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ca1a0e10ca
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added example for layout
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2021-06-14 09:06:30 +01:00 |
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8fa9faa17d
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added another aa dict type to reference_dict.py and calculated electrostatisc changes for muts based on adding these properties to mcsm mut stule snps. This will allow the calculation on a given file type since the ref dict can now easily be adapted.
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2021-06-11 17:12:21 +01:00 |
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f88e2665e9
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calculating af_or using function and cmd options now
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2021-06-11 15:12:08 +01:00 |
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7686aa39b4
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added script to test af_or_calcs
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2021-06-11 13:33:25 +01:00 |
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931f8ec2f9
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added mychisq_or.R and af_or_calcs.R
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2021-06-11 13:28:07 +01:00 |
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b6df47a0cd
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moved old af_or_calcs.R to redundant
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2021-06-11 13:27:40 +01:00 |
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acda9f13e5
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saving the correct af or script
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2021-06-11 13:26:28 +01:00 |
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e78707067c
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saving work before converting to a function
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2021-06-11 13:25:02 +01:00 |
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a2431b59e5
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minor tweak to plotting_globals.R to make gene_match a global var
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2021-06-11 11:21:20 +01:00 |
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f6259aa517
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moved functions/ in the scripts dir
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2021-06-11 11:11:39 +01:00 |
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0c3645705d
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moved old bp scripts to redundant
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2021-06-10 16:18:08 +01:00 |
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dccdfe9742
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moved plotting_func to functions and replaced 3 basic_barplots scripts with 1
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2021-06-10 16:09:58 +01:00 |
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5c018e23be
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added function for position_count_bp.R
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2021-06-10 14:46:11 +01:00 |
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4bee48f545
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added functions dir for further tidying and tested this with ind scripts for stability
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2021-06-09 18:13:18 +01:00 |
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786eaabe1a
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moved bp function script to function/
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2021-06-09 17:08:56 +01:00 |
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225360fb93
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added shiny app and turned stability bp to function
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2021-06-09 17:05:02 +01:00 |
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3f58a5c64c
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saving work
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2021-06-09 16:27:05 +01:00 |
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776c4e0279
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repuposed and ran basic_barplots for lig and foldx including filenames
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2021-06-09 11:33:08 +01:00 |
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d45a9499a2
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repurposed basic_barplots_foldx.R
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2021-06-09 11:24:50 +01:00 |
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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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