed, 23 Jan 2008 09:37:33 +0000 (09:37 +0000)]
+ renamed main dir in order to create python module hierarchy

git-svn-id: http://svn.tuebingen.mpg.de/ag-raetsch/projects/QPalma@7537 e1793c9e-67f9-0310-80fc-b846ff1f7b36

12 years ago+ moved pythn data tools to new dir
fabio [Wed, 23 Jan 2008 09:31:16 +0000 (09:31 +0000)]
+ moved pythn data tools to new dir

git-svn-id: http://svn.tuebingen.mpg.de/ag-raetsch/projects/QPalma@7536 e1793c9e-67f9-0310-80fc-b846ff1f7b36

12 years ago+ small changes
fabio [Wed, 23 Jan 2008 09:27:22 +0000 (09:27 +0000)]
+ small changes

git-svn-id: http://svn.tuebingen.mpg.de/ag-raetsch/projects/QPalma@7535 e1793c9e-67f9-0310-80fc-b846ff1f7b36

12 years ago+ check in latest changes
fabio [Wed, 23 Jan 2008 09:16:43 +0000 (09:16 +0000)]
+ check in latest changes
TODO
+ rearrange directory structure a bit

git-svn-id: http://svn.tuebingen.mpg.de/ag-raetsch/projects/QPalma@7534 e1793c9e-67f9-0310-80fc-b846ff1f7b36

12 years ago+ fixed bug in the label feature calculation
fabio [Tue, 22 Jan 2008 15:30:15 +0000 (15:30 +0000)]
+ fixed bug in the label feature calculation
+ seems to work with constant quality scores

git-svn-id: http://svn.tuebingen.mpg.de/ag-raetsch/projects/QPalma@7532 e1793c9e-67f9-0310-80fc-b846ff1f7b36