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6f24fc1fac
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uddated how to run plotting scripts. This is a cleaner version to keep up-to-date
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2021-06-08 16:53:07 +01:00 |
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ce8abafdfe
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wrapper script basic_barplots_PS.R now takes cmd and calls functions to generate plots.Tested and verfiied.
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2021-06-08 16:48:19 +01:00 |
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b25511a239
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tidied plotting_data.R as a function returning a lits of dfs
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2021-06-08 16:00:28 +01:00 |
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b8d0bc416a
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added plotting_globals and text file with info on how to run plotting scripst
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2021-06-04 17:26:01 +01:00 |
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d21605b31f
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tweaking baic bp to make generic
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2021-06-04 17:23:41 +01:00 |
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4f60e93abb
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minor updates to dir.R
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2021-06-04 15:05:52 +01:00 |
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7242b3516b
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adpated combining_dfs.py and plotting.R for gid and attempting to make it generic
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2021-06-04 14:36:16 +01:00 |
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d52534f676
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test branch commit
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2021-06-04 09:43:48 +01:00 |
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18af246c24
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saving before starting work
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2021-06-04 09:38:17 +01:00 |
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8009c3fe3d
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updated counts.py with wt seq counts
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2021-03-03 11:54:48 +00:00 |
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c59e3f178d
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added adjusted p-values for DM muts comparison
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2021-02-27 10:42:04 +00:00 |
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bbec97b00c
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updated count.py with indel and stop codon count
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2021-02-24 09:56:36 +00:00 |
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9062751790
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retrieved results for gid b8 and b9
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2021-02-23 08:59:01 +00:00 |
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77efd0b76d
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retrieved gid b7 and submitted b8,b9 and b10
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2021-02-22 09:31:29 +00:00 |
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88dad2696f
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retrieved results for gid b6
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2021-02-21 16:23:22 +00:00 |
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34c0b808ea
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added count.py to count samples for quick checks
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2021-02-21 16:07:33 +00:00 |
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05562399ce
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saving work and generating revised_figure7
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2021-02-20 16:17:38 +00:00 |
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9f03e6a6fd
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dynamut retrieved b5 and b6, submitted 6 and 7
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2021-02-20 13:05:30 +00:00 |
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2995299179
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code to retrieve results from batch 4 and 5 once ready
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2021-02-19 12:09:26 +00:00 |
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f9249d7bf2
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updated .gitignore
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2021-02-18 12:01:04 +00:00 |
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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
|
added mcsm_na_temp
|
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
|
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
|
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
|
separated defs and calls and added a separate script to test examples
|
2021-02-12 14:15:55 +00:00 |
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4e19961283
|
updating and cleaning get_results script
|
2021-02-12 12:04:49 +00:00 |
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7116b45bf8
|
updating get_results_def.py
|
2021-02-12 11:38:21 +00:00 |
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28521104f8
|
added example files to test dynamut results fetching for single and multiple urls
|
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
|
2021-02-11 19:21:26 +00:00 |
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2e047fd548
|
extracting single mut url from the batch processing step
|
2021-02-11 17:19:04 +00:00 |
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5d6ddb7639
|
added submit_def.py with example to run batch of 50
|
2021-02-11 14:36:32 +00:00 |
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cfe9028a9c
|
added split_csv.sh
|
2021-02-11 13:42:14 +00:00 |
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2eab17cb9e
|
uncommented some debug output for mcsm, pandas and numpy conflict. So temporarily resolved it by running from base env
|
2021-02-11 10:53:23 +00:00 |
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d159a81cfb
|
saving work in dynamut submit
|
2021-02-11 09:46:11 +00:00 |
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fad1526ce5
|
dynamut scripts and minor change dir for rd_df.py
|
2021-02-10 15:40:33 +00:00 |
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0fd3e75ab0
|
renamed files
|
2021-02-10 11:53:20 +00:00 |
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600f829972
|
added sample test_snps
|
2021-02-10 10:38:08 +00:00 |
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d139342074
|
updated minor changes
|
2021-02-10 10:37:44 +00:00 |
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491b317752
|
added depricated shell scripts
|
2021-02-10 10:36:02 +00:00 |
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98287b3c20
|
updated testing cmds for foldx
|
2021-02-10 10:32:09 +00:00 |
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ab7bed9f4b
|
added test2/ for testing updated foldx script
|
2021-02-10 10:16:28 +00:00 |
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56ca9db40d
|
added script to submit jobs
|
2021-02-09 20:16:27 +00:00 |
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5e735af323
|
adding and saving files
|
2021-02-09 18:30:47 +00:00 |
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0c95b3a512
|
testing dynamut script
|
2021-02-09 18:28:16 +00:00 |
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bcf4467c44
|
Merge branch 'master' of https://git.tunstall.in/tanu/LSHTM_analysis
|
2021-02-09 16:12:34 +00:00 |
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64018cce4c
|
added dynamut dir
|
2021-02-09 16:11:07 +00:00 |
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6b6921d45f
|
work from thinkpad
|
2021-02-09 16:03:02 +00:00 |
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534a6754cd
|
add foldx5 wrapper
|
2021-02-09 15:45:21 +00:00 |
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4163ede798
|
dont break when the pdb file is in a weird place with a weird name
|
2021-02-09 15:20:55 +00:00 |
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8302d01867
|
check to handle missing I/O/P dirs if drug unset
|
2021-02-09 15:00:03 +00:00 |
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725e9b53ca
|
test2 runfoldx symlink
|
2021-02-09 14:43:03 +00:00 |
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56150ae3c8
|
various changes
|
2021-02-09 14:42:44 +00:00 |
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ca68996264
|
renamed file runFoldx.py in test2/ to reflect this
|
2021-02-09 10:54:35 +00:00 |
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86670bbac3
|
remove shell scripts run with subprocess() and launch foldx directly from python
|
2021-02-08 18:06:02 +00:00 |
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9df3913a84
|
modifying script to avoid invoking bash as a subprocess
|
2021-02-08 16:59:42 +00:00 |
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99b77434b5
|
more debug
|
2021-02-08 16:16:53 +00:00 |
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fa25a30dcf
|
fixup broken shell scripts
|
2021-02-08 15:44:21 +00:00 |
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1f8cfc2403
|
test2 bugfixes
|
2021-02-08 15:24:22 +00:00 |
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7a9b16255a
|
added user defined option for processing dir to allow me to specify external storage device for running it
|
2020-12-02 11:26:26 +00:00 |
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08ad16adbb
|
added chain_extract.py and pdb_chain_extract.py
|
2020-11-30 14:11:46 +00:00 |
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fc4313045f
|
adding options to specify files by user
|
2020-11-27 13:02:15 +00:00 |
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20bba2ad70
|
added my_pdbtools containing pdbtools cloned from a git repo
|
2020-11-17 13:56:23 +00:00 |
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802522d1c6
|
updating notes to running_scripts.py as running for another drug-target
|
2020-11-17 13:55:16 +00:00 |
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|
ac5b86a9cd
|
modified running script to mention chain info for foldx
|
2020-11-16 16:16:24 +00:00 |
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2ac4ea8f5c
|
added script to interrogate pdb files mainly for res numbers
|
2020-11-16 16:01:31 +00:00 |
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ccdd6029be
|
updated results summary in the data_extraction.py
|
2020-11-12 17:05:29 +00:00 |
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|
f9fd74812a
|
handling missing dir for data_extraction.py
|
2020-11-12 13:21:06 +00:00 |
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b0b9e91af7
|
added what is required as a minimum to run data_extraction
|
2020-11-06 19:04:27 +00:00 |
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b2284f7216
|
added base histogram script for af and or
|
2020-10-13 13:38:17 +01:00 |
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|
1f9ea3f789
|
added ns prefix to SNPs for unambiguity
|
2020-10-13 13:37:22 +01:00 |
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|
59911687c8
|
changing labels in graphs for frontiers journal
|
2020-10-09 13:10:08 +01:00 |
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|
2f1f02e1de
|
renamed other_plots.R to other_plots_combined.R and changing labels to capital letters for journal
|
2020-10-09 12:17:24 +01:00 |
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|
667804ad83
|
saving work minor changes perhaps
|
2020-10-08 16:03:12 +01:00 |
|
|
|
7f5ca7f5a4
|
added af and OR columns in the data
|
2020-10-06 19:39:59 +01:00 |
|
|
|
69f3629cc0
|
indicated hardcoded active site residues for pnca
|
2020-10-06 19:12:32 +01:00 |
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|
be50636b15
|
script to subset data for dnds cals
|
2020-10-06 19:11:34 +01:00 |
|
|
|
4285bbd59f
|
added barplot_subcolours_aa_combined.R to combine and label these plots
|
2020-10-06 18:43:20 +01:00 |
|
|
|
18b6407539
|
adjusted x axis position label for barplot_subcols_aa_LIG.R
|
2020-10-06 18:42:24 +01:00 |
|
|
|
9784cba232
|
generated labelled ps_plots_combined.R and capital "P" for position in barplots coloured aa for Lig
|
2020-10-06 18:15:50 +01:00 |
|
|
|
e60b4c5492
|
output corr plots with coloured dots
|
2020-10-06 17:47:24 +01:00 |
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|
9d2d6cfd84
|
updated TASK in hist_af_or_combined.R
|
2020-10-06 16:43:59 +01:00 |
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|
a549e52825
|
renamed dist_plots.R to dist_plots_check.R as its exploratory
|
2020-10-06 16:39:24 +01:00 |
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|
5f441d09d9
|
added hist_af_or_combined.R to generate plots for output and moved previosu run to scratch_plots/
|
2020-10-06 16:33:25 +01:00 |
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|
f240c969ec
|
added hist_af.R
|
2020-10-06 15:07:42 +01:00 |
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|
07104a8c8e
|
updated .gitignore
|
2020-10-06 09:55:19 +01:00 |
|
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|
74c4ef16ae
|
added basic_barplots_foldx.R for supp figure
|
2020-10-06 09:53:34 +01:00 |
|
|
|
4c345ea9f4
|
moved not required plots to scratch
|
2020-10-06 09:52:54 +01:00 |
|
|
|
9597997741
|
saving predictions script
|
2020-09-30 14:09:08 +01:00 |
|
|
|
8a6c7968f5
|
added predictions for ps and lig and output to results
|
2020-09-30 13:12:05 +01:00 |
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|
|
a77b472dfa
|
added prediction.R to do logistic regression
|
2020-09-30 10:04:49 +01:00 |
|
|
|
d2093e7a4c
|
added ../data_extraction_epistasis.py for getting list for epistasis work
|
2020-09-29 16:09:54 +01:00 |
|
|
|
81796df71a
|
added corr_data.R corr_PS_LIG_all.R corr_PS_LIG_v2.R
|
2020-09-29 16:08:25 +01:00 |
|
|
|
c58fa8cd4d
|
added dist_plot.R to generate plots for writing results
|
2020-09-23 19:24:42 +01:00 |
|
|
|
48050752db
|
added more analysis in extreme_muts.R to be tidied later
|
2020-09-23 19:23:34 +01:00 |
|
|
|
a3aab4556a
|
added fold and duet agreement to extreme_muts.R
|
2020-09-23 11:20:22 +01:00 |
|
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|
6d08b646fc
|
added foldx scaled and foldx outcome to plotting_data.R
|
2020-09-23 11:12:41 +01:00 |
|
|
|
5579e9527b
|
updated extreme_muts.R with number of budding hotspots and mult muts numbers
|
2020-09-23 11:02:13 +01:00 |
|
tgttunstall
|
f7280ceada
|
Update README.md
|
2020-09-21 18:11:24 +01:00 |
|
tgttunstall
|
807876d919
|
Update README.md
|
2020-09-21 18:11:10 +01:00 |
|
tgttunstall
|
baedea8c5b
|
Update README.md
|
2020-09-21 18:09:55 +01:00 |
|
tgttunstall
|
0eca5cf859
|
Update README.md
|
2020-09-21 18:08:49 +01:00 |
|
tgttunstall
|
ac3c8a8086
|
Update README.md
|
2020-09-21 18:07:58 +01:00 |
|
|
|
5ceea2e7b7
|
updated gitignore for more tidying
|
2020-09-21 17:58:51 +01:00 |
|
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|
63fa0c596a
|
updated gitignore to tidyup
|
2020-09-21 17:54:54 +01:00 |
|
|
|
7239ab220b
|
remove unneeded dir
|
2020-09-21 17:49:19 +01:00 |
|
|
|
2297617af2
|
added ks_test_all_PS.R, ks_test_dr_PS.R, ks_test_dr_others_PS.R
|
2020-09-21 17:46:22 +01:00 |
|
|
|
be8fa7e639
|
saving combined bubble plot with labels
|
2020-09-18 18:19:55 +01:00 |
|
|
|
7e8d5c869e
|
updated .gitignore to include .RData
|
2020-09-18 18:10:23 +01:00 |
|
|
|
edabe0d776
|
added script basic_barplots_combined.R to combine basic barplots for PS and lig
|
2020-09-18 18:09:24 +01:00 |
|
|
|
771995d1ab
|
saving work
|
2020-09-18 18:07:48 +01:00 |
|
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|
093ae0d832
|
added ggcorr all plot figure for supp
|
2020-09-18 12:46:12 +01:00 |
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|
369c906a33
|
added ggcorr plots combined for all params
|
2020-09-18 11:56:19 +01:00 |
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|
|
24b1cc2440
|
saving work
|
2020-09-18 11:55:08 +01:00 |
|
|
|
5e1c920a0c
|
updated Header file and saving work
|
2020-09-17 20:12:08 +01:00 |
|
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|
b8575c6e69
|
logo_combined.R, outputs logo plot with multiple mutations and log_or
|
2020-09-17 20:01:57 +01:00 |
|
|
|
40e4ddd70a
|
minor tweaks in logo and corr plots
|
2020-09-17 20:00:34 +01:00 |
|
|
|
8ddca4a8b1
|
updated corr plots to show points with no colours
|
2020-09-17 17:17:11 +01:00 |
|
|
|
883207bc4b
|
updated corr_PS_LIG.R to output both styles of corr plots
|
2020-09-17 17:04:03 +01:00 |
|
|
|
ea5d5bda44
|
renamed corr_plot scripts
|
2020-09-17 16:38:40 +01:00 |
|
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|
f0ee1ff6c9
|
updated plot name in corr_plots_foldx.R
|
2020-09-17 16:36:45 +01:00 |
|
|
|
1b5280145b
|
renamed file to denote corr adjusted and plain
|
2020-09-17 16:35:35 +01:00 |
|
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|
fb0646373b
|
added scratch_plots/ggpairs_test.R to play with ggally for future
|
2020-09-17 15:32:40 +01:00 |
|
|
|
5f335a5051
|
added plotting/corr_plots_style2.Radded my version of pairs.panel with lower panel turned off. Also added new script for corr plots using my version of pairs.panel
|
2020-09-17 15:31:37 +01:00 |
|
|
|
63e04ae600
|
saving work
|
2020-09-17 15:29:17 +01:00 |
|
|
|
375cdc2068
|
added new layput for dm_om and facet_lineage plot
|
2020-09-17 14:01:04 +01:00 |
|
|
|
a5b03e53e8
|
updated with two outputs: labelled and unlabelled
|
2020-09-16 15:37:56 +01:00 |
|
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|
351e472e73
|
renaming and moving files
|
2020-09-16 14:57:51 +01:00 |
|
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|
b36bfc9e9d
|
renamed file in scratch plot/
|
2020-09-16 14:53:53 +01:00 |
|
|
|
25f2f9e4a2
|
playing with lineage_dist_dm_om
|
2020-09-16 13:23:49 +01:00 |
|
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|
ba02107e23
|
added dir scratch_plots/ to practice extra plots
|
2020-09-16 11:51:17 +01:00 |
|
|
|
0f6bf3875d
|
updated plotting_data.R with stability colours as variables
|
2020-09-16 11:47:38 +01:00 |
|
|
|
83deb64e1c
|
saving work
|
2020-09-15 13:34:26 +01:00 |
|
|
|
445f3e2047
|
updated distribution scripts to try adding points
|
2020-09-15 13:33:28 +01:00 |
|
|
|
44d1f64e88
|
updating lineage_country.R with different data slices
|
2020-09-15 13:14:33 +01:00 |
|
|
|
645827570f
|
added ggridges_lineage_country.R for dist by country
|
2020-09-15 12:50:25 +01:00 |
|
|
|
ee69445f11
|
updated gitignore to include TO_DO/
|
2020-09-14 17:26:28 +01:00 |
|
|
|
09e20cf7b3
|
added mutate.py and run_mutate.sh to create MSA aligbments for mutant sequences required to generate logoplot from sequence in R
|
2020-09-14 15:17:49 +01:00 |
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3612ef0f2d
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saving logoplot attempts
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2020-09-14 15:13:52 +01:00 |
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a5fdf01d25
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added corr_plots_foldx.R
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2020-09-11 20:28:18 +01:00 |
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e1da853cf1
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updated figure for multi mut plot
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2020-09-11 19:30:20 +01:00 |
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968b57105f
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added logo_multiple_muts.R
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2020-09-11 18:12:06 +01:00 |
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431e606448
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added check for active site mut count
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2020-09-11 17:41:40 +01:00 |
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fadd61bf57
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saving extreme muts analysis
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2020-09-11 16:43:27 +01:00 |
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7e4be21575
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added extreme_muts.R
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2020-09-11 16:07:23 +01:00 |
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8d9ede186c
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added delta symbol to plotting_data.R and pretty labels for dr_other_muts figure
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2020-09-11 14:40:37 +01:00 |
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ecbc7541e9
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added plotting/other_plots_data.R
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2020-09-11 12:52:17 +01:00 |
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1262df40c9
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results for electrostatic changes
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2020-09-11 10:27:56 +01:00 |
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078644c322
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write merged_df3 files from combining_dfs_plotting
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2020-09-11 09:51:53 +01:00 |
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c124f49041
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add scripts/mut_electrostatic_changes.py
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2020-09-10 20:18:35 +01:00 |
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26d0d7f42d
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updated notes with supp table colnames
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2020-09-10 20:15:00 +01:00 |
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c1041ad273
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updated logo plot data to source from combining_df_plotting.R
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2020-09-10 19:58:33 +01:00 |
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e690f5beba
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added logo plot
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2020-09-10 19:56:33 +01:00 |
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c4225cec4f
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updated Header file with Logolas and ggseqlogo
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2020-09-10 19:55:21 +01:00 |
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d4e75d5f64
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added merged_df3_short.csv for supp tables and struct figures
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2020-09-10 19:17:05 +01:00 |
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8be1418a32
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saving work
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2020-09-10 19:16:24 +01:00 |
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6934faca10
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saving other_plots.R
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2020-09-10 17:53:49 +01:00 |
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5102bbea1b
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Merge branch 'master' of github.com:tgttunstall/LSHTM_analysis
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2020-09-10 16:14:46 +01:00 |
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f415b0b239
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changes
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2020-09-10 16:06:14 +01:00 |
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cf732a3bcc
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saving work yet again to be extra sure
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2020-09-10 16:03:04 +01:00 |
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65841e4f5b
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saving recovered combining_dfs_plotting.R after editing
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2020-09-10 15:52:22 +01:00 |
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68050a93b4
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move combining_dfs_plotting.R
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2020-09-10 15:36:17 +01:00 |
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fdecc944fc
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re-adding deleted combining_dfs_plotting.R
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2020-09-10 15:28:10 +01:00 |
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d43ecfa1dc
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updated gitignore and saving workk
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2020-09-10 14:45:10 +01:00 |
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1708194912
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added boxplots and stats for other numerical params
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2020-09-10 14:09:40 +01:00 |
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fc47c58f91
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saving work after correlation plots
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2020-09-09 20:56:07 +01:00 |
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9bee97052e
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added correlation plots
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2020-09-09 20:48:21 +01:00 |
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f3f86d6651
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renamed file
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2020-09-09 19:11:06 +01:00 |
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2c2c2c1a60
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regenerated combined_or figure with correct muts
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2020-09-09 19:03:52 +01:00 |
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f85b1bd902
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script to generate combined ps plot wit af and or
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2020-09-09 18:57:28 +01:00 |
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e570454cf2
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saving work
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2020-09-09 18:56:59 +01:00 |
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5025e47983
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renamed lineage_dist
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2020-09-09 17:34:32 +01:00 |
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f424f4e2d6
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corrected subcols_axis name in sucols_all_PS
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2020-09-09 13:36:37 +01:00 |
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080cd6375d
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lineage dist plots combined generated
Please enter the commit message for your changes. Lines starting
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2020-09-09 13:18:57 +01:00 |
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19a984f228
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generated lineage dist plots combined. needs tweaking
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2020-09-09 12:53:53 +01:00 |
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31b98fb3d3
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plotting script with resolved gene metadata
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2020-09-09 12:00:42 +01:00 |
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774b34ef00
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updated dir.R
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2020-09-09 11:45:09 +01:00 |
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09e4f7bfbd
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add dirs and resolving_ambiguous_muts
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2020-09-09 11:36:40 +01:00 |
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b7c7ffc018
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`resolved ambiguous muts and generated clean output. Also seaprated dir.R
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2020-09-09 11:26:13 +01:00 |
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46b43cf261
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changing category of ambiguous muts
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2020-09-08 18:51:03 +01:00 |
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eb5491aad9
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outputting revised all params file
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2020-09-08 17:52:45 +01:00 |
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42986bb119
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hopefully finally sorted data merges!
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2020-09-08 17:46:52 +01:00 |
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fe49a45447
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various changes
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2020-09-08 17:13:02 +01:00 |
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5d9561f88a
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trying other num param plots
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2020-09-07 17:17:56 +01:00 |
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648be02665
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ks test script added
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2020-09-07 15:27:53 +01:00 |
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b4affa0c94
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Combining dfs for PS and lig in one
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2020-09-07 14:05:46 +01:00 |
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2ef767f046
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lineage barplot script
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2020-09-07 11:29:28 +01:00 |
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db87f98d32
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updated giignore
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2020-09-04 22:46:07 +01:00 |
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7460c7c97f
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updated combining_two_df.R for plots
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2020-09-04 22:43:30 +01:00 |
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dd1158a66c
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script to plot lineage dist plots
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2020-09-04 22:40:49 +01:00 |
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645868ea27
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adding missing mutation col in combining_dfs
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2020-09-04 21:04:18 +01:00 |
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ddefcd7841
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resolving missing mutation info in combining script
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2020-09-04 20:56:16 +01:00 |
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bba3487829
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added running scripts doc
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2020-08-26 17:20:01 +01:00 |
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3f8d6695a4
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all barplots generated for ps and lig
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2020-08-26 17:18:45 +01:00 |
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0220960975
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reflected change in running_scripts doc
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2020-08-26 16:41:10 +01:00 |
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89e881b5d4
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renamed file to reflect sucols_axis is commons script sourced by ps and lig plots
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2020-08-26 16:40:36 +01:00 |
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0e3f9e584b
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sorted subcols_axis script to generate correct axis cols for both PS and lig plots
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2020-08-26 16:39:10 +01:00 |
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482eeadb9a
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generated subcolour bps for PS
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2020-08-26 12:45:09 +01:00 |
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ed739aeb71
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sourcing plotting_data for subcols_axis_PS
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2020-08-26 12:07:04 +01:00 |
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b754f26f9b
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added ligand df in plotting
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2020-08-26 10:02:44 +01:00 |
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73877942f4
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added instructions on running plot scripts
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2020-08-24 14:38:45 +01:00 |
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75273cebbf
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generated replaced Bfactor pdbs
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2020-08-24 14:37:28 +01:00 |
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54f9fd073b
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rectified mcsm_mean_stability to avereage on raw values and then scale
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2020-08-24 13:04:25 +01:00 |
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d76345c3de
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saving work to check merge conflicts resolved
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2020-08-24 11:20:58 +01:00 |
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f468554427
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sourced plotting script in mean_stability calcs
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2020-08-21 17:33:09 +01:00 |
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a448d9276b
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added plotting scripts from old run
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2020-08-21 13:25:01 +01:00 |
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d78626048c
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script to format snp_info.txt
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2020-08-21 13:23:29 +01:00 |
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acd0b8355b
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updated script to combine dfs
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2020-08-21 13:22:28 +01:00 |
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841d18d10b
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sorted df by position for output in data_extraction
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2020-08-14 17:57:12 +01:00 |
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48773a19ef
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tidy script for linking or_kinship with missense variant info
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2020-08-14 16:41:11 +01:00 |
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f8f33abad8
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removed if clause for filenames
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2020-08-13 18:39:16 +01:00 |
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2d8cb01cb7
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added output file for checking
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2020-08-11 18:34:02 +01:00 |
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dcd9a985ec
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saving work, ready for more remote working
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2020-08-07 13:35:02 +01:00 |
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13203e6fe0
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added data cjeckings script
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2020-08-07 13:34:24 +01:00 |
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61e41f1697
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saving work
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2020-08-07 13:33:44 +01:00 |
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efe0178f4e
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separting data processing from plotting, started with basic_barplots_PS script
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2020-07-16 18:59:17 +01:00 |
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7d1ecbb660
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replaced single quotes with double in R scripts
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2020-07-16 14:18:18 +01:00 |
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5e1b39cea0
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mean stability values calcs and replaceBfactor plots
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2020-07-16 14:12:08 +01:00 |
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1f44f8ec0a
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calculating mean stabilty per position
please enter the commit message for your changes. Lines starting
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2020-07-16 10:37:40 +01:00 |
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1e785a08a1
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scripts generating axis coloured subcols bp for PS
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2020-07-15 16:31:10 +01:00 |
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3cb33df009
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made tweaks to output plot filenames
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2020-07-15 16:29:36 +01:00 |
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55f03bc343
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adding plots as I tidy and generate
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2020-07-15 13:50:07 +01:00 |
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e41fb78e37
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saved work before adding plots
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2020-07-15 13:36:20 +01:00 |
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e4270b67c8
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saving work for today
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2020-07-14 16:13:17 +01:00 |
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2bc5be20b9
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resolving merge conflicts dur to shoddy data
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2020-07-14 14:09:42 +01:00 |
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7d36e0e36b
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fixed white space prob with mcsm input with merge
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2020-07-14 14:07:23 +01:00 |
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46b1505fdf
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remove white space in colnames before mcsm format output
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2020-07-14 12:59:40 +01:00 |
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83383b4493
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finding discrepancy in merging or dfs,grrrr
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2020-07-13 18:31:29 +01:00 |
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9e8469abe3
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trying to resolve copy warning in code
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2020-07-13 12:20:43 +01:00 |
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57a966c7c4
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added sanity checks for or_kinship calcs
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2020-07-13 11:37:43 +01:00 |
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f9500d5324
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added sanity checks for or_kin
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2020-07-10 15:24:57 +01:00 |
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5677175423
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refactoring or_kin script minor changes only
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2020-07-10 12:38:42 +01:00 |
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c80faef0bf
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refactoring or_kin script minor changes only
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2020-07-10 12:37:41 +01:00 |
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aaf3f5e084
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added cleaned up af_or_calcs.R
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2020-07-09 15:55:16 +01:00 |
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d3d82623d2
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added consistent style scripts to format kd & rd values
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2020-07-09 14:08:27 +01:00 |
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e4a7deae7b
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minor tidy up in foldx, mcsm and dssp scripts
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2020-07-09 14:04:16 +01:00 |
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0379d3e241
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renamed mcsm_wrapper to run_mcsm
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2020-07-09 13:33:56 +01:00 |
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91348aaae2
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added dssp.py with refactored argeparse
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2020-07-09 12:58:55 +01:00 |
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f8e345f5bc
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adding default dirs and filenames to argparse in foldx and mcsm
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2020-07-09 12:57:08 +01:00 |
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6402990154
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minor edits to format mcsm data like sorting df
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2020-07-09 11:15:56 +01:00 |
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01fbc2a87b
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ran foldx and mcsm (get) for 33k dataset
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2020-07-08 20:30:32 +01:00 |
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0e71b23759
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modified extraction to be explicit for extracting nsSNP for specified gene
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2020-07-08 18:47:22 +01:00 |
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1fa0dc6ad4
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minor changes in data extraction
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2020-07-08 16:01:54 +01:00 |
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c958cc1081
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data extraction tidy up
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2020-07-08 13:26:33 +01:00 |
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a4670b9944
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saving work for the day
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2020-07-07 18:31:14 +01:00 |
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a7f21cfb14
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adding clean files for rerrun 35k dataset
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2020-07-07 18:28:55 +01:00 |
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943513a338
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added script to combine all files in one
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2020-07-07 16:06:11 +01:00 |
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5addb85851
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renamed files that combine dfs
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2020-07-07 15:46:13 +01:00 |
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a220288c5f
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testing combining df script
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2020-07-03 19:23:23 +01:00 |
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262bd79204
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stil fiddling iwth combining dfs
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2020-07-03 19:22:46 +01:00 |
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90cbb49560
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added fixme: for some necessary required changes
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2020-07-02 14:16:40 +01:00 |
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f758c01159
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added combining funct & combining_mcsm_foldx script
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2020-07-01 16:41:58 +01:00 |
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4d686e2933
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refactor foldx pipeline to include:
* command-line args
* creating necessary dirs automagically
* code cleanup, syntax errors, etc etc
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2020-06-30 17:14:30 +01:00 |
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af65a86ff9
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updated code and made it tidy
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2020-06-25 14:40:44 +01:00 |
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3c6122a296
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tidying script
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2020-06-25 13:12:09 +01:00 |
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b82cc11dbe
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updated ref dict to create separate dicts
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2020-06-24 14:10:39 +01:00 |
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626ed3a57b
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added commonly used mutation format for missense muts in the gene_specific nssnp_info file
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2020-06-24 13:34:35 +01:00 |
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a298071309
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combined and output all ors
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2020-06-23 17:34:54 +01:00 |
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003b22ce3f
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script for calcuating various OR & output csv
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2020-06-23 13:07:29 +01:00 |
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a1cc7ee33d
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further tidy for OR calcs
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2020-06-23 12:19:26 +01:00 |
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1e43ca8136
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tody scracth script for various OR calcs
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2020-06-23 11:57:51 +01:00 |
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18998092f4
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all OR calcs using sapply and output as df
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2020-06-22 18:17:06 +01:00 |
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8f272bdc17
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extracting other params from logistic
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2020-06-22 14:11:16 +01:00 |
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ada205962b
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script to combine ors and afs
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2020-06-22 13:07:26 +01:00 |
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0c3c6fd143
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script to combine all ors
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2020-06-19 14:43:23 +01:00 |
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3497d1ef54
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renamed files & added or kinship link file
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2020-06-19 10:33:26 +01:00 |
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fa2bcb5f05
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updated Af and OR calcs script with argeparse and minor tidyup
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2020-06-18 18:37:55 +01:00 |
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76ecb65a1a
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getopt and commandArgs examples, and AF/OR update to use getopt()
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2020-06-18 17:59:28 +01:00 |
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6c2c7e0a90
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removed merging df for AF_OR
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2020-06-18 16:10:02 +01:00 |
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b33419c939
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af and or calcs, not merging
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2020-06-18 15:57:25 +01:00 |
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010ef133dd
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foramtting and adding or
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2020-06-18 13:55:45 +01:00 |
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fdba990b80
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added AF_and OR calcs script and making it generic
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2020-06-17 19:36:34 +01:00 |
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8d1daabff4
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ran struc param analysis
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2020-06-17 19:36:02 +01:00 |
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e21635fe02
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inlcuded the revised master file for 35k isolates
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2020-06-16 11:39:11 +01:00 |
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e2f319ba42
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various debug, doc, and args
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2020-05-25 14:27:25 +01:00 |
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f6fc6e47ab
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added scratch/
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2020-05-22 12:03:11 +01:00 |
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3fe1d35df5
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building script for inspecting pdb
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2020-05-22 11:57:59 +01:00 |
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ca36e004c1
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fixing hetatm script
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2020-05-21 12:54:10 +01:00 |
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15dea0cbf6
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added script for pairwise alignment
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2020-05-15 17:58:14 +01:00 |
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548d9a5192
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tidy up code
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2020-05-15 13:48:50 +01:00 |
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f7e371a585
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script for saving pdb chains in single file
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2020-05-15 13:44:57 +01:00 |
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01a7cbf26e
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renamed extract chain file
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2020-05-15 10:59:19 +01:00 |
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65db4a090e
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added pdb_chain splitter code and wrapper
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2020-05-13 16:54:20 +01:00 |
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3425d8fa2b
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added pdbtools from github source and modified seq.py to exclude hetatm seq extraction
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2020-05-12 14:08:08 +01:00 |
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7f66d5d19e
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adding commands for use of pdbtools
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2020-05-12 12:50:49 +01:00 |
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b28d866237
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handle not ready (refresh) url
Please enter the commit message for your changes. Lines starting
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2020-04-21 17:12:18 +01:00 |
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a405aa17c3
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moved scripts to /ind_scripts & added add col to formatting script
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2020-04-20 12:52:10 +01:00 |
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e94da61871
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fixed indentation error and ran mcsm_wrapper dcs
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2020-04-17 12:19:08 +01:00 |
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e50466da39
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add wrapper and mcsm library
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2020-04-16 17:45:24 +01:00 |
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7aafa72e10
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defined method for formatting mcsm_results
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2020-04-14 11:30:36 +01:00 |
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45889990e7
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saving work for the day
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2020-04-11 19:00:39 +01:00 |
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7d2241ad81
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added lambda func to normalise duet and aff values
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2020-04-11 18:52:57 +01:00 |
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398eccd246
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added script to format results
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2020-04-10 19:32:47 +01:00 |
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f5241048b4
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saving work for today
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2020-04-09 16:40:45 +01:00 |
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0550cfe0e2
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adding separae script for getting results for mcsm
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2020-04-09 15:42:56 +01:00 |
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7cee9b21e2
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refactoring bash into python to run mcsm
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2020-04-08 18:27:51 +01:00 |
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7a8bbc6595
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minor tweaks
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2020-04-08 18:27:09 +01:00 |
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fe3d431a3d
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combine df script with command line args and added method
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2020-04-08 12:44:17 +01:00 |
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c025a22343
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correcting indendation
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2020-04-08 12:43:37 +01:00 |
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30aa64fd2b
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refactoring: added command line args to combine_dfs
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2020-04-08 11:44:53 +01:00 |
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49a38dd1ae
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saving work for today
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2020-04-07 17:57:34 +01:00 |
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569b7c6c7f
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adapted rd_df script to make it take command line args and define function
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2020-04-07 17:42:59 +01:00 |
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811027e34d
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tidy kd_df script
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2020-04-07 17:42:06 +01:00 |
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02488ea23e
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adapted kd calc script with command line args and made it into a function
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2020-04-07 16:45:59 +01:00 |
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6afe202931
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kd script with command line args and as function
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2020-04-07 16:39:50 +01:00 |
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44577b4a0c
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updating kd script to take command line args
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2020-04-07 16:13:54 +01:00 |
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24c7ade7c4
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renamed file for consistency
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2020-04-07 16:04:01 +01:00 |
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f690c75ca0
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modified dssp_df to handle multiple chains
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2020-04-07 16:02:19 +01:00 |
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d161fcd0f3
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added dssp.py that runs, processes and outputs csv
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2020-04-07 15:08:18 +01:00 |
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b0e56328ef
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adding settings params
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2020-04-06 19:04:35 +01:00 |
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cc9cdbcad5
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refactoring code to make it take command line args
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2020-04-06 19:03:41 +01:00 |
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b5aa524914
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logoplot from df and seqs with custom height
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2020-03-29 17:11:17 +01:00 |
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34a2057d29
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added R header file to base dir to allow general access by R scripts
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2020-03-28 17:56:39 +00:00 |
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b1e4dcd376
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tidied combining plot scripts
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2020-03-28 17:54:45 +00:00 |
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e7f2a3aada
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added mutate.py script for msa generation
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2020-03-27 17:11:16 +00:00 |
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ab541aa3de
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saving work for the day
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2020-03-27 17:08:33 +00:00 |
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d1da203df0
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changed filename to the new combined output (mcsm+struct params)
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2020-03-27 12:43:48 +00:00 |
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82e96fcdba
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combining mcsm and struct params
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2020-03-27 12:39:02 +00:00 |
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afd6ca8881
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tidy code and saving work for the day
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2020-03-26 17:58:39 +00:00 |
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69e2567ffc
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added script to combined dfs of structural params like kd, dssp & rd
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2020-03-26 17:14:20 +00:00 |
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c0bac6fd7b
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changed outcols in dssp and kd outputs
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2020-03-26 17:12:59 +00:00 |
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5bab99c15f
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added residue depth processing to generate df
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2020-03-26 15:44:20 +00:00 |
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0b7a938fbd
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tidy code and renamed kd.py to kd_df.py
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2020-03-26 15:43:13 +00:00 |
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4c2fa2b600
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tidied and updated kd and dssp scripts & generated their respective outputs
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2020-03-25 18:19:23 +00:00 |
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87a847109a
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updated kd.py to relfect a merging col for combining num params later
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2020-03-25 15:20:54 +00:00 |
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de1822f491
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output from comb script & electrostatic mut changes calculated
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2020-03-25 13:42:18 +00:00 |
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96ebb85069
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updated combining df scripts for duet & lig
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2020-03-24 18:28:52 +00:00 |
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c184841951
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minor changes to variable names in .R & .py
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2020-03-24 10:36:51 +00:00 |
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dd91692673
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renamed files to make more generic
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2020-03-23 18:13:02 +00:00 |
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22a0d38563
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renamed files to make more generic
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2020-03-23 17:48:39 +00:00 |
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d42e6fbdb3
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fixed bugs and tidy code
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2020-03-23 17:43:06 +00:00 |
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b4dbad7e54
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delete old file
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2020-03-23 17:40:19 +00:00 |
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b331227023
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updated pnca_extraction and AF_OR calcs
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2020-03-23 17:36:42 +00:00 |
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eb021349fe
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bug fixes and massive clean up of data extraction script
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2020-03-23 13:33:25 +00:00 |
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8df0b7d920
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saving from work
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2020-02-27 15:16:20 +00:00 |
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77cc5bf42c
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renamed file and updated logo plot code
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2020-02-26 12:00:32 +00:00 |
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95e8205189
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added 2 logo plot scripts
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2020-02-25 19:09:43 +00:00 |
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f9837b474c
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updating mut_seq script
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2020-02-25 18:13:18 +00:00 |
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e9a95e9d3a
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hydrophobicity script
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2020-02-25 10:42:58 +00:00 |
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ed8fc4d488
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remove old surface_res3.py
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2020-02-20 12:23:56 +00:00 |
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d7ef8ef51e
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fixup
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2020-02-20 10:41:49 +00:00 |
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b56c0b8b68
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adding scripts for struct params
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2020-02-16 15:14:36 +00:00 |
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4ef68bdc1b
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remove __pycache__, update .gitignore
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2020-02-16 15:08:45 +00:00 |
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b97712edb0
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test commit
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2020-02-16 15:00:49 +00:00 |
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9e4b3c5dce
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added script to calculate electrostatic changes of mutations
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2020-02-11 15:03:21 +00:00 |
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0653a8c1e3
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updated ref dict to inc aa_calcprop
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2020-02-11 15:02:32 +00:00 |
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d12ef0ef00
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saving a and b labels in bubble plot with brackets
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2020-02-02 11:39:35 +00:00 |
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d9519b6262
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added script for KS_test for DUET
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2020-02-02 11:36:17 +00:00 |
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134dea609d
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tidy code for lineage_dist_PS
|
2020-02-02 11:14:25 +00:00 |
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8c7c389562
|
tidying script for lineage dist PS and separating KS test results
|
2020-02-02 11:11:49 +00:00 |
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632b78320a
|
added bubble plot
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2020-02-02 09:17:11 +00:00 |
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c15d1a8a95
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added script for coloured axis for ligand affinity
|
2020-01-31 16:39:22 +00:00 |
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3390f80168
|
remove .Rhistory
|
2020-01-31 15:35:25 +00:00 |
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1d80186ab9
|
Merge branch 'master' of https://git.tunstall.in/tanu/LSHTM_analysis
|
2020-01-31 15:34:58 +00:00 |
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15daa6dfc1
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remove .Rhistory
|
2020-01-31 15:32:32 +00:00 |
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ac34de9e79
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added subaxis plots for PS and lig separately
|
2020-01-31 15:30:08 +00:00 |
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f1584bddb1
|
saving previous stuff from work
|
2020-01-30 08:26:21 +00:00 |
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6cbef0c3d7
|
tidy script for data extraction
|
2020-01-28 11:53:10 +00:00 |
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1edfe3f8f8
|
Merge branch 'master' of github.com:tgttunstall/LSHTM_analysis
|
2020-01-28 10:17:24 +00:00 |
|
tgttunstall
|
8d2456f7f2
|
Update README.md
|
2020-01-28 10:14:08 +00:00 |
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15391a5700
|
saving data_extraction from home
|
2020-01-28 10:13:01 +00:00 |
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c3c50f65f2
|
saving previous work from home pc
|
2020-01-28 10:13:01 +00:00 |
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4d2d03f634
|
added coloured axis barplots
|
2020-01-28 10:13:01 +00:00 |
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bcf822d6e4
|
updated lineage dist for LIG for consistency
|
2020-01-28 10:13:01 +00:00 |
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4f06e42ee4
|
graphs for PS lineage dist for all and dr muts
|
2020-01-28 10:13:01 +00:00 |
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4bcb81e9be
|
saving data_extraction from home
|
2020-01-28 10:10:16 +00:00 |
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be213cb7e9
|
saving previous work from home pc
|
2020-01-23 09:31:35 +00:00 |
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cae9c550a4
|
added coloured axis barplots
|
2020-01-22 15:09:21 +00:00 |
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2df031c02a
|
updated lineage dist for LIG for consistency
|
2020-01-22 11:34:59 +00:00 |
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c1ea688c5c
|
graphs for PS lineage dist for all and dr muts
|
2020-01-22 10:12:09 +00:00 |
|
tgttunstall
|
ec37e3c1f6
|
Update README.md
Updated README.md
|
2020-01-14 11:29:13 +00:00 |
|
tgttunstall
|
50ade050c2
|
Update README.md
|
2020-01-14 11:22:41 +00:00 |
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