Commits · master · Andrew Lyon / GenLibrary

06 Feb, 2020 32 commits
- Actually correctly handle completely ordered sequences in run_iupred · e79c7b35
  Andrew Lyon authored Feb 06, 2020
  
  e79c7b35
- Correctly handle completely ordered sequences in run_iupred · a9c15e8a
  Andrew Lyon authored Feb 06, 2020
  
  a9c15e8a
- Handle completely ordered sequences in run_iupred · 09019e59
  Andrew Lyon authored Feb 06, 2020
  
  09019e59
- Handle completely ordered sequences in get_regions_from_do_str · cc1ed535
  Andrew Lyon authored Feb 06, 2020
  
  cc1ed535
- Fix indexing when returning disordered regions · c7ecbf4b
  Andrew Lyon authored Feb 06, 2020
  
  c7ecbf4b
- Fix variable reference so that processed fasta is written instead of original · 0bce3a05
  Andrew Lyon authored Feb 06, 2020
  
  0bce3a05
- Print worker_output for testing, but after actually putting data into it · c82704fd
  Andrew Lyon authored Feb 06, 2020
  
  c82704fd
- Print worker_output for testing · ce783988
  Andrew Lyon authored Feb 06, 2020
  
  ce783988
- Early return for testing · e22e6076
  Andrew Lyon authored Feb 06, 2020
  
  e22e6076
- Changes in MobiDBLite.py to allow use with runPredictors.py, add "D" elements... · 47d238da
  Andrew Lyon authored Feb 06, 2020
```
Changes in MobiDBLite.py to allow use with runPredictors.py, add "D" elements to disorder region outputs in Predictors.py, implement commandline script runPredictors.py
```
  47d238da
- Fix parameters for disembl again · 34ee302d
  Andrew Lyon authored Feb 06, 2020
  
  34ee302d
- Fix parameters for disembl · 1adffcf9
  Andrew Lyon authored Feb 06, 2020
  
  1adffcf9
- Add default arg for nn_exec · e2861be6
  Andrew Lyon authored Feb 06, 2020
  
  e2861be6
- Add all predictors to runPredictors.py · 18f5cd73
  Andrew Lyon authored Feb 06, 2020
  
  18f5cd73
- Missing "\n" in split... annoying · b2493800
  Andrew Lyon authored Feb 06, 2020
  
  b2493800
- Add print(line) diagnostic · 6ba358f2
  Andrew Lyon authored Feb 06, 2020
  
  6ba358f2
- Add "if line" avoid trailing newline issue · e12e7057
  Andrew Lyon authored Feb 06, 2020
  
  e12e7057
- Change .split('\n') to readlines() to avoid trailing newline issue · b8cdf027
  Andrew Lyon authored Feb 06, 2020
  
  b8cdf027
- Add missing parentheses · 39c037e2
  Andrew Lyon authored Feb 06, 2020
  
  39c037e2
- Fix TypeError in IUPred output parsing · 56a82fc5
  Andrew Lyon authored Feb 06, 2020
  
  56a82fc5
- Implement parsing IUpred output · ad0287ca
  Andrew Lyon authored Feb 06, 2020
  
  ad0287ca
- Try shell=True for subprocess · 819b0901
  Andrew Lyon authored Feb 06, 2020
  
  819b0901
- Fix subprocess command formatting again · fb22d40c
  Andrew Lyon authored Feb 06, 2020
  
  fb22d40c
- Fix subprocess command formatting · ffce3c7b
  Andrew Lyon authored Feb 06, 2020
  
  ffce3c7b
- Fix flushing tempfile · ffbb3a3e
  Andrew Lyon authored Feb 06, 2020
  
  ffbb3a3e
- Change IUPred tempfile to NamedTemporaryFile · 516c4e40
  Andrew Lyon authored Feb 06, 2020
  
  516c4e40
- Change runEspritz.py to runPredictors.py and add run_iupred to it · c1a7c4db
  Andrew Lyon authored Feb 06, 2020
  
  c1a7c4db
- Add IUpred to Predictors.py · 31711750
  Andrew Lyon authored Feb 06, 2020
  
  31711750
- Create new function get_regions_from_do_str() to parse Espritz output in a way that actually works · e71970c9
  Andrew Lyon authored Feb 06, 2020
  
  e71970c9
- Fixes to subprocess call · 9854e725
  Andrew Lyon authored Feb 06, 2020
  
  9854e725
- Fix error in Predictors.py · d7ce6aae
  Andrew Lyon authored Feb 06, 2020
  
  d7ce6aae
- Implement module Predictors.py, with tests, add a template SLURM sbatch script · 72a4281a
  Andrew Lyon authored Feb 06, 2020
  
  72a4281a
31 Jan, 2020 8 commits
- Merge remote-tracking branch 'origin/master' · 33addccd
  Andrew Lyon authored Jan 31, 2020
  
  33addccd
- Add missing argument to score_mseq_smart in PScore.position_scores() · 1328c434
  Andrew Lyon authored Jan 31, 2020
  
  1328c434
- Update README.md · 9c8098cf
  Andrew Lyon authored Jan 31, 2020
  
  9c8098cf
- Merge remote-tracking branch 'origin/master' · 408bd817
  Andrew Lyon authored Jan 31, 2020
  
  408bd817
- Expand tildes · fe5cb903
  Andrew Lyon authored Jan 31, 2020
  
  fe5cb903
- Update README.md · db15703f
  Andrew Lyon authored Jan 31, 2020
  
  db15703f
- Add README.md · 67389b46
  Andrew Lyon authored Jan 31, 2020
  
  67389b46
- Hard code unique LARKS sequences in Larks.py, refactor PScore.py and... · c58da387
  Andrew Lyon authored Jan 31, 2020
```
Hard code unique LARKS sequences in Larks.py, refactor PScore.py and genLibrary.py to load DBs and constants in genLibrary.py, change default file paths in parse_args()
```
  c58da387