qpalma.git
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

12 years ago+ solved some issues with the data generation
fabio [Tue, 22 Jan 2008 13:02:26 +0000 (13:02 +0000)]
+ solved some issues with the data generation
+ first test with Palma works ! alignments are reconstructed properly
TODO
+ test now with extended model using quality scores

git-svn-id: http://svn.tuebingen.mpg.de/ag-raetsch/projects/QPalma@7523 e1793c9e-67f9-0310-80fc-b846ff1f7b36

12 years agoan example shows how to integrate into qpalma
ong [Tue, 22 Jan 2008 11:38:21 +0000 (11:38 +0000)]
an example shows how to integrate into qpalma

git-svn-id: http://svn.tuebingen.mpg.de/ag-raetsch/projects/QPalma@7521 e1793c9e-67f9-0310-80fc-b846ff1f7b36

12 years agoFirst try at splice site scores. Not yet integrated.
ong [Mon, 21 Jan 2008 18:12:56 +0000 (18:12 +0000)]
First try at splice site scores. Not yet integrated.

git-svn-id: http://svn.tuebingen.mpg.de/ag-raetsch/projects/QPalma@7518 e1793c9e-67f9-0310-80fc-b846ff1f7b36

12 years ago+ added some assertions concerning scores
fabio [Mon, 21 Jan 2008 16:13:04 +0000 (16:13 +0000)]
+ added some assertions concerning scores
+ changed data generator

git-svn-id: http://svn.tuebingen.mpg.de/ag-raetsch/projects/QPalma@7514 e1793c9e-67f9-0310-80fc-b846ff1f7b36

12 years ago+ added prediction script with evaluation functions to test QPalma
fabio [Mon, 21 Jan 2008 11:29:42 +0000 (11:29 +0000)]
+ added prediction script with evaluation functions to test QPalma
+ changed parameter storage
+ removed obsolete script

git-svn-id: http://svn.tuebingen.mpg.de/ag-raetsch/projects/QPalma@7509 e1793c9e-67f9-0310-80fc-b846ff1f7b36

12 years ago+ fixed bug in the assertion whether scalar prod + loss equals viterbi output
fabio [Mon, 21 Jan 2008 10:23:15 +0000 (10:23 +0000)]
+ fixed bug in the assertion whether scalar prod + loss equals viterbi output
+ now check before whether states have distinct scores

git-svn-id: http://svn.tuebingen.mpg.de/ag-raetsch/projects/QPalma@7508 e1793c9e-67f9-0310-80fc-b846ff1f7b36

12 years ago+ added a toy data random generator
fabio [Fri, 18 Jan 2008 13:03:04 +0000 (13:03 +0000)]
+ added a toy data random generator
+ removed num exons == 3 restriction from computeSpliceAlignWithQuality
TODO
- check difference in the DP recurrences of the ../standalone vs. ../python
  versions, choose one to make predictions with.

git-svn-id: http://svn.tuebingen.mpg.de/ag-raetsch/projects/QPalma@7504 e1793c9e-67f9-0310-80fc-b846ff1f7b36

12 years ago+ minor fixes
fabio [Thu, 17 Jan 2008 16:30:44 +0000 (16:30 +0000)]
+ minor fixes

git-svn-id: http://svn.tuebingen.mpg.de/ag-raetsch/projects/QPalma@7499 e1793c9e-67f9-0310-80fc-b846ff1f7b36

12 years ago+ minor changes
fabio [Thu, 17 Jan 2008 14:17:01 +0000 (14:17 +0000)]
+ minor changes

git-svn-id: http://svn.tuebingen.mpg.de/ag-raetsch/projects/QPalma@7496 e1793c9e-67f9-0310-80fc-b846ff1f7b36

12 years ago+ found feature count bug in the quality scores
fabio [Thu, 17 Jan 2008 11:18:03 +0000 (11:18 +0000)]
+ found feature count bug in the quality scores
+ using lookup_penalty instead of own implementation
TODO
+ still +/- 1 between alignment score and dot_prod + loss

git-svn-id: http://svn.tuebingen.mpg.de/ag-raetsch/projects/QPalma@7489 e1793c9e-67f9-0310-80fc-b846ff1f7b36

12 years agoused the last value of quality plifs to fill out the substitution matrix. Some cosmet...
ong [Wed, 16 Jan 2008 19:23:02 +0000 (19:23 +0000)]
used the last value of quality plifs to fill out the substitution matrix. Some cosmetic improvements to plots

git-svn-id: http://svn.tuebingen.mpg.de/ag-raetsch/projects/QPalma@7409 e1793c9e-67f9-0310-80fc-b846ff1f7b36

12 years ago+ fixed matchmatrix for the quality case to be a 1x6 matrix
fabio [Wed, 16 Jan 2008 16:10:26 +0000 (16:10 +0000)]
+ fixed matchmatrix for the quality case to be a 1x6 matrix
+ cleaned up the code a bit

git-svn-id: http://svn.tuebingen.mpg.de/ag-raetsch/projects/QPalma@7401 e1793c9e-67f9-0310-80fc-b846ff1f7b36

12 years agoplot the parameter vector in a useful way
ong [Wed, 16 Jan 2008 15:42:54 +0000 (15:42 +0000)]
plot the parameter vector in a useful way

git-svn-id: http://svn.tuebingen.mpg.de/ag-raetsch/projects/QPalma@7398 e1793c9e-67f9-0310-80fc-b846ff1f7b36

12 years ago+ some minor fixes
fabio [Wed, 16 Jan 2008 14:12:57 +0000 (14:12 +0000)]
+ some minor fixes
+ correct init of quality params
+ additional asserions in c-code
+ undefined chars are now '-1' gaps are '0'

git-svn-id: http://svn.tuebingen.mpg.de/ag-raetsch/projects/QPalma@7392 e1793c9e-67f9-0310-80fc-b846ff1f7b36

12 years ago+ added info file
fabio [Wed, 16 Jan 2008 10:24:23 +0000 (10:24 +0000)]
+ added info file

git-svn-id: http://svn.tuebingen.mpg.de/ag-raetsch/projects/QPalma@7383 e1793c9e-67f9-0310-80fc-b846ff1f7b36

12 years ago+ fixded index bug in feature count
fabio [Tue, 15 Jan 2008 17:04:49 +0000 (17:04 +0000)]
+ fixded index bug in feature count
+ now it works for all quality scores usually [-1,40]

git-svn-id: http://svn.tuebingen.mpg.de/ag-raetsch/projects/QPalma@7363 e1793c9e-67f9-0310-80fc-b846ff1f7b36

12 years ago+ added some assertions
fabio [Tue, 15 Jan 2008 15:26:45 +0000 (15:26 +0000)]
+ added some assertions
+ can switch now between 'normal' palma and qpalma
+ compared result values with qpalma matlab version -> correct
TODO
+ check values/indices for qpalma
+ train!

git-svn-id: http://svn.tuebingen.mpg.de/ag-raetsch/projects/QPalma@7360 e1793c9e-67f9-0310-80fc-b846ff1f7b36

12 years ago+ fixed Swig/python double free bug
fabio [Tue, 15 Jan 2008 11:28:08 +0000 (11:28 +0000)]
+ fixed Swig/python double free bug

git-svn-id: http://svn.tuebingen.mpg.de/ag-raetsch/projects/QPalma@7358 e1793c9e-67f9-0310-80fc-b846ff1f7b36

12 years ago+ fixed if/else cases bug in the increaseFeatureCount function of result_align
fabio [Tue, 15 Jan 2008 11:10:22 +0000 (11:10 +0000)]
+ fixed if/else cases bug in the increaseFeatureCount function of result_align
TODO
+ fix Swig/python double free issue

git-svn-id: http://svn.tuebingen.mpg.de/ag-raetsch/projects/QPalma@7356 e1793c9e-67f9-0310-80fc-b846ff1f7b36

12 years ago+ changed interface for decoded plif features -> directly access double array
fabio [Mon, 14 Jan 2008 17:17:44 +0000 (17:17 +0000)]
+ changed interface for decoded plif features -> directly access double array
+ using now a 5x6 matrix of plifs for scoring / features
TODO
- find annoying double free problem of python/swig interface

git-svn-id: http://svn.tuebingen.mpg.de/ag-raetsch/projects/QPalma@7351 e1793c9e-67f9-0310-80fc-b846ff1f7b36

12 years ago+ disabled don/acc scores properly
fabio [Mon, 14 Jan 2008 11:55:31 +0000 (11:55 +0000)]
+ disabled don/acc scores properly
+ fixed a bug in the feature calculation -> incorrect init of plif.limits
+ added prb value passing to result_align
TODO
- calculate features counts for gaps

git-svn-id: http://svn.tuebingen.mpg.de/ag-raetsch/projects/QPalma@7344 e1793c9e-67f9-0310-80fc-b846ff1f7b36

12 years ago+ modifications and bugfixes
fabio [Fri, 11 Jan 2008 18:17:53 +0000 (18:17 +0000)]
+ modifications and bugfixes
+ added some checks for correct dimensions
+ replaced magic numbers by Configuration.varname
TODO
- check features / parameters matrices for correct values

git-svn-id: http://svn.tuebingen.mpg.de/ag-raetsch/projects/QPalma@7294 e1793c9e-67f9-0310-80fc-b846ff1f7b36

12 years ago*** empty log message ***
raetsch [Fri, 11 Jan 2008 17:08:56 +0000 (17:08 +0000)]
*** empty log message ***

git-svn-id: http://svn.tuebingen.mpg.de/ag-raetsch/projects/QPalma@7293 e1793c9e-67f9-0310-80fc-b846ff1f7b36

12 years ago+ fixed some index bugs in the c code
fabio [Thu, 10 Jan 2008 16:30:14 +0000 (16:30 +0000)]
+ fixed some index bugs in the c code
+ fixed feature count calculation for the label features

git-svn-id: http://svn.tuebingen.mpg.de/ag-raetsch/projects/QPalma@7284 e1793c9e-67f9-0310-80fc-b846ff1f7b36

12 years ago+ added fasta parser for TAIR7 sequences
fabio [Wed, 9 Jan 2008 14:36:56 +0000 (14:36 +0000)]
+ added fasta parser for TAIR7 sequences
+ added loading function for solexa data
+ fixed bug in the filterReads
+ minor changes to qpalma in order to work with new data

git-svn-id: http://svn.tuebingen.mpg.de/ag-raetsch/projects/QPalma@7273 e1793c9e-67f9-0310-80fc-b846ff1f7b36

12 years ago+ restored old filtering functionality -> reads have to start/stop at exon boundaries
fabio [Wed, 9 Jan 2008 11:44:33 +0000 (11:44 +0000)]
+ restored old filtering functionality -> reads have to start/stop at  exon boundaries
+ added regex functionality to extract gene ids from gff files

git-svn-id: http://svn.tuebingen.mpg.de/ag-raetsch/projects/QPalma@7265 e1793c9e-67f9-0310-80fc-b846ff1f7b36

12 years ago+ minor changes
fabio [Tue, 8 Jan 2008 12:54:14 +0000 (12:54 +0000)]
+ minor changes
+ changed older functions to work with new config

git-svn-id: http://svn.tuebingen.mpg.de/ag-raetsch/projects/QPalma@7255 e1793c9e-67f9-0310-80fc-b846ff1f7b36

12 years ago+ added feature calculation for the labels
fabio [Tue, 8 Jan 2008 11:23:31 +0000 (11:23 +0000)]
+ added feature calculation for the labels
+ moved all parameter to central config file
TODO
- clean up code, eliminate some redundancies
- add more assertions

git-svn-id: http://svn.tuebingen.mpg.de/ag-raetsch/projects/QPalma@7254 e1793c9e-67f9-0310-80fc-b846ff1f7b36

12 years ago+ changed reads combination in order to allow for overlaps at both exon borders
fabio [Mon, 7 Jan 2008 16:03:15 +0000 (16:03 +0000)]
+ changed reads combination in order to allow for overlaps at both exon borders
+ fixed index bug in the remove_ambiguities function

git-svn-id: http://svn.tuebingen.mpg.de/ag-raetsch/projects/QPalma@7245 e1793c9e-67f9-0310-80fc-b846ff1f7b36

12 years ago+ parameter transfer to python layer works
fabio [Mon, 7 Jan 2008 10:35:42 +0000 (10:35 +0000)]
+ parameter transfer to python layer works
+ first version of feature count is running
TODO
+ stack all Plif values into the weight vector
+ implement feature count for dna gaps

git-svn-id: http://svn.tuebingen.mpg.de/ag-raetsch/projects/QPalma@7243 e1793c9e-67f9-0310-80fc-b846ff1f7b36

12 years ago+ added part of the feature calculation for the quality score values
fabio [Sun, 6 Jan 2008 16:12:07 +0000 (16:12 +0000)]
+ added part of the feature calculation for the quality score values
+ rearranged some code to eliminate redundancies -> Plif class
+ computeSpliceAlignWithQuality is responsible for the extraction of the feature
counts. this method could be combined with the "normal" computeSpliceAlign later
on.
TODO:
- fix GC problem during parameter returning of the alignemnt
- enable the use of quality scores in the result_align function

git-svn-id: http://svn.tuebingen.mpg.de/ag-raetsch/projects/QPalma@7235 e1793c9e-67f9-0310-80fc-b846ff1f7b36

12 years ago+ incorporated feature count for prb and chastity Plifs in result_align
fabio [Sun, 30 Dec 2007 15:03:42 +0000 (15:03 +0000)]
+ incorporated feature count for prb and chastity Plifs in result_align
+ feature counts are returned as swigged array of plifs
TODO
- write a converter from wrapped swig arrays to numpy matrices
- might be useful to switch from structs to classes for convenience reasons

git-svn-id: http://svn.tuebingen.mpg.de/ag-raetsch/projects/QPalma@7222 e1793c9e-67f9-0310-80fc-b846ff1f7b36

12 years ago+ changed parameter transfer to support array of plifs
fabio [Sat, 29 Dec 2007 20:51:41 +0000 (20:51 +0000)]
+ changed parameter transfer to support array of plifs
+ the quality scores are stored in an array of plifs
TODO
- calculate feature scores for quality plifs

git-svn-id: http://svn.tuebingen.mpg.de/ag-raetsch/projects/QPalma@7221 e1793c9e-67f9-0310-80fc-b846ff1f7b36

12 years ago+ changed filter criteria
fabio [Fri, 28 Dec 2007 14:36:15 +0000 (14:36 +0000)]
+ changed filter criteria
+ added some counters to infer why certain reads are excluded
+ disabled smoothness checks for now

git-svn-id: http://svn.tuebingen.mpg.de/ag-raetsch/projects/QPalma@7216 e1793c9e-67f9-0310-80fc-b846ff1f7b36

12 years ago+ loosened filtering criterion
fabio [Sat, 22 Dec 2007 16:14:34 +0000 (16:14 +0000)]
+ loosened filtering criterion
+ fixed memory leaks

git-svn-id: http://svn.tuebingen.mpg.de/ag-raetsch/projects/QPalma@7210 e1793c9e-67f9-0310-80fc-b846ff1f7b36

12 years ago+ found bug which caused ~10 reads of overlap "0"
fabio [Sat, 22 Dec 2007 02:03:57 +0000 (02:03 +0000)]
+ found bug which caused ~10 reads of overlap "0"
TODO
+ still a memory leak -> check all malloc/free occurrences
+ read line skipping can be made faster

git-svn-id: http://svn.tuebingen.mpg.de/ag-raetsch/projects/QPalma@7209 e1793c9e-67f9-0310-80fc-b846ff1f7b36

12 years ago+ added missing check for strand orientation
fabio [Fri, 21 Dec 2007 15:44:52 +0000 (15:44 +0000)]
+ added missing check for strand orientation
+ added function remove_ambiguities which is responsible for the differences
between annotation and reads ( the [XY] pairs in the sequence string)

git-svn-id: http://svn.tuebingen.mpg.de/ag-raetsch/projects/QPalma@7207 e1793c9e-67f9-0310-80fc-b846ff1f7b36

12 years ago+ added support for writing in result file
fabio [Thu, 20 Dec 2007 16:29:37 +0000 (16:29 +0000)]
+ added support for writing in result file
+ changed number of attributes which are stored in result file

git-svn-id: http://svn.tuebingen.mpg.de/ag-raetsch/projects/QPalma@7200 e1793c9e-67f9-0310-80fc-b846ff1f7b36

12 years ago+ optimized and fixed map file parser
fabio [Thu, 20 Dec 2007 15:05:19 +0000 (15:05 +0000)]
+ optimized and fixed map file parser

git-svn-id: http://svn.tuebingen.mpg.de/ag-raetsch/projects/QPalma@7199 e1793c9e-67f9-0310-80fc-b846ff1f7b36

12 years ago+ compacted parser code
fabio [Thu, 20 Dec 2007 08:18:56 +0000 (08:18 +0000)]
+ compacted parser code
+ found conceptual error

git-svn-id: http://svn.tuebingen.mpg.de/ag-raetsch/projects/QPalma@7191 e1793c9e-67f9-0310-80fc-b846ff1f7b36

12 years ago+ parser works now with mmap and sscanf
fabio [Wed, 19 Dec 2007 16:26:28 +0000 (16:26 +0000)]
+ parser works now with mmap and sscanf
TODO
+ perform some logical checks -> orientation...

git-svn-id: http://svn.tuebingen.mpg.de/ag-raetsch/projects/QPalma@7178 e1793c9e-67f9-0310-80fc-b846ff1f7b36