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e67a716d82
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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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91f214f014
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added split_csv.sh
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2021-02-11 13:42:14 +00:00 |
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e302aafacf
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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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acd51ab3e4
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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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e3189df74b
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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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21451789e7
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renamed files
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2021-02-10 11:53:20 +00:00 |
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53ff6a9a1a
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added sample test_snps
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2021-02-10 10:38:08 +00:00 |
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af1446253b
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updated minor changes
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2021-02-10 10:37:44 +00:00 |
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8d0bd8011f
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added depricated shell scripts
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2021-02-10 10:36:02 +00:00 |
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6103254442
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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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3280cdb2a1
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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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c8feba90bc
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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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4f25acfa35
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adding and saving files
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2021-02-09 18:30:47 +00:00 |
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d77491b507
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testing dynamut script
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2021-02-09 18:28:16 +00:00 |
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aec61e2c1f
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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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d26b17fd19
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added dynamut dir
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2021-02-09 16:11:07 +00:00 |
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660ab31ce8
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work from thinkpad
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2021-02-09 16:03:02 +00:00 |
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2f0e508679
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add foldx5 wrapper
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2021-02-09 15:45:21 +00:00 |
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b5b54c7658
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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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73b705a563
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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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0d2f5c55ef
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test2 runfoldx symlink
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2021-02-09 14:43:03 +00:00 |
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93f6707b8f
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various changes
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2021-02-09 14:42:44 +00:00 |
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80e00b0dfa
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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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f95f2a3c93
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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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d4a7e3b635
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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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fab1fb0492
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more debug
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2021-02-08 16:16:53 +00:00 |
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c9698d7550
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fixup broken shell scripts
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2021-02-08 15:44:21 +00:00 |
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a67156bc87
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test2 bugfixes
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2021-02-08 15:24:22 +00:00 |
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4d03a43c4a
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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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619a828659
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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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a7d7bceb00
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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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50744f046f
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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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2911678177
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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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d4cd5aea0a
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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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91b7f73a63
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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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073381e5a2
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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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e67fbfd986
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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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c7194b7423
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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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719f18a226
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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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784199d48f
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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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02fae30c29
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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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e91d704929
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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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bf3e830f64
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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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7158f5b2c9
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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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da3b23d502
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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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10e1baee82
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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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4157b8137c
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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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861b2a7ee1
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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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4368c061c7
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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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315f7b1e0e
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output corr plots with coloured dots
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2020-10-06 17:47:24 +01:00 |
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