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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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