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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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99b77434b5
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more debug
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2021-02-08 16:16:53 +00:00 |
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fa25a30dcf
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fixup broken shell scripts
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2021-02-08 15:44:21 +00:00 |
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1f8cfc2403
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test2 bugfixes
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2021-02-08 15:24:22 +00:00 |
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7a9b16255a
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added user defined option for processing dir to allow me to specify external storage device for running it
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2020-12-02 11:26:26 +00:00 |
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08ad16adbb
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added chain_extract.py and pdb_chain_extract.py
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2020-11-30 14:11:46 +00:00 |
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fc4313045f
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adding options to specify files by user
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2020-11-27 13:02:15 +00:00 |
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20bba2ad70
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added my_pdbtools containing pdbtools cloned from a git repo
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2020-11-17 13:56:23 +00:00 |
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802522d1c6
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updating notes to running_scripts.py as running for another drug-target
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2020-11-17 13:55:16 +00:00 |
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ac5b86a9cd
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modified running script to mention chain info for foldx
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2020-11-16 16:16:24 +00:00 |
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2ac4ea8f5c
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added script to interrogate pdb files mainly for res numbers
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2020-11-16 16:01:31 +00:00 |
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ccdd6029be
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updated results summary in the data_extraction.py
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2020-11-12 17:05:29 +00:00 |
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f9fd74812a
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handling missing dir for data_extraction.py
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2020-11-12 13:21:06 +00:00 |
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b0b9e91af7
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added what is required as a minimum to run data_extraction
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2020-11-06 19:04:27 +00:00 |
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b2284f7216
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added base histogram script for af and or
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2020-10-13 13:38:17 +01:00 |
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1f9ea3f789
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added ns prefix to SNPs for unambiguity
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2020-10-13 13:37:22 +01:00 |
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59911687c8
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changing labels in graphs for frontiers journal
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2020-10-09 13:10:08 +01:00 |
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2f1f02e1de
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renamed other_plots.R to other_plots_combined.R and changing labels to capital letters for journal
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2020-10-09 12:17:24 +01:00 |
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667804ad83
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saving work minor changes perhaps
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2020-10-08 16:03:12 +01:00 |
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7f5ca7f5a4
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added af and OR columns in the data
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2020-10-06 19:39:59 +01:00 |
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69f3629cc0
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indicated hardcoded active site residues for pnca
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2020-10-06 19:12:32 +01:00 |
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be50636b15
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script to subset data for dnds cals
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2020-10-06 19:11:34 +01:00 |
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4285bbd59f
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added barplot_subcolours_aa_combined.R to combine and label these plots
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2020-10-06 18:43:20 +01:00 |
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18b6407539
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adjusted x axis position label for barplot_subcols_aa_LIG.R
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2020-10-06 18:42:24 +01:00 |
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9784cba232
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generated labelled ps_plots_combined.R and capital "P" for position in barplots coloured aa for Lig
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2020-10-06 18:15:50 +01:00 |
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