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d683e971d4
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updated .gitignore to include temp dirs
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2021-02-18 11:54:36 +00:00 |
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8dc3a790c0
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add files
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2021-02-18 11:50:46 +00:00 |
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69b62e54a5
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running dynamut in batches
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2021-02-18 11:27:20 +00:00 |
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cfdd18086a
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renamed files in dynamut for consistency
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2021-02-18 10:52:51 +00:00 |
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9a0e98eb24
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renamed file in mcsm_na to be consistent
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2021-02-18 10:51:17 +00:00 |
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2168007f12
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renaming file
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2021-02-18 10:48:06 +00:00 |
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19d89230f5
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renamed file run_submit to run_submit_dynamut
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2021-02-18 10:45:35 +00:00 |
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a9a4483aee
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renamed file run_results to run_get_results
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2021-02-18 10:43:45 +00:00 |
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cd06a83e13
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ran mcsm_na for all 26 batches for gid
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2021-02-16 13:55:31 +00:00 |
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013bba2503
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sunmitting mcsm_na jobs manually
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2021-02-16 10:51:06 +00:00 |
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b69d9d729a
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added get_results_mcsm_na.py run_get_results.py to retrieve results for each batch run of 20 for mcsm_na
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2021-02-15 12:22:52 +00:00 |
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7a74fecbda
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saving work for mcsm_na
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2021-02-15 12:22:19 +00:00 |
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322979406c
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added mcsm_na_temp
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2021-02-12 17:40:02 +00:00 |
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1f72001689
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added shell script to format muts for mcsm NA
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2021-02-12 17:38:42 +00:00 |
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c99f1cac92
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added mcsm_na scripts to submit batches of 20
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2021-02-12 16:51:41 +00:00 |
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b2397ea99d
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minor cody tidy up
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2021-02-12 16:50:34 +00:00 |
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9c221e6786
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tested and added note to reflect that tar.gz needs to be made into a cmd line option
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2021-02-12 15:32:16 +00:00 |
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7f75b92553
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checked tar.gz downlaod from the script with example
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2021-02-12 15:25:32 +00:00 |
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56f5479c0b
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added tar.gz download within get_results.py
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2021-02-12 15:24:51 +00:00 |
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80f7e039ab
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separated defs and calls and added a separate script to test examples
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2021-02-12 14:15:55 +00:00 |
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4e19961283
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updating and cleaning get_results script
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2021-02-12 12:04:49 +00:00 |
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7116b45bf8
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updating get_results_def.py
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2021-02-12 11:38:21 +00:00 |
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28521104f8
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added example files to test dynamut results fetching for single and multiple urls
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2021-02-11 19:22:19 +00:00 |
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1d8e6f0d75
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updated with def for get_results.py for dynamut
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2021-02-11 19:21:26 +00:00 |
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2e047fd548
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extracting single mut url from the batch processing step
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2021-02-11 17:19:04 +00:00 |
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5d6ddb7639
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added submit_def.py with example to run batch of 50
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2021-02-11 14:36:32 +00:00 |
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cfe9028a9c
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added split_csv.sh
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2021-02-11 13:42:14 +00:00 |
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2eab17cb9e
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uncommented some debug output for mcsm, pandas and numpy conflict. So temporarily resolved it by running from base env
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2021-02-11 10:53:23 +00:00 |
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d159a81cfb
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saving work in dynamut submit
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2021-02-11 09:46:11 +00:00 |
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fad1526ce5
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dynamut scripts and minor change dir for rd_df.py
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2021-02-10 15:40:33 +00:00 |
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0fd3e75ab0
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renamed files
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2021-02-10 11:53:20 +00:00 |
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600f829972
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added sample test_snps
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2021-02-10 10:38:08 +00:00 |
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d139342074
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updated minor changes
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2021-02-10 10:37:44 +00:00 |
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491b317752
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added depricated shell scripts
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2021-02-10 10:36:02 +00:00 |
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98287b3c20
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updated testing cmds for foldx
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2021-02-10 10:32:09 +00:00 |
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ab7bed9f4b
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added test2/ for testing updated foldx script
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2021-02-10 10:16:28 +00:00 |
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56ca9db40d
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added script to submit jobs
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2021-02-09 20:16:27 +00:00 |
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5e735af323
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adding and saving files
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2021-02-09 18:30:47 +00:00 |
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0c95b3a512
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testing dynamut script
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2021-02-09 18:28:16 +00:00 |
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bcf4467c44
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Merge branch 'master' of https://git.tunstall.in/tanu/LSHTM_analysis
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2021-02-09 16:12:34 +00:00 |
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64018cce4c
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added dynamut dir
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2021-02-09 16:11:07 +00:00 |
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6b6921d45f
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work from thinkpad
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2021-02-09 16:03:02 +00:00 |
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534a6754cd
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add foldx5 wrapper
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2021-02-09 15:45:21 +00:00 |
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4163ede798
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dont break when the pdb file is in a weird place with a weird name
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2021-02-09 15:20:55 +00:00 |
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8302d01867
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check to handle missing I/O/P dirs if drug unset
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2021-02-09 15:00:03 +00:00 |
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725e9b53ca
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test2 runfoldx symlink
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2021-02-09 14:43:03 +00:00 |
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56150ae3c8
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various changes
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2021-02-09 14:42:44 +00:00 |
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ca68996264
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renamed file runFoldx.py in test2/ to reflect this
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2021-02-09 10:54:35 +00:00 |
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86670bbac3
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remove shell scripts run with subprocess() and launch foldx directly from python
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2021-02-08 18:06:02 +00:00 |
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9df3913a84
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modifying script to avoid invoking bash as a subprocess
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2021-02-08 16:59:42 +00:00 |
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