Commits · d379a356a29828b21685756f016cc17d00492eeb · Matej Lexa / nested

Feb 26, 2020
- Fixed database creation, working on problems with bad result accuracy · d379a356
  Jakub Horváth authored Feb 26, 2020
  
  d379a356
Feb 24, 2020
- Working on ltr_finder integration · a96a00ea
  Jakub Horváth authored Feb 24, 2020
  
  a96a00ea
Feb 23, 2020
- Major changes to functionality and optimisation · 5733ae64
  Jakub Horváth authored Feb 23, 2020
  
  5733ae64
- removed unnecessary files created during initial phase · 09a2b678
  Jakub Horváth authored Feb 23, 2020
  
  09a2b678
Feb 22, 2020
- fixed @click arguments · 287579f3
  Jakub Horváth authored Feb 22, 2020
  
  287579f3
- fixing get_accuracy() · 723eaaf1
  Jakub Horváth authored Feb 22, 2020
  
  723eaaf1
- added todos · c4cc74a3
  Jakub Horváth authored Feb 22, 2020
  
  c4cc74a3
- fixed indentation error in gff_parser.py · 0d199065
  Jakub Horváth authored Feb 22, 2020
  
  0d199065
Feb 20, 2020
- cleared up junk code in gff_parser.py · 57e07706
  Jakub Horváth authored Feb 20, 2020
  
  57e07706
- Merge branch 'xhorvat9-branch' of gitlab.fi.muni.cz:lexa/nested into xhorvat9-branch · 9e7b6983
  Jakub Horváth authored Feb 20, 2020
  
  9e7b6983
- added comments · a73e5a77
  Jakub Horváth authored Feb 20, 2020
  
  a73e5a77
- Update gff_parser_changed.py · 386f776b
  Jakub Horváth authored Feb 20, 2020
  
  386f776b
- added todos · 01b9c58d
  Jakub Horváth authored Feb 20, 2020
  
  01b9c58d
- added post-analysis config.yml setup and nester final run · cbd72872
  Jakub Horváth authored Feb 20, 2020
  
  cbd72872
Feb 19, 2020
- fixed parameter -u setting in config.yml · 7e4305f6
  Jakub Horváth authored Feb 19, 2020
  
  7e4305f6
- Started work on evaluating the parametrisation results, fixing -u parameter bug · 5b5cce4f
  Jakub Horváth authored Feb 19, 2020
  
  5b5cce4f
Feb 18, 2020
- added new TODOs · c97a7878
  Jakub Horváth authored Feb 18, 2020
  
  c97a7878
- Update TODO.txt · 102b3c50
  Jakub Horváth authored Feb 18, 2020
  
  102b3c50
- TODOs file · dc5f4f4c
  Jakub Horváth authored Feb 18, 2020
  
  dc5f4f4c
- Fixed case where Regex wasnt matching negative numbers · 19e43d67
  Jakub Horváth authored Feb 18, 2020
  
  19e43d67
Feb 13, 2020
- working on case where no reference database is given · 8439123f
  Jakub Horváth authored Feb 13, 2020
  
  8439123f
Feb 06, 2020

Deleted TEster/TEster.egg-info/PKG-INFO, TEster/TEster.egg-info/SOURCES.txt,... · 4d464283

Jakub Horváth authored Feb 06, 2020

Deleted TEster/TEster.egg-info/PKG-INFO, TEster/TEster.egg-info/SOURCES.txt, TEster/TEster.egg-info/dependency_links.txt, TEster/TEster.egg-info/entry_points.txt, TEster/TEster.egg-info/requires.txt, TEster/TEster.egg-info/top_level.txt, TEster/build/lib/analysis/__init__.py, TEster/build/lib/testingTools/__init__.py, TEster/build/lib/testingTools/compare.py, TEster/build/lib/testingTools/detection_region_analyser.py, TEster/build/lib/testingTools/get_average_lengths.py, TEster/build/lib/testingTools/gff_parser.py, TEster/build/lib/testingTools/plot_bases.py, TEster/build/lib/testingTools/position_analysis.py, TEster/build/lib/toolchain/TEster.py, TEster/build/lib/toolchain/__init__.py, TEster/build/lib/toolchain/analyser.py, TEster/build/lib/toolchain/config_parameter.py, TEster/build/lib/toolchain/database_loader.py, TEster/build/lib/toolchain/gff_compare.py, TEster/build/lib/toolchain/input_load.py, TEster/build/lib/toolchain/nester_run.py, TEster/build/lib/toolchain/run_finder.py, TEster/build/lib/toolchain/sequence_generator.py, TEster/dist/TEster-1.0.0-py3.6.egg, TEster/testingTools/__init__.py, TEster/testingTools/compare.py, TEster/testingTools/detection_region_analyser.py, TEster/testingTools/get_average_lengths.py, TEster/testingTools/gff_parser.py, TEster/testingTools/plot_bases.py, TEster/testingTools/position_analysis.py files

4d464283

skipped fixing packaging issues, will focus on building the program and extending behavior · 1185db42
Jakub Horváth authored Feb 06, 2020

1185db42

Feb 05, 2020

fixed minor function call issues · b39300ee
Jakub Horváth authored Feb 05, 2020

b39300ee
Merge branch 'xhorvat9-branch' of gitlab.fi.muni.cz:lexa/nested into xhorvat9-branch · 74a4e4ce
Jakub Horváth authored Feb 05, 2020

74a4e4ce
moved analysis file creation to cwd · 217c8563
Jakub Horváth authored Feb 05, 2020

217c8563

Deleted TE-tester/testingTools/compare.py,... · 8bc5649b

Jakub Horváth authored Feb 05, 2020

Deleted TE-tester/testingTools/compare.py, TE-tester/testingTools/detection_region_analyser.py, TE-tester/testingTools/get_average_lengths.py, TE-tester/testingTools/gff_parser.py, TE-tester/testingTools/plot_bases.py, TE-tester/testingTools/position_analysis.py, TE-tester/toolchain/TEster.py, TE-tester/toolchain/analyser.py, TE-tester/toolchain/config_parameter.py, TE-tester/toolchain/database_loader.py, TE-tester/toolchain/gff_compare.py, TE-tester/toolchain/input_load.py, TE-tester/toolchain/nester_run.py, TE-tester/toolchain/run_finder.py, TE-tester/toolchain/sequence_generator.py, TE-tester/toolchain/temporary.txt files

8bc5649b

Fixed issue with running nester, moved generated folder to /tmp · 43da6537
Jakub Horváth authored Feb 05, 2020

43da6537

Feb 04, 2020
- Adapted the analysing part for TEster, fixed file path problems · aa5eef2e
  Jakub Horváth authored Feb 04, 2020
  
  aa5eef2e
Jan 30, 2020
- added comments and TODOs · f01201ea
  Jakub Horváth authored Jan 30, 2020
  
  f01201ea
- Created parameter class to reduce arguments · 5da338f9
  Jakub Horváth authored Jan 30, 2020
  
  5da338f9
Jan 29, 2020
- Finished implementation of changing the parameters in config.yml · 4244ed28
  Jakub Horváth authored Jan 29, 2020
  
  4244ed28
- working on the parametrisation and 'sed' command on config.yml · 83fa6d12
  Jakub Horváth authored Jan 29, 2020
  
  83fa6d12
Jan 28, 2020
- finished parameter loading and generating · 84930c56
  Jakub Horváth authored Jan 28, 2020
  
  84930c56
Jan 24, 2020
- generating code is written · c0bc0eef
  Jakub Horváth authored Jan 24, 2020
  
  c0bc0eef
Jan 19, 2020
- created the package structure for te-tester · 9a173c09
  Jakub Horváth authored Jan 19, 2020
  
  9a173c09
- created the package structure for te-tester · 44189dcf
  Jakub Horváth authored Jan 19, 2020
  
  44189dcf
Oct 04, 2019
- Merge branch 'xhorvat9-branch' of gitlab.fi.muni.cz:lexa/nested into xhorvat9-branch · f4ebed75
  Jakub Horváth authored Oct 04, 2019
  
  f4ebed75
- added false positive recognition · 6d1bd22e
  Jakub Horváth authored Oct 04, 2019
  
  6d1bd22e
Oct 02, 2019
- Update nested_generator_automated.sh · 24a09f65
  Jakub Horváth authored Oct 02, 2019
  
  24a09f65

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