qpalma.git
11 years ago+ minor changes in the paths
fabio [Mon, 1 Sep 2008 12:21:29 +0000 (12:21 +0000)]
+ minor changes in the paths
+ fixed some stuff in the approximation
+ freeze version for git checkout

git-svn-id: http://svn.tuebingen.mpg.de/ag-raetsch/projects/QPalma@10491 e1793c9e-67f9-0310-80fc-b846ff1f7b36

11 years ago+ added raw framework of workflow
fabio [Thu, 21 Aug 2008 12:56:52 +0000 (12:56 +0000)]
+ added raw framework of workflow

git-svn-id: http://svn.tuebingen.mpg.de/ag-raetsch/projects/QPalma@10392 e1793c9e-67f9-0310-80fc-b846ff1f7b36

11 years ago+ fixed bug in reads stemming from negative strand
fabio [Thu, 21 Aug 2008 11:30:12 +0000 (11:30 +0000)]
+ fixed bug in reads stemming from negative strand

git-svn-id: http://svn.tuebingen.mpg.de/ag-raetsch/projects/QPalma@10391 e1793c9e-67f9-0310-80fc-b846ff1f7b36

11 years ago+ added convenient script
fabio [Thu, 14 Aug 2008 10:43:12 +0000 (10:43 +0000)]
+ added convenient script

git-svn-id: http://svn.tuebingen.mpg.de/ag-raetsch/projects/QPalma@10370 e1793c9e-67f9-0310-80fc-b846ff1f7b36

11 years ago+ found negative strand bug
fabio [Mon, 11 Aug 2008 07:34:50 +0000 (07:34 +0000)]
+ found negative strand bug
+ fix this version as a base for the distribution

git-svn-id: http://svn.tuebingen.mpg.de/ag-raetsch/projects/QPalma@10357 e1793c9e-67f9-0310-80fc-b846ff1f7b36

11 years ago+ fixed bug in position calculation for negative strand
fabio [Thu, 7 Aug 2008 14:47:01 +0000 (14:47 +0000)]
+ fixed bug in position calculation for negative strand

git-svn-id: http://svn.tuebingen.mpg.de/ag-raetsch/projects/QPalma@10352 e1793c9e-67f9-0310-80fc-b846ff1f7b36

11 years ago+ minor mods in sequence_utils
fabio [Wed, 6 Aug 2008 16:12:19 +0000 (16:12 +0000)]
+ minor mods in sequence_utils
+ addded alignment viz to Utils

git-svn-id: http://svn.tuebingen.mpg.de/ag-raetsch/projects/QPalma@10345 e1793c9e-67f9-0310-80fc-b846ff1f7b36

11 years ago+ added some testcases
fabio [Wed, 6 Aug 2008 15:21:08 +0000 (15:21 +0000)]
+ added some testcases

git-svn-id: http://svn.tuebingen.mpg.de/ag-raetsch/projects/QPalma@10342 e1793c9e-67f9-0310-80fc-b846ff1f7b36

11 years ago+ higher level cluster tasks interface for qpalma
fabio [Tue, 5 Aug 2008 10:25:32 +0000 (10:25 +0000)]
+ higher level cluster tasks interface for qpalma

git-svn-id: http://svn.tuebingen.mpg.de/ag-raetsch/projects/QPalma@10328 e1793c9e-67f9-0310-80fc-b846ff1f7b36

11 years ago+ minor modifications for the prefetching the whole negative strand
fabio [Mon, 4 Aug 2008 14:34:00 +0000 (14:34 +0000)]
+ minor modifications for the prefetching the whole negative strand

git-svn-id: http://svn.tuebingen.mpg.de/ag-raetsch/projects/QPalma@10316 e1793c9e-67f9-0310-80fc-b846ff1f7b36

11 years ago+ minor fixes
fabio [Mon, 4 Aug 2008 12:23:17 +0000 (12:23 +0000)]
+ minor fixes

git-svn-id: http://svn.tuebingen.mpg.de/ag-raetsch/projects/QPalma@10313 e1793c9e-67f9-0310-80fc-b846ff1f7b36

11 years ago+ fixed quality conversion: According to new specs quality of prb is `ascii value...
fabio [Thu, 31 Jul 2008 21:15:48 +0000 (21:15 +0000)]
+ fixed quality conversion: According to new specs quality of prb is `ascii value - 64` _not_ 50 anymore !

git-svn-id: http://svn.tuebingen.mpg.de/ag-raetsch/projects/QPalma@10276 e1793c9e-67f9-0310-80fc-b846ff1f7b36

11 years ago+ modifications in order to use new data format / access methods
fabio [Thu, 31 Jul 2008 09:50:53 +0000 (09:50 +0000)]
+ modifications in order to use new data format / access methods

git-svn-id: http://svn.tuebingen.mpg.de/ag-raetsch/projects/QPalma@10268 e1793c9e-67f9-0310-80fc-b846ff1f7b36

11 years ago+ changed PipelinHeuristic to support new data access functions
fabio [Thu, 31 Jul 2008 09:22:34 +0000 (09:22 +0000)]
+ changed PipelinHeuristic to support new data access functions
+ fixed bug in the split_file utility function
+ minor changes in grid_ file

git-svn-id: http://svn.tuebingen.mpg.de/ag-raetsch/projects/QPalma@10267 e1793c9e-67f9-0310-80fc-b846ff1f7b36

11 years ago+ added some testcases for sequence_utils module
fabio [Tue, 29 Jul 2008 17:36:12 +0000 (17:36 +0000)]
+ added some testcases for sequence_utils module

git-svn-id: http://svn.tuebingen.mpg.de/ag-raetsch/projects/QPalma@10220 e1793c9e-67f9-0310-80fc-b846ff1f7b36

11 years ago+ adapted Lookup table to new data interface
fabio [Tue, 29 Jul 2008 15:20:38 +0000 (15:20 +0000)]
+ adapted Lookup table to new data interface

git-svn-id: http://svn.tuebingen.mpg.de/ag-raetsch/projects/QPalma@10219 e1793c9e-67f9-0310-80fc-b846ff1f7b36

11 years ago+ changed sequence utils to support more general genomic/splice dirs and filenames
fabio [Tue, 29 Jul 2008 15:02:41 +0000 (15:02 +0000)]
+ changed sequence utils to support more general genomic/splice dirs and filenames

git-svn-id: http://svn.tuebingen.mpg.de/ag-raetsch/projects/QPalma@10218 e1793c9e-67f9-0310-80fc-b846ff1f7b36

11 years ago+ fix version before moving to new format
fabio [Tue, 29 Jul 2008 10:44:03 +0000 (10:44 +0000)]
+ fix version before moving to new format

git-svn-id: http://svn.tuebingen.mpg.de/ag-raetsch/projects/QPalma@10216 e1793c9e-67f9-0310-80fc-b846ff1f7b36

11 years ago+ Fixed issue with g being last element of a sequence (one donor score too much)
fabio [Thu, 10 Jul 2008 14:39:42 +0000 (14:39 +0000)]
+ Fixed issue with g being last element of a sequence (one donor score too much)

git-svn-id: http://svn.tuebingen.mpg.de/ag-raetsch/projects/QPalma@9991 e1793c9e-67f9-0310-80fc-b846ff1f7b36

11 years ago+ modified Lookup table to work with negative strands
fabio [Thu, 10 Jul 2008 09:24:52 +0000 (09:24 +0000)]
+ modified Lookup table to work with negative strands
+ added correct negative strand processing to the pipeline

git-svn-id: http://svn.tuebingen.mpg.de/ag-raetsch/projects/QPalma@9968 e1793c9e-67f9-0310-80fc-b846ff1f7b36

11 years ago+ wrapped sequence and score functions in order to reduce function calls
fabio [Wed, 9 Jul 2008 17:16:25 +0000 (17:16 +0000)]
+ wrapped sequence and score functions in order to reduce function calls

git-svn-id: http://svn.tuebingen.mpg.de/ag-raetsch/projects/QPalma@9953 e1793c9e-67f9-0310-80fc-b846ff1f7b36

11 years ago+ some bugfixes
fabio [Wed, 9 Jul 2008 14:39:16 +0000 (14:39 +0000)]
+ some bugfixes

git-svn-id: http://svn.tuebingen.mpg.de/ag-raetsch/projects/QPalma@9939 e1793c9e-67f9-0310-80fc-b846ff1f7b36

11 years ago+ interesting version : it crashes but valgrind detects 0 errors
fabio [Fri, 4 Jul 2008 14:12:59 +0000 (14:12 +0000)]
+ interesting version : it crashes but valgrind detects 0 errors

git-svn-id: http://svn.tuebingen.mpg.de/ag-raetsch/projects/QPalma@9878 e1793c9e-67f9-0310-80fc-b846ff1f7b36

11 years ago+ recalculating exons boundaries fixed
fabio [Fri, 4 Jul 2008 08:50:57 +0000 (08:50 +0000)]
+ recalculating exons boundaries fixed

git-svn-id: http://svn.tuebingen.mpg.de/ag-raetsch/projects/QPalma@9861 e1793c9e-67f9-0310-80fc-b846ff1f7b36

11 years ago+ added reverse complementation to filter reads function
fabio [Fri, 4 Jul 2008 07:04:04 +0000 (07:04 +0000)]
+ added reverse complementation to filter reads function

git-svn-id: http://svn.tuebingen.mpg.de/ag-raetsch/projects/QPalma@9860 e1793c9e-67f9-0310-80fc-b846ff1f7b36

11 years ago+ moved tools from training dataset generation to their own folder
fabio [Thu, 3 Jul 2008 10:53:48 +0000 (10:53 +0000)]
+ moved tools from training dataset generation to their own folder

git-svn-id: http://svn.tuebingen.mpg.de/ag-raetsch/projects/QPalma@9854 e1793c9e-67f9-0310-80fc-b846ff1f7b36

11 years ago+ saving changes in the dataset generation
fabio [Thu, 3 Jul 2008 10:52:59 +0000 (10:52 +0000)]
+ saving changes in the dataset generation

git-svn-id: http://svn.tuebingen.mpg.de/ag-raetsch/projects/QPalma@9853 e1793c9e-67f9-0310-80fc-b846ff1f7b36

11 years ago+ some optimization
fabio [Wed, 2 Jul 2008 17:34:10 +0000 (17:34 +0000)]
+ some optimization

git-svn-id: http://svn.tuebingen.mpg.de/ag-raetsch/projects/QPalma@9837 e1793c9e-67f9-0310-80fc-b846ff1f7b36

11 years ago+ pruned a lot of import declarations
fabio [Mon, 30 Jun 2008 15:16:48 +0000 (15:16 +0000)]
+ pruned a lot of import declarations
+ switched to new pythongrid version
+ renamed some ambiguous variables
+ cleaned up code base a bit

git-svn-id: http://svn.tuebingen.mpg.de/ag-raetsch/projects/QPalma@9800 e1793c9e-67f9-0310-80fc-b846ff1f7b36

11 years ago+ moved penalty lookup and compute_doncc to Plif module
fabio [Thu, 26 Jun 2008 09:32:24 +0000 (09:32 +0000)]
+ moved penalty lookup and compute_doncc to Plif module
+ added Param class to svn

git-svn-id: http://svn.tuebingen.mpg.de/ag-raetsch/projects/QPalma@9780 e1793c9e-67f9-0310-80fc-b846ff1f7b36

11 years ago+ removed unnecessary file
fabio [Wed, 25 Jun 2008 12:15:21 +0000 (12:15 +0000)]
+ removed unnecessary file
+ changed configuration file usage

git-svn-id: http://svn.tuebingen.mpg.de/ag-raetsch/projects/QPalma@9773 e1793c9e-67f9-0310-80fc-b846ff1f7b36

11 years ago+ cleaning up code base
fabio [Wed, 25 Jun 2008 10:12:29 +0000 (10:12 +0000)]
+ cleaning up code base

git-svn-id: http://svn.tuebingen.mpg.de/ag-raetsch/projects/QPalma@9772 e1793c9e-67f9-0310-80fc-b846ff1f7b36

11 years ago+ added small program for intron-position comparison
fabio [Tue, 24 Jun 2008 13:01:14 +0000 (13:01 +0000)]
+ added small program for intron-position comparison

git-svn-id: http://svn.tuebingen.mpg.de/ag-raetsch/projects/QPalma@9736 e1793c9e-67f9-0310-80fc-b846ff1f7b36

11 years ago+ added proper treatment of reads overlapping into first/last 250 nucleotides of
fabio [Mon, 23 Jun 2008 08:43:31 +0000 (08:43 +0000)]
+ added proper treatment of reads overlapping into first/last 250 nucleotides of
a chromosome

git-svn-id: http://svn.tuebingen.mpg.de/ag-raetsch/projects/QPalma@9708 e1793c9e-67f9-0310-80fc-b846ff1f7b36

11 years ago+ added checks to see whether reads lie in the 250nuc are from the start/stop of...
fabio [Fri, 20 Jun 2008 13:32:31 +0000 (13:32 +0000)]
+ added checks to see whether reads lie in the 250nuc are from the start/stop of a genomic
sequence as there are no splice scores present

git-svn-id: http://svn.tuebingen.mpg.de/ag-raetsch/projects/QPalma@9695 e1793c9e-67f9-0310-80fc-b846ff1f7b36

11 years ago+ optimized dataset generation/storage
fabio [Fri, 20 Jun 2008 12:31:35 +0000 (12:31 +0000)]
+ optimized dataset generation/storage
+ added some assertions

git-svn-id: http://svn.tuebingen.mpg.de/ag-raetsch/projects/QPalma@9694 e1793c9e-67f9-0310-80fc-b846ff1f7b36

11 years ago+ cleaning up scripts directory
fabio [Wed, 18 Jun 2008 14:50:56 +0000 (14:50 +0000)]
+ cleaning up scripts directory

git-svn-id: http://svn.tuebingen.mpg.de/ag-raetsch/projects/QPalma@9657 e1793c9e-67f9-0310-80fc-b846ff1f7b36

11 years ago+ added alignment reconstruction function
fabio [Wed, 18 Jun 2008 12:59:28 +0000 (12:59 +0000)]
+ added alignment reconstruction function
+ add script for est2gff processing

git-svn-id: http://svn.tuebingen.mpg.de/ag-raetsch/projects/QPalma@9653 e1793c9e-67f9-0310-80fc-b846ff1f7b36

11 years ago+ added two scripts for the psl2gff step
fabio [Mon, 16 Jun 2008 14:48:38 +0000 (14:48 +0000)]
+ added two scripts for the psl2gff step

git-svn-id: http://svn.tuebingen.mpg.de/ag-raetsch/projects/QPalma@9622 e1793c9e-67f9-0310-80fc-b846ff1f7b36

11 years ago+ saving alignment information now in array container (saves factor 8 memory
fabio [Sun, 15 Jun 2008 22:01:10 +0000 (22:01 +0000)]
+ saving alignment information now in array container (saves factor 8 memory
requirement)
TODO
+ check for all other places where it could be useful to use array.array instead
of [] (for example quality scores)

git-svn-id: http://svn.tuebingen.mpg.de/ag-raetsch/projects/QPalma@9613 e1793c9e-67f9-0310-80fc-b846ff1f7b36

11 years ago+ added selection option for alignment format
fabio [Thu, 12 Jun 2008 12:36:11 +0000 (12:36 +0000)]
+ added selection option for alignment format
+ added pythongrid script for alignment output

git-svn-id: http://svn.tuebingen.mpg.de/ag-raetsch/projects/QPalma@9579 e1793c9e-67f9-0310-80fc-b846ff1f7b36

11 years ago+ changed output format of alignment file script to be compatible with est2gff
fabio [Wed, 11 Jun 2008 15:36:05 +0000 (15:36 +0000)]
+ changed output format of alignment file script to be compatible with est2gff
+ modified PipelineHeuristic to support faster parsers

git-svn-id: http://svn.tuebingen.mpg.de/ag-raetsch/projects/QPalma@9571 e1793c9e-67f9-0310-80fc-b846ff1f7b36

11 years ago+ minor changes to support transcriptome data
fabio [Wed, 11 Jun 2008 10:30:14 +0000 (10:30 +0000)]
+ minor changes to support transcriptome data

git-svn-id: http://svn.tuebingen.mpg.de/ag-raetsch/projects/QPalma@9561 e1793c9e-67f9-0310-80fc-b846ff1f7b36

11 years ago+ fixed some bugs in the negative strand lookup table
fabio [Thu, 5 Jun 2008 15:24:51 +0000 (15:24 +0000)]
+ fixed some bugs in the negative strand lookup table

git-svn-id: http://svn.tuebingen.mpg.de/ag-raetsch/projects/QPalma@9406 e1793c9e-67f9-0310-80fc-b846ff1f7b36

11 years ago+ extended Lookup object to support negative strand
fabio [Wed, 4 Jun 2008 17:49:08 +0000 (17:49 +0000)]
+ extended Lookup object to support negative strand

git-svn-id: http://svn.tuebingen.mpg.de/ag-raetsch/projects/QPalma@9395 e1793c9e-67f9-0310-80fc-b846ff1f7b36

11 years ago+ fixed other bug (missing n last entries of the acceptor scores)
fabio [Wed, 4 Jun 2008 14:30:17 +0000 (14:30 +0000)]
+ fixed other bug (missing n last entries of the acceptor scores)

git-svn-id: http://svn.tuebingen.mpg.de/ag-raetsch/projects/QPalma@9389 e1793c9e-67f9-0310-80fc-b846ff1f7b36

11 years ago+ fixed index error for negative stand queries of splice scores
fabio [Wed, 4 Jun 2008 10:12:12 +0000 (10:12 +0000)]
+ fixed index error for negative stand queries of splice scores

git-svn-id: http://svn.tuebingen.mpg.de/ag-raetsch/projects/QPalma@9383 e1793c9e-67f9-0310-80fc-b846ff1f7b36

11 years ago+ added code for negative strand processing
fabio [Tue, 3 Jun 2008 15:59:42 +0000 (15:59 +0000)]
+ added code for negative strand processing

git-svn-id: http://svn.tuebingen.mpg.de/ag-raetsch/projects/QPalma@9374 e1793c9e-67f9-0310-80fc-b846ff1f7b36

11 years ago+ added script to parallelize QPalma heuristic on the cluster
fabio [Tue, 3 Jun 2008 10:32:05 +0000 (10:32 +0000)]
+ added script to parallelize QPalma heuristic on the cluster
+ added datafile splitting and rejoining method to Utils

git-svn-id: http://svn.tuebingen.mpg.de/ag-raetsch/projects/QPalma@9360 e1793c9e-67f9-0310-80fc-b846ff1f7b36

11 years ago+ return value is a tuple now containing the original line as second element
fabio [Tue, 3 Jun 2008 08:18:14 +0000 (08:18 +0000)]
+ return value is a tuple now containing the original line as second element

git-svn-id: http://svn.tuebingen.mpg.de/ag-raetsch/projects/QPalma@9352 e1793c9e-67f9-0310-80fc-b846ff1f7b36

11 years ago+ added compatiblity to PipelineHeuristic parser
fabio [Mon, 2 Jun 2008 16:57:29 +0000 (16:57 +0000)]
+ added compatiblity to PipelineHeuristic parser

git-svn-id: http://svn.tuebingen.mpg.de/ag-raetsch/projects/QPalma@9342 e1793c9e-67f9-0310-80fc-b846ff1f7b36

11 years ago+ removed stupid temp file
fabio [Mon, 2 Jun 2008 15:34:46 +0000 (15:34 +0000)]
+ removed stupid temp file

git-svn-id: http://svn.tuebingen.mpg.de/ag-raetsch/projects/QPalma@9337 e1793c9e-67f9-0310-80fc-b846ff1f7b36

11 years ago+ added VECTOR and MAP mode to ParaParser in order to handle entries with same
fabio [Mon, 2 Jun 2008 15:24:36 +0000 (15:24 +0000)]
+ added VECTOR and MAP mode to ParaParser in order to handle entries with same
ids

git-svn-id: http://svn.tuebingen.mpg.de/ag-raetsch/projects/QPalma@9335 e1793c9e-67f9-0310-80fc-b846ff1f7b36

11 years ago+ added some assertions
fabio [Mon, 2 Jun 2008 14:15:03 +0000 (14:15 +0000)]
+ added some assertions
+ fixed bug for smaller format strings

git-svn-id: http://svn.tuebingen.mpg.de/ag-raetsch/projects/QPalma@9333 e1793c9e-67f9-0310-80fc-b846ff1f7b36

11 years ago+ found string splitting bug
fabio [Mon, 2 Jun 2008 12:18:51 +0000 (12:18 +0000)]
+ found string splitting bug

git-svn-id: http://svn.tuebingen.mpg.de/ag-raetsch/projects/QPalma@9330 e1793c9e-67f9-0310-80fc-b846ff1f7b36

11 years ago+ rewrote some data storage code
fabio [Mon, 2 Jun 2008 11:44:41 +0000 (11:44 +0000)]
+ rewrote some data storage code
+ still have to find pointer-to-entry related problem

git-svn-id: http://svn.tuebingen.mpg.de/ag-raetsch/projects/QPalma@9329 e1793c9e-67f9-0310-80fc-b846ff1f7b36

11 years ago+ fix starting point for rewrite of data accession for PipelineHeuristic
fabio [Mon, 2 Jun 2008 09:52:55 +0000 (09:52 +0000)]
+ fix starting point for rewrite of data accession for PipelineHeuristic

git-svn-id: http://svn.tuebingen.mpg.de/ag-raetsch/projects/QPalma@9328 e1793c9e-67f9-0310-80fc-b846ff1f7b36

11 years ago+ added generice parser code
fabio [Mon, 2 Jun 2008 07:41:24 +0000 (07:41 +0000)]
+ added generice parser code

git-svn-id: http://svn.tuebingen.mpg.de/ag-raetsch/projects/QPalma@9327 e1793c9e-67f9-0310-80fc-b846ff1f7b36

11 years ago+ original reads sequence now has to be reconstructred automatically as we have
fabio [Fri, 30 May 2008 12:00:47 +0000 (12:00 +0000)]
+ original reads sequence now has to be reconstructred automatically as we have
no ground truth file anymore

git-svn-id: http://svn.tuebingen.mpg.de/ag-raetsch/projects/QPalma@9309 e1793c9e-67f9-0310-80fc-b846ff1f7b36

11 years ago+ added missing modules imports
fabio [Fri, 30 May 2008 11:59:12 +0000 (11:59 +0000)]
+ added missing modules imports

git-svn-id: http://svn.tuebingen.mpg.de/ag-raetsch/projects/QPalma@9308 e1793c9e-67f9-0310-80fc-b846ff1f7b36

11 years ago+ shell script for the heuristic run
fabio [Fri, 30 May 2008 10:19:53 +0000 (10:19 +0000)]
+ shell script for the heuristic run

git-svn-id: http://svn.tuebingen.mpg.de/ag-raetsch/projects/QPalma@9305 e1793c9e-67f9-0310-80fc-b846ff1f7b36

11 years ago+ removed unnecessary numpy dependency
fabio [Fri, 30 May 2008 10:06:26 +0000 (10:06 +0000)]
+ removed unnecessary numpy dependency

git-svn-id: http://svn.tuebingen.mpg.de/ag-raetsch/projects/QPalma@9304 e1793c9e-67f9-0310-80fc-b846ff1f7b36

11 years ago+ added modifications of parser to repo
fabio [Fri, 30 May 2008 10:04:01 +0000 (10:04 +0000)]
+ added modifications of parser to repo

git-svn-id: http://svn.tuebingen.mpg.de/ag-raetsch/projects/QPalma@9303 e1793c9e-67f9-0310-80fc-b846ff1f7b36

11 years ago+ removed files
fabio [Fri, 30 May 2008 09:53:36 +0000 (09:53 +0000)]
+ removed files

git-svn-id: http://svn.tuebingen.mpg.de/ag-raetsch/projects/QPalma@9302 e1793c9e-67f9-0310-80fc-b846ff1f7b36

11 years ago+ minor changes
fabio [Fri, 30 May 2008 09:30:59 +0000 (09:30 +0000)]
+ minor changes

git-svn-id: http://svn.tuebingen.mpg.de/ag-raetsch/projects/QPalma@9301 e1793c9e-67f9-0310-80fc-b846ff1f7b36

11 years ago+ moved sequence access functions to own module
fabio [Fri, 30 May 2008 09:29:59 +0000 (09:29 +0000)]
+ moved sequence access functions to own module

git-svn-id: http://svn.tuebingen.mpg.de/ag-raetsch/projects/QPalma@9300 e1793c9e-67f9-0310-80fc-b846ff1f7b36

11 years ago+ added dataset generation function to dataset specific scripts dir.
fabio [Fri, 30 May 2008 09:25:43 +0000 (09:25 +0000)]
+ added dataset generation function to dataset specific scripts dir.

git-svn-id: http://svn.tuebingen.mpg.de/ag-raetsch/projects/QPalma@9299 e1793c9e-67f9-0310-80fc-b846ff1f7b36

11 years ago+ moved qpalma dataset generation scripts
fabio [Fri, 30 May 2008 09:08:13 +0000 (09:08 +0000)]
+ moved qpalma dataset generation scripts

git-svn-id: http://svn.tuebingen.mpg.de/ag-raetsch/projects/QPalma@9298 e1793c9e-67f9-0310-80fc-b846ff1f7b36

11 years ago+ added a script that processes the single lane files to create a full dataset
fabio [Fri, 30 May 2008 09:00:10 +0000 (09:00 +0000)]
+ added a script that processes the single lane files to create a full dataset

git-svn-id: http://svn.tuebingen.mpg.de/ag-raetsch/projects/QPalma@9297 e1793c9e-67f9-0310-80fc-b846ff1f7b36

11 years ago+ added some more scripts from the dataset processing
fabio [Fri, 30 May 2008 08:08:20 +0000 (08:08 +0000)]
+ added some more scripts from the dataset processing

git-svn-id: http://svn.tuebingen.mpg.de/ag-raetsch/projects/QPalma@9295 e1793c9e-67f9-0310-80fc-b846ff1f7b36

11 years ago+ added small counting script
fabio [Fri, 30 May 2008 08:06:27 +0000 (08:06 +0000)]
+ added small counting script

git-svn-id: http://svn.tuebingen.mpg.de/ag-raetsch/projects/QPalma@9294 e1793c9e-67f9-0310-80fc-b846ff1f7b36

11 years ago+ minor changes
fabio [Mon, 26 May 2008 07:13:53 +0000 (07:13 +0000)]
+ minor changes
+ changed data representation a bit
+ moved some code to other modules
+ removed / commented some debugging code lines

git-svn-id: http://svn.tuebingen.mpg.de/ag-raetsch/projects/QPalma@9188 e1793c9e-67f9-0310-80fc-b846ff1f7b36

11 years ago+ added script which draws the coverage bar plots presented in the QPalma paper
fabio [Wed, 21 May 2008 19:43:10 +0000 (19:43 +0000)]
+ added script which draws the coverage bar plots presented in the QPalma paper

git-svn-id: http://svn.tuebingen.mpg.de/ag-raetsch/projects/QPalma@9134 e1793c9e-67f9-0310-80fc-b846ff1f7b36

11 years ago+ changed data loading procedures
fabio [Wed, 21 May 2008 19:42:33 +0000 (19:42 +0000)]
+ changed data loading procedures
+ made functions generic

git-svn-id: http://svn.tuebingen.mpg.de/ag-raetsch/projects/QPalma@9133 e1793c9e-67f9-0310-80fc-b846ff1f7b36

11 years ago+ added missing free for line array
fabio [Fri, 16 May 2008 07:58:21 +0000 (07:58 +0000)]
+ added missing free for line array
+ added check to ensure consistency with python parser
+ parsing is much faster now

git-svn-id: http://svn.tuebingen.mpg.de/ag-raetsch/projects/QPalma@9044 e1793c9e-67f9-0310-80fc-b846ff1f7b36

11 years ago+ minor modifications
fabio [Thu, 15 May 2008 16:59:59 +0000 (16:59 +0000)]
+ minor modifications
TODO
+ fix bug in the array access (fetch function)

git-svn-id: http://svn.tuebingen.mpg.de/ag-raetsch/projects/QPalma@9040 e1793c9e-67f9-0310-80fc-b846ff1f7b36

11 years ago+ modified module in order to act like a database returning a dictionary of the
fabio [Thu, 15 May 2008 16:37:57 +0000 (16:37 +0000)]
+ modified module in order to act like a database returning a dictionary of the
line given a particular id

git-svn-id: http://svn.tuebingen.mpg.de/ag-raetsch/projects/QPalma@9039 e1793c9e-67f9-0310-80fc-b846ff1f7b36

11 years ago+ coded alternative implementation using a list per line
fabio [Thu, 15 May 2008 13:17:09 +0000 (13:17 +0000)]
+ coded alternative implementation using a list per line
+ got rid of qualities scores as they are not needed for evaluation anyways
+ modified check script in order to be able to check dict/line entries
separately

git-svn-id: http://svn.tuebingen.mpg.de/ag-raetsch/projects/QPalma@9027 e1793c9e-67f9-0310-80fc-b846ff1f7b36

11 years ago+ fixed seq size bug
fabio [Thu, 15 May 2008 12:06:01 +0000 (12:06 +0000)]
+ fixed seq size bug
+ added check to ensure that this c code does the same as the old python code

git-svn-id: http://svn.tuebingen.mpg.de/ag-raetsch/projects/QPalma@9024 e1793c9e-67f9-0310-80fc-b846ff1f7b36

11 years ago+ fixed a bug in the sscanf
fabio [Thu, 15 May 2008 11:40:10 +0000 (11:40 +0000)]
+ fixed a bug in the sscanf

git-svn-id: http://svn.tuebingen.mpg.de/ag-raetsch/projects/QPalma@9023 e1793c9e-67f9-0310-80fc-b846ff1f7b36

11 years ago+ removed binaries
fabio [Thu, 15 May 2008 10:32:45 +0000 (10:32 +0000)]
+ removed binaries
+ added input conversion for quality array

git-svn-id: http://svn.tuebingen.mpg.de/ag-raetsch/projects/QPalma@9020 e1793c9e-67f9-0310-80fc-b846ff1f7b36

11 years ago+ added python module for reads parsing as plain python code is to slow
fabio [Thu, 15 May 2008 10:26:35 +0000 (10:26 +0000)]
+ added python module for reads parsing as plain python code is to slow

git-svn-id: http://svn.tuebingen.mpg.de/ag-raetsch/projects/QPalma@9019 e1793c9e-67f9-0310-80fc-b846ff1f7b36

11 years ago+ take into account multiple hits per unique read
fabio [Wed, 14 May 2008 16:23:07 +0000 (16:23 +0000)]
+ take into account multiple hits per unique read
+ change prediction file name to include current set_flag

git-svn-id: http://svn.tuebingen.mpg.de/ag-raetsch/projects/QPalma@9012 e1793c9e-67f9-0310-80fc-b846ff1f7b36

11 years ago+ made original reads file location a parameter for the command line
fabio [Wed, 14 May 2008 16:06:10 +0000 (16:06 +0000)]
+ made original reads file location a parameter for the command line

git-svn-id: http://svn.tuebingen.mpg.de/ag-raetsch/projects/QPalma@9011 e1793c9e-67f9-0310-80fc-b846ff1f7b36

11 years ago+ First fully working version.
fabio [Wed, 14 May 2008 15:26:28 +0000 (15:26 +0000)]
+ First fully working version.

git-svn-id: http://svn.tuebingen.mpg.de/ag-raetsch/projects/QPalma@9010 e1793c9e-67f9-0310-80fc-b846ff1f7b36

11 years ago+ changed dataset compiler to take the two different map files into account
fabio [Wed, 14 May 2008 08:13:55 +0000 (08:13 +0000)]
+ changed dataset compiler to take the two different map files into account

git-svn-id: http://svn.tuebingen.mpg.de/ag-raetsch/projects/QPalma@9002 e1793c9e-67f9-0310-80fc-b846ff1f7b36

11 years ago+ first version of a script that uses pythongrid
fabio [Wed, 14 May 2008 07:43:03 +0000 (07:43 +0000)]
+ first version of a script that uses pythongrid

git-svn-id: http://svn.tuebingen.mpg.de/ag-raetsch/projects/QPalma@9001 e1793c9e-67f9-0310-80fc-b846ff1f7b36

11 years ago+ added configuration variables to main config file
fabio [Tue, 13 May 2008 14:53:57 +0000 (14:53 +0000)]
+ added configuration variables to main config file
+ extended parameter checking script
+ wrote pipeline framework for vmatch and heuristic steps

git-svn-id: http://svn.tuebingen.mpg.de/ag-raetsch/projects/QPalma@8999 e1793c9e-67f9-0310-80fc-b846ff1f7b36

11 years ago+ sanity checks for the global config file
fabio [Tue, 13 May 2008 13:31:20 +0000 (13:31 +0000)]
+ sanity checks for the global config file

git-svn-id: http://svn.tuebingen.mpg.de/ag-raetsch/projects/QPalma@8992 e1793c9e-67f9-0310-80fc-b846ff1f7b36

11 years ago+ adapted training method to use new dataset standard
fabio [Tue, 13 May 2008 11:34:37 +0000 (11:34 +0000)]
+ adapted training method to use new dataset standard

git-svn-id: http://svn.tuebingen.mpg.de/ag-raetsch/projects/QPalma@8984 e1793c9e-67f9-0310-80fc-b846ff1f7b36

11 years ago+ changed dataset representation
fabio [Mon, 12 May 2008 20:58:54 +0000 (20:58 +0000)]
+ changed dataset representation
+ fixed datatype bug in the numpy exons array

git-svn-id: http://svn.tuebingen.mpg.de/ag-raetsch/projects/QPalma@8980 e1793c9e-67f9-0310-80fc-b846ff1f7b36

11 years ago+ removed obsolete code
fabio [Sun, 11 May 2008 19:04:09 +0000 (19:04 +0000)]
+ removed obsolete code
+ changed dataset loading/processing

git-svn-id: http://svn.tuebingen.mpg.de/ag-raetsch/projects/QPalma@8979 e1793c9e-67f9-0310-80fc-b846ff1f7b36

11 years ago+ removed lot of redundant/old code from the dataset generation functions
fabio [Sun, 11 May 2008 12:07:20 +0000 (12:07 +0000)]
+ removed lot of redundant/old code from the dataset generation functions
TODO
- think about faster filtered reads parser

git-svn-id: http://svn.tuebingen.mpg.de/ag-raetsch/projects/QPalma@8978 e1793c9e-67f9-0310-80fc-b846ff1f7b36

11 years ago+ fix changes we made so far
fabio [Tue, 22 Apr 2008 08:44:58 +0000 (08:44 +0000)]
+ fix changes we made so far
+ right after final ECCB submission

git-svn-id: http://svn.tuebingen.mpg.de/ag-raetsch/projects/QPalma@8751 e1793c9e-67f9-0310-80fc-b846ff1f7b36

11 years ago+ Aaaarghh found stupid bug in the parser (Case statement of "one key - n elements...
fabio [Mon, 21 Apr 2008 03:31:59 +0000 (03:31 +0000)]
+ Aaaarghh found stupid bug in the parser (Case statement of "one key - n elements" was wrong)

git-svn-id: http://svn.tuebingen.mpg.de/ag-raetsch/projects/QPalma@8720 e1793c9e-67f9-0310-80fc-b846ff1f7b36

11 years ago+ support dangling end for unspliced reads in computeSpliceAlignWithQ
fabio [Sat, 19 Apr 2008 15:37:04 +0000 (15:37 +0000)]
+ support dangling end for unspliced reads in computeSpliceAlignWithQ
+ made parsers a bit faster by using mmap

git-svn-id: http://svn.tuebingen.mpg.de/ag-raetsch/projects/QPalma@8701 e1793c9e-67f9-0310-80fc-b846ff1f7b36

11 years ago+ added faster evaluation function
fabio [Sat, 19 Apr 2008 15:35:52 +0000 (15:35 +0000)]
+ added faster evaluation function
+ in PipelineHeuristic fixed bug in returning alternatives
+ corrected if statements in Lookup

git-svn-id: http://svn.tuebingen.mpg.de/ag-raetsch/projects/QPalma@8700 e1793c9e-67f9-0310-80fc-b846ff1f7b36

11 years ago+ fixed some index bugs in the evaluation
fabio [Sat, 19 Apr 2008 01:54:03 +0000 (01:54 +0000)]
+ fixed some index bugs in the evaluation

git-svn-id: http://svn.tuebingen.mpg.de/ag-raetsch/projects/QPalma@8698 e1793c9e-67f9-0310-80fc-b846ff1f7b36

11 years ago+ using new parsers now
fabio [Fri, 18 Apr 2008 23:52:29 +0000 (23:52 +0000)]
+ using new parsers now
+ store only minimum amount of information needed to perform prediction

git-svn-id: http://svn.tuebingen.mpg.de/ag-raetsch/projects/QPalma@8697 e1793c9e-67f9-0310-80fc-b846ff1f7b36

11 years ago+ changed code for prediction -> easier and faster
fabio [Fri, 18 Apr 2008 23:51:15 +0000 (23:51 +0000)]
+ changed code for prediction -> easier and faster

git-svn-id: http://svn.tuebingen.mpg.de/ag-raetsch/projects/QPalma@8696 e1793c9e-67f9-0310-80fc-b846ff1f7b36