LSHTM_analysis

tanu/LSHTM_analysis

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7f75b92553 checked tar.gz downlaod from the script with example Tanushree Tunstall 2021-02-12 15:25:32 +00:00
2b6ffec100 checked tar.gz downlaod from the script with example Tanushree Tunstall 2021-02-12 15:25:32 +00:00
56f5479c0b added tar.gz download within get_results.py Tanushree Tunstall 2021-02-12 15:24:51 +00:00
a5f1878158 added tar.gz download within get_results.py Tanushree Tunstall 2021-02-12 15:24:51 +00:00
80f7e039ab separated defs and calls and added a separate script to test examples Tanushree Tunstall 2021-02-12 14:15:55 +00:00
deb0aa8e58 separated defs and calls and added a separate script to test examples Tanushree Tunstall 2021-02-12 14:15:55 +00:00
4e19961283 updating and cleaning get_results script Tanushree Tunstall 2021-02-12 12:04:49 +00:00
6c458f8883 updating and cleaning get_results script Tanushree Tunstall 2021-02-12 12:04:49 +00:00
7116b45bf8 updating get_results_def.py Tanushree Tunstall 2021-02-12 11:38:21 +00:00
db1c950c39 updating get_results_def.py Tanushree Tunstall 2021-02-12 11:38:21 +00:00
28521104f8 added example files to test dynamut results fetching for single and multiple urls Tanushree Tunstall 2021-02-11 19:22:19 +00:00
c146ea0f43 added example files to test dynamut results fetching for single and multiple urls Tanushree Tunstall 2021-02-11 19:22:19 +00:00
1d8e6f0d75 updated with def for get_results.py for dynamut Tanushree Tunstall 2021-02-11 19:21:26 +00:00
72426fd949 updated with def for get_results.py for dynamut Tanushree Tunstall 2021-02-11 19:21:26 +00:00
2e047fd548 extracting single mut url from the batch processing step Tanushree Tunstall 2021-02-11 17:19:04 +00:00
9629d24169 extracting single mut url from the batch processing step Tanushree Tunstall 2021-02-11 17:19:04 +00:00
5d6ddb7639 added submit_def.py with example to run batch of 50 Tanushree Tunstall 2021-02-11 14:36:32 +00:00
e67a716d82 added submit_def.py with example to run batch of 50 Tanushree Tunstall 2021-02-11 14:36:32 +00:00
cfe9028a9c added split_csv.sh Tanushree Tunstall 2021-02-11 13:42:14 +00:00
91f214f014 added split_csv.sh Tanushree Tunstall 2021-02-11 13:42:14 +00:00
2eab17cb9e uncommented some debug output for mcsm, pandas and numpy conflict. So temporarily resolved it by running from base env Tanushree Tunstall 2021-02-11 10:53:23 +00:00
e302aafacf uncommented some debug output for mcsm, pandas and numpy conflict. So temporarily resolved it by running from base env Tanushree Tunstall 2021-02-11 10:53:23 +00:00
d159a81cfb saving work in dynamut submit Tanushree Tunstall 2021-02-11 09:46:11 +00:00
acd51ab3e4 saving work in dynamut submit Tanushree Tunstall 2021-02-11 09:46:11 +00:00
fad1526ce5 dynamut scripts and minor change dir for rd_df.py Tanushree Tunstall 2021-02-10 15:40:33 +00:00
e3189df74b dynamut scripts and minor change dir for rd_df.py Tanushree Tunstall 2021-02-10 15:40:33 +00:00
0fd3e75ab0 renamed files Tanushree Tunstall 2021-02-10 11:53:20 +00:00
21451789e7 renamed files Tanushree Tunstall 2021-02-10 11:53:20 +00:00
600f829972 added sample test_snps Tanushree Tunstall 2021-02-10 10:38:08 +00:00
53ff6a9a1a added sample test_snps Tanushree Tunstall 2021-02-10 10:38:08 +00:00
d139342074 updated minor changes Tanushree Tunstall 2021-02-10 10:37:44 +00:00
af1446253b updated minor changes Tanushree Tunstall 2021-02-10 10:37:44 +00:00
491b317752 added depricated shell scripts Tanushree Tunstall 2021-02-10 10:36:02 +00:00
8d0bd8011f added depricated shell scripts Tanushree Tunstall 2021-02-10 10:36:02 +00:00
98287b3c20 updated testing cmds for foldx Tanushree Tunstall 2021-02-10 10:32:09 +00:00
6103254442 updated testing cmds for foldx Tanushree Tunstall 2021-02-10 10:32:09 +00:00
ab7bed9f4b added test2/ for testing updated foldx script Tanushree Tunstall 2021-02-10 10:16:28 +00:00
3280cdb2a1 added test2/ for testing updated foldx script Tanushree Tunstall 2021-02-10 10:16:28 +00:00
56ca9db40d added script to submit jobs Tanushree Tunstall 2021-02-09 20:16:27 +00:00
c8feba90bc added script to submit jobs Tanushree Tunstall 2021-02-09 20:16:27 +00:00
5e735af323 adding and saving files Tanushree Tunstall 2021-02-09 18:30:47 +00:00
4f25acfa35 adding and saving files Tanushree Tunstall 2021-02-09 18:30:47 +00:00
0c95b3a512 testing dynamut script Tanushree Tunstall 2021-02-09 18:28:16 +00:00
d77491b507 testing dynamut script Tanushree Tunstall 2021-02-09 18:28:16 +00:00
bcf4467c44 Merge branch 'master' of https://git.tunstall.in/tanu/LSHTM_analysis Tanushree Tunstall 2021-02-09 16:12:34 +00:00
aec61e2c1f Merge branch 'master' of https://git.tunstall.in/tanu/LSHTM_analysis Tanushree Tunstall 2021-02-09 16:12:34 +00:00
64018cce4c added dynamut dir Tanushree Tunstall 2021-02-09 16:11:07 +00:00
d26b17fd19 added dynamut dir Tanushree Tunstall 2021-02-09 16:11:07 +00:00
6b6921d45f work from thinkpad Tanushree Tunstall 2021-02-09 16:03:02 +00:00
660ab31ce8 work from thinkpad Tanushree Tunstall 2021-02-09 16:03:02 +00:00
534a6754cd add foldx5 wrapper Tanushree Tunstall 2021-02-09 15:45:21 +00:00
2f0e508679 add foldx5 wrapper Tanushree Tunstall 2021-02-09 15:45:21 +00:00
4163ede798 dont break when the pdb file is in a weird place with a weird name Tanushree Tunstall 2021-02-09 15:20:55 +00:00
b5b54c7658 dont break when the pdb file is in a weird place with a weird name Tanushree Tunstall 2021-02-09 15:20:55 +00:00
8302d01867 check to handle missing I/O/P dirs if drug unset Tanushree Tunstall 2021-02-09 15:00:03 +00:00
73b705a563 check to handle missing I/O/P dirs if drug unset Tanushree Tunstall 2021-02-09 15:00:03 +00:00
725e9b53ca test2 runfoldx symlink Tanushree Tunstall 2021-02-09 14:43:03 +00:00
0d2f5c55ef test2 runfoldx symlink Tanushree Tunstall 2021-02-09 14:43:03 +00:00
56150ae3c8 various changes Tanushree Tunstall 2021-02-09 14:42:44 +00:00
93f6707b8f various changes Tanushree Tunstall 2021-02-09 14:42:44 +00:00
ca68996264 renamed file runFoldx.py in test2/ to reflect this Tanushree Tunstall 2021-02-09 10:54:35 +00:00
80e00b0dfa renamed file runFoldx.py in test2/ to reflect this Tanushree Tunstall 2021-02-09 10:54:35 +00:00
86670bbac3 remove shell scripts run with subprocess() and launch foldx directly from python Tanushree Tunstall 2021-02-08 18:06:02 +00:00
f95f2a3c93 remove shell scripts run with subprocess() and launch foldx directly from python Tanushree Tunstall 2021-02-08 18:06:02 +00:00
9df3913a84 modifying script to avoid invoking bash as a subprocess Tanushree Tunstall 2021-02-08 16:59:42 +00:00
d4a7e3b635 modifying script to avoid invoking bash as a subprocess Tanushree Tunstall 2021-02-08 16:59:42 +00:00
99b77434b5 more debug Tanushree Tunstall 2021-02-08 16:16:53 +00:00
fab1fb0492 more debug Tanushree Tunstall 2021-02-08 16:16:53 +00:00
fa25a30dcf fixup broken shell scripts Tanushree Tunstall 2021-02-08 15:44:21 +00:00
c9698d7550 fixup broken shell scripts Tanushree Tunstall 2021-02-08 15:44:21 +00:00
1f8cfc2403 test2 bugfixes Tanushree Tunstall 2021-02-08 15:24:22 +00:00
a67156bc87 test2 bugfixes Tanushree Tunstall 2021-02-08 15:24:22 +00:00
7a9b16255a added user defined option for processing dir to allow me to specify external storage device for running it Tanushree Tunstall 2020-12-02 11:26:26 +00:00
4d03a43c4a added user defined option for processing dir to allow me to specify external storage device for running it Tanushree Tunstall 2020-12-02 11:26:26 +00:00
08ad16adbb added chain_extract.py and pdb_chain_extract.py Tanushree Tunstall 2020-11-30 14:11:46 +00:00
619a828659 added chain_extract.py and pdb_chain_extract.py Tanushree Tunstall 2020-11-30 14:11:46 +00:00
fc4313045f adding options to specify files by user Tanushree Tunstall 2020-11-27 13:02:15 +00:00
a7d7bceb00 adding options to specify files by user Tanushree Tunstall 2020-11-27 13:02:15 +00:00
20bba2ad70 added my_pdbtools containing pdbtools cloned from a git repo Tanushree Tunstall 2020-11-17 13:56:23 +00:00
50744f046f added my_pdbtools containing pdbtools cloned from a git repo Tanushree Tunstall 2020-11-17 13:56:23 +00:00
802522d1c6 updating notes to running_scripts.py as running for another drug-target Tanushree Tunstall 2020-11-17 13:55:16 +00:00
2911678177 updating notes to running_scripts.py as running for another drug-target Tanushree Tunstall 2020-11-17 13:55:16 +00:00
ac5b86a9cd modified running script to mention chain info for foldx Tanushree Tunstall 2020-11-16 16:16:24 +00:00
d4cd5aea0a modified running script to mention chain info for foldx Tanushree Tunstall 2020-11-16 16:16:24 +00:00
2ac4ea8f5c added script to interrogate pdb files mainly for res numbers Tanushree Tunstall 2020-11-16 16:01:31 +00:00
91b7f73a63 added script to interrogate pdb files mainly for res numbers Tanushree Tunstall 2020-11-16 16:01:31 +00:00
ccdd6029be updated results summary in the data_extraction.py Tanushree Tunstall 2020-11-12 17:05:29 +00:00
073381e5a2 updated results summary in the data_extraction.py Tanushree Tunstall 2020-11-12 17:05:29 +00:00
f9fd74812a handling missing dir for data_extraction.py Tanushree Tunstall 2020-11-12 13:21:06 +00:00
e67fbfd986 handling missing dir for data_extraction.py Tanushree Tunstall 2020-11-12 13:21:06 +00:00
b0b9e91af7 added what is required as a minimum to run data_extraction Tanushree Tunstall 2020-11-06 19:04:27 +00:00
c7194b7423 added what is required as a minimum to run data_extraction Tanushree Tunstall 2020-11-06 19:04:27 +00:00
b2284f7216 added base histogram script for af and or Tanushree Tunstall 2020-10-13 13:38:17 +01:00
719f18a226 added base histogram script for af and or Tanushree Tunstall 2020-10-13 13:38:17 +01:00
1f9ea3f789 added ns prefix to SNPs for unambiguity Tanushree Tunstall 2020-10-13 13:37:22 +01:00
784199d48f added ns prefix to SNPs for unambiguity Tanushree Tunstall 2020-10-13 13:37:22 +01:00
59911687c8 changing labels in graphs for frontiers journal Tanushree Tunstall 2020-10-09 13:10:08 +01:00
02fae30c29 changing labels in graphs for frontiers journal Tanushree Tunstall 2020-10-09 13:10:08 +01:00
2f1f02e1de renamed other_plots.R to other_plots_combined.R and changing labels to capital letters for journal Tanushree Tunstall 2020-10-09 12:17:24 +01:00
e91d704929 renamed other_plots.R to other_plots_combined.R and changing labels to capital letters for journal Tanushree Tunstall 2020-10-09 12:17:24 +01:00