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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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0cdc507ba5
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updated TASK in hist_af_or_combined.R
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2020-10-06 16:43:59 +01:00 |
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711781933c
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renamed dist_plots.R to dist_plots_check.R as its exploratory
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2020-10-06 16:39:24 +01:00 |
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cc8443c7d4
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added hist_af_or_combined.R to generate plots for output and moved previosu run to scratch_plots/
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2020-10-06 16:33:25 +01:00 |
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9b9ee07801
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added hist_af.R
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2020-10-06 15:07:42 +01:00 |
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66db9ddd9c
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updated .gitignore
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2020-10-06 09:55:19 +01:00 |
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3ecba79eb9
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added basic_barplots_foldx.R for supp figure
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2020-10-06 09:53:34 +01:00 |
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b63bbd6f15
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moved not required plots to scratch
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2020-10-06 09:52:54 +01:00 |
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923cad81b5
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saving predictions script
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2020-09-30 14:09:08 +01:00 |
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4f32ffd3b6
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added predictions for ps and lig and output to results
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2020-09-30 13:12:05 +01:00 |
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c95db27b06
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added prediction.R to do logistic regression
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2020-09-30 10:04:49 +01:00 |
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8e16b2635e
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added ../data_extraction_epistasis.py for getting list for epistasis work
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2020-09-29 16:09:54 +01:00 |
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6354caae3c
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added corr_data.R corr_PS_LIG_all.R corr_PS_LIG_v2.R
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2020-09-29 16:08:25 +01:00 |
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9ba7b32c14
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added dist_plot.R to generate plots for writing results
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2020-09-23 19:24:42 +01:00 |
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a0755eeab6
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added more analysis in extreme_muts.R to be tidied later
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2020-09-23 19:23:34 +01:00 |
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5f10ad8075
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added fold and duet agreement to extreme_muts.R
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2020-09-23 11:20:22 +01:00 |
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4398c049ca
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added foldx scaled and foldx outcome to plotting_data.R
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2020-09-23 11:12:41 +01:00 |
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5deb12187e
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updated extreme_muts.R with number of budding hotspots and mult muts numbers
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2020-09-23 11:02:13 +01:00 |
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3318f3f85a
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Update README.md
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2020-09-21 18:11:24 +01:00 |
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e0561f29c0
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Update README.md
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2020-09-21 18:11:10 +01:00 |
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7c6581f19a
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Update README.md
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2020-09-21 18:09:55 +01:00 |
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e8aff6129a
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Update README.md
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2020-09-21 18:08:49 +01:00 |
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