Commits · 898d9ad2b42c1a7aa5af64daf9cbfaf09cf501a3 · Mustafa Tekpinar / PRESCOTT

01 Jun, 2023 1 commit

Added --verbose option to the esgemme.py arguments. · 898d9ad2

--verbose option controls if epistatic and independent
results files will be written or not. It is False by
default and therefore, the files are not written.

authored Jun 01, 2023

898d9ad2 Browse Files

30 May, 2023 1 commit
- Updated the documentation. · 3509620e
  Mustafa Tekpinar authored May 30, 2023
  
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27 May, 2023 2 commits
- Added reformat.pl script to the image. · 7298ac7d
  Mustafa Tekpinar authored May 28, 2023
  
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- Added hhsuite to the Dockerfile. · fbe4ff55
  Mustafa Tekpinar authored May 27, 2023
  
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26 May, 2023 1 commit
- Changed Dockerfile slightly to include more tools. · e6303622
  Mustafa Tekpinar authored May 26, 2023
  
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25 May, 2023 1 commit
- Improved prot_normPred_evolCombiTransposed.txt output. · fe0d5632
  Mustafa Tekpinar authored May 25, 2023
  
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24 May, 2023 1 commit
- Transposed classical GEMME output for better legibility! · 461e81ee
  Mustafa Tekpinar authored May 24, 2023
  
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05 May, 2023 1 commit
- Created docs folder and its content with sphinx. · ae5d1c5f
  Mustafa Tekpinar authored May 05, 2023
  
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15 Apr, 2023 1 commit
- Changed max_load from 2*10^6 to 8*10^6. · a46cad97
  Mustafa Tekpinar authored Apr 15, 2023
  
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14 Apr, 2023 1 commit
- Changed java memory from 4096 to 8192 for big proteins. · 9fa8780f
  Mustafa Tekpinar authored Apr 14, 2023
  
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06 Apr, 2023 1 commit
- Added esgemme logo to the README.md. · 910931e6
  Mustafa Tekpinar authored Apr 06, 2023
  
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03 Apr, 2023 1 commit
- Removed Linux grep command calls. · cce7cb89
  Mustafa Tekpinar authored Apr 03, 2023
  
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31 Mar, 2023 1 commit
- Commented unused code in pred.R and computePred.R · 2d117e24
  Mustafa Tekpinar authored Mar 31, 2023
  
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30 Mar, 2023 1 commit
- The program won't write *_pred_evolEpi.txt and *_pred_evolInd.txt files anymore. · 5647766c
  Mustafa Tekpinar authored Mar 30, 2023
  
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29 Mar, 2023 1 commit
- Some more documentation and Dockerfile · f5de1a26
  Mustafa Tekpinar authored Mar 29, 2023
  
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28 Mar, 2023 1 commit
- Updated README file. · 2403b757
  Mustafa Tekpinar authored Mar 28, 2023
  
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20 Mar, 2023 1 commit
- Changed normWeightMode options. · e7a7207f
```
Convert trace->tjet, maxhalftracepchalftracecvhalfcvpc->max
and ssjetormax->sstjetormax in ESGEMME.
```
  Mustafa Tekpinar authored Mar 20, 2023
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16 Mar, 2023 1 commit
- Separated data from code by putting all data into data/ folder. · eb8c519b
  Mustafa Tekpinar authored Mar 16, 2023
  
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15 Mar, 2023 6 commits
- Improved cleanTheMess fucntion esgemme.py · facba872
  Mustafa Tekpinar authored Mar 15, 2023
  
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- Commented the lines containing pssm output. · 7f40b9ac
  Mustafa Tekpinar authored Mar 15, 2023
  
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- Commented bfactor-related unused code. · 8e2a131c
  Mustafa Tekpinar authored Mar 15, 2023
  
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- Corrected a bug in computePred.R when there is only one mutation in the mut file. · 83ba006d
  Mustafa Tekpinar authored Mar 15, 2023
  
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- Changed default.conf file copy process from bash to more Pythonic way. · f469ecb8
  Mustafa Tekpinar authored Mar 15, 2023
  
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- Removed dynamics related functions: calcPercentDFI, calcBfactors and getBfactors. · b20bee53
  Mustafa Tekpinar authored Mar 15, 2023
  
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10 Mar, 2023 1 commit
- Removed unused normWeightMode options in esgemme.py and computePred.R. · 5ffaa0e3
  Mustafa Tekpinar authored Mar 10, 2023
  
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09 Mar, 2023 2 commits
- Removed some commented/unused code from computePred.R · 4e510021
  Mustafa Tekpinar authored Mar 09, 2023
  
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- Changed editConfJET to editConfJETpython to reduce bash dependency. · 4e82cee0
  Mustafa Tekpinar authored Mar 09, 2023
  
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08 Mar, 2023 2 commits
- Changed SGEMME_PATH to ESGEMME_PATH · aabe1568
  Mustafa Tekpinar authored Mar 08, 2023
  
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- Removed (unused) bin calculation based jetormax option from computePred.R. · e7a02f1e
  Mustafa Tekpinar authored Mar 08, 2023
  
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06 Mar, 2023 4 commits
- Removed unnecessary combinedv[1-4] normWeightMode options. · e1a03717
  Mustafa Tekpinar authored Mar 06, 2023
  
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- Added calculateSecondaryStructure and countCoilSegments functions. · 7a52b1c1
  Mustafa Tekpinar authored Mar 06, 2023
  
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- Removed local SGEMME_DEV_PATH calls. · ecd6817e
  Mustafa Tekpinar authored Mar 06, 2023
  
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- Added ssjetormax normalization weight mode. · 90e5f3e6
  Mustafa Tekpinar authored Mar 06, 2023
  
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21 Feb, 2023 2 commits
- Removed gemmeAnal.py. Not needed anymore. · fcd3b21b
  Mustafa Tekpinar authored Feb 21, 2023
  
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- Moved editConf and launchJET from gemmeAnal.py to sgemme.py · 8f6e1b64
  Mustafa Tekpinar authored Feb 21, 2023
  
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17 Feb, 2023 1 commit
- Removed some commented lines in launchJET function in gemmeAnal.py. · 9f20b4c1
  Mustafa Tekpinar authored Feb 17, 2023
  
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16 Feb, 2023 1 commit
- Moved createPDB function in gemmeAnal.py to sgemme.py. · 96910f1f
  Mustafa Tekpinar authored Feb 16, 2023
  
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14 Feb, 2023 2 commits
- Moved getNbSeq function from gemmeAnal.py to sgemme.py. · 594c5761
  Mustafa Tekpinar authored Feb 14, 2023
  
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- Moved the main function under if(__name__) block in sgemme.py. · 7b3f2711
  Mustafa Tekpinar authored Feb 14, 2023
  
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01 Feb, 2023 1 commit
- Added jetormax to the normalization options · a823960e
  Mustafa Tekpinar authored Feb 01, 2023
  
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