qpalma.git
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

12 years ago+ added processing function for reads
fabio [Wed, 19 Dec 2007 11:43:54 +0000 (11:43 +0000)]
+ added processing function for reads
TODO
- figure out how to use sscanf together with mmap

git-svn-id: http://svn.tuebingen.mpg.de/ag-raetsch/projects/QPalma@7170 e1793c9e-67f9-0310-80fc-b846ff1f7b36

12 years ago+ wrote faster parser / file processing tools in C
fabio [Tue, 18 Dec 2007 14:44:40 +0000 (14:44 +0000)]
+ wrote faster parser / file processing tools in C
TODO
+ finish solexa reads parser

git-svn-id: http://svn.tuebingen.mpg.de/ag-raetsch/projects/QPalma@7164 e1793c9e-67f9-0310-80fc-b846ff1f7b36

12 years ago+ added python parsers for gff and solexa / read files
fabio [Mon, 17 Dec 2007 15:11:15 +0000 (15:11 +0000)]
+ added python parsers for gff and solexa / read files

git-svn-id: http://svn.tuebingen.mpg.de/ag-raetsch/projects/QPalma@7156 e1793c9e-67f9-0310-80fc-b846ff1f7b36

12 years ago+ started to add quality scoring function to C code
fabio [Fri, 14 Dec 2007 16:48:46 +0000 (16:48 +0000)]
+ started to add quality scoring function to C code

TODO
- think about apropriate replacement for global vars
- think about how dnaest should be visible to the python layer

git-svn-id: http://svn.tuebingen.mpg.de/ag-raetsch/projects/QPalma@7100 e1793c9e-67f9-0310-80fc-b846ff1f7b36

12 years ago+ started to extend fill_matrix in order to be able to use quality scores
fabio [Thu, 13 Dec 2007 18:51:36 +0000 (18:51 +0000)]
+ started to extend fill_matrix in order to be able to use quality scores
+ started to extend qpalma.py accordingly

git-svn-id: http://svn.tuebingen.mpg.de/ag-raetsch/projects/QPalma@7066 e1793c9e-67f9-0310-80fc-b846ff1f7b36

12 years ago+ fixed a parameter name bug in the exporter script
fabio [Thu, 13 Dec 2007 14:09:29 +0000 (14:09 +0000)]
+ fixed a parameter name bug in the exporter script
+ minor changes to qpalma

git-svn-id: http://svn.tuebingen.mpg.de/ag-raetsch/projects/QPalma@7059 e1793c9e-67f9-0310-80fc-b846ff1f7b36

12 years ago+ fixed a bug in the C++ interface
fabio [Wed, 12 Dec 2007 16:32:22 +0000 (16:32 +0000)]
+ fixed a bug in the C++ interface
+ removed some debugging printfs
+ added first version of an evaluation script
+ added standalone code to svn

git-svn-id: http://svn.tuebingen.mpg.de/ag-raetsch/projects/QPalma@7048 e1793c9e-67f9-0310-80fc-b846ff1f7b36

12 years ago+ added small scripts for EST filtering
fabio [Tue, 11 Dec 2007 18:20:07 +0000 (18:20 +0000)]
+ added small scripts for EST filtering

git-svn-id: http://svn.tuebingen.mpg.de/ag-raetsch/projects/QPalma@7018 e1793c9e-67f9-0310-80fc-b846ff1f7b36

12 years ago+ added export_param function to export parameters to "palma definition files" (param...
fabio [Mon, 10 Dec 2007 15:00:42 +0000 (15:00 +0000)]
+ added export_param function to export parameters to "palma definition files" (parameter files)
+ added parameter saving function which is called after training
+ fixed some indices for the splice weights

git-svn-id: http://svn.tuebingen.mpg.de/ag-raetsch/projects/QPalma@6978 e1793c9e-67f9-0310-80fc-b846ff1f7b36

12 years ago+ fixed some index bugs
fabio [Mon, 10 Dec 2007 12:14:34 +0000 (12:14 +0000)]
+ fixed some index bugs
+ added debugging output

git-svn-id: http://svn.tuebingen.mpg.de/ag-raetsch/projects/QPalma@6961 e1793c9e-67f9-0310-80fc-b846ff1f7b36

12 years ago+ removed accidently checked in vim swap files
fabio [Fri, 7 Dec 2007 16:56:33 +0000 (16:56 +0000)]
+ removed accidently checked in vim swap files

git-svn-id: http://svn.tuebingen.mpg.de/ag-raetsch/projects/QPalma@6946 e1793c9e-67f9-0310-80fc-b846ff1f7b36

12 years ago+ found index bug in SWIG interface
fabio [Fri, 7 Dec 2007 16:53:09 +0000 (16:53 +0000)]
+ found index bug in SWIG interface
+ added more checks
+ adapted SIQP_CPX solver from the RFP project to work with QPalma
TODO
- check newWeights -> still a +2 offset at some positions

git-svn-id: http://svn.tuebingen.mpg.de/ag-raetsch/projects/QPalma@6945 e1793c9e-67f9-0310-80fc-b846ff1f7b36

12 years ago+ found bug in SWIG interface dna_len vs. dna_len-1 because of '\0' in matlab
fabio [Fri, 7 Dec 2007 13:08:45 +0000 (13:08 +0000)]
+ found bug in SWIG interface dna_len vs. dna_len-1 because of '\0' in matlab

git-svn-id: http://svn.tuebingen.mpg.de/ag-raetsch/projects/QPalma@6941 e1793c9e-67f9-0310-80fc-b846ff1f7b36

12 years ago+ changed interface array_function to array_class
fabio [Thu, 6 Dec 2007 12:04:46 +0000 (12:04 +0000)]
+ changed interface array_function to array_class
+ removed bug in alignmentscores

git-svn-id: http://svn.tuebingen.mpg.de/ag-raetsch/projects/QPalma@6935 e1793c9e-67f9-0310-80fc-b846ff1f7b36

12 years ago+ changed design
fabio [Thu, 6 Dec 2007 12:03:46 +0000 (12:03 +0000)]
+ changed design
+ fixed variable names
+ introduced more auxiliary functions

git-svn-id: http://svn.tuebingen.mpg.de/ag-raetsch/projects/QPalma@6934 e1793c9e-67f9-0310-80fc-b846ff1f7b36

12 years ago+ fixed some index bugs in the weights calculation
fabio [Wed, 5 Dec 2007 17:39:01 +0000 (17:39 +0000)]
+ fixed some index bugs in the weights calculation
+ fixed array bug in SWIG interface

git-svn-id: http://svn.tuebingen.mpg.de/ag-raetsch/projects/QPalma@6931 e1793c9e-67f9-0310-80fc-b846ff1f7b36

12 years ago+ Extended C/C++ interface to return results easily
fabio [Wed, 5 Dec 2007 14:34:37 +0000 (14:34 +0000)]
+ Extended C/C++ interface to return results easily
+ First running version of QPalma SWIG interface
TODO

- still some index issues remain
- add evaluation after wrong alignment generation

git-svn-id: http://svn.tuebingen.mpg.de/ag-raetsch/projects/QPalma@6929 e1793c9e-67f9-0310-80fc-b846ff1f7b36

12 years ago- python code is now checked and complete
fabio [Wed, 5 Dec 2007 10:10:18 +0000 (10:10 +0000)]
- python code is now checked and complete
- interface is complete
TODO

- Change logic in the myalign function
- Modify training loop accordingly

git-svn-id: http://svn.tuebingen.mpg.de/ag-raetsch/projects/QPalma@6927 e1793c9e-67f9-0310-80fc-b846ff1f7b36

12 years ago+ removed several index bugs
fabio [Tue, 4 Dec 2007 14:36:29 +0000 (14:36 +0000)]
+ removed several index bugs
+ added checks to compare against matlab version
+ added convenience functions
TODO
- go on with value checks

git-svn-id: http://svn.tuebingen.mpg.de/ag-raetsch/projects/QPalma@6923 e1793c9e-67f9-0310-80fc-b846ff1f7b36

12 years ago+ rewrote C interface for SWIG/Python
fabio [Mon, 3 Dec 2007 12:19:09 +0000 (12:19 +0000)]
+ rewrote C interface for SWIG/Python
+ extended qpalma algorithm
+ added evalutation script for alignments
TODO

- added preprocessing scripts
- create an evaluation score

git-svn-id: http://svn.tuebingen.mpg.de/ag-raetsch/projects/QPalma@6915 e1793c9e-67f9-0310-80fc-b846ff1f7b36

12 years ago+ using correct interface now
fabio [Sun, 2 Dec 2007 20:11:22 +0000 (20:11 +0000)]
+ using correct interface now
+ added some assertions for range checks
+ added two new python scripts translated from the matlab version
TODO
- dimension and range checking for all other structures/array after set_param_palma
- decide between numpy and lists for smaller arrays

git-svn-id: http://svn.tuebingen.mpg.de/ag-raetsch/projects/QPalma@6913 e1793c9e-67f9-0310-80fc-b846ff1f7b36

12 years ago+ created necessary interfaces
fabio [Sat, 1 Dec 2007 00:59:22 +0000 (00:59 +0000)]
+ created necessary interfaces
+ wrote some convenience python functions in set_param_palma

TODO

- complete python training loop

git-svn-id: http://svn.tuebingen.mpg.de/ag-raetsch/projects/QPalma@6906 e1793c9e-67f9-0310-80fc-b846ff1f7b36

12 years ago+ added c code from the palma project
fabio [Fri, 30 Nov 2007 15:53:57 +0000 (15:53 +0000)]
+ added c code from the palma project
+ added own version of the swig interface

TODO

- think about wrapper for structs / cells
  user either SWIG constrcuts or native python object

git-svn-id: http://svn.tuebingen.mpg.de/ag-raetsch/projects/QPalma@6902 e1793c9e-67f9-0310-80fc-b846ff1f7b36

12 years ago+ added first converted scripts
fabio [Fri, 30 Nov 2007 13:13:42 +0000 (13:13 +0000)]
+ added first converted scripts
+ SpliceAlign computation works

git-svn-id: http://svn.tuebingen.mpg.de/ag-raetsch/projects/QPalma@6888 e1793c9e-67f9-0310-80fc-b846ff1f7b36