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8931441fa5
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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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172fa18420
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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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436125745d
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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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65e6b28d9e
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data extraction tidy up
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2020-07-08 13:26:33 +01:00 |
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e4328df255
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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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8f460347b4
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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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0973717287
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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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01ef04613a
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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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56d1617561
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testing combining df script
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2020-07-03 19:23:23 +01:00 |
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b09c15004b
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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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e0ba3108f6
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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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fb277a1484
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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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973a1a33da
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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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e8a66a7a94
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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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7032baa08d
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tidying script
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2020-06-25 13:12:09 +01:00 |
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cdb1ea1476
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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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27a656dba1
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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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a9498f8e08
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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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d8b272b0ae
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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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c80c87235e
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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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e3ae1c3a95
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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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263527f576
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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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6b5ced65e5
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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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28e52d4194
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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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c98ca7c8ae
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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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07258120de
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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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c36197d75e
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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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f9a8ed3dc7
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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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864f814e1b
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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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3d1536f2b6
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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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c4f9e24007
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foramtting and adding or
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2020-06-18 13:55:45 +01:00 |
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b73c506587
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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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2cebd338ba
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ran struc param analysis
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2020-06-17 19:36:02 +01:00 |
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96da4d8ed5
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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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b28d0afded
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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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3a0ff9b35e
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added scratch/
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2020-05-22 12:03:11 +01:00 |
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73762568e8
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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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bdad2dcfda
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fixing hetatm script
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2020-05-21 12:54:10 +01:00 |
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bc368be4b7
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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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cf3e507475
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tidy up code
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2020-05-15 13:48:50 +01:00 |
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f28b287c86
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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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bc2844dffb
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renamed extract chain file
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2020-05-15 10:59:19 +01:00 |
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ea213d09aa
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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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6b527baaff
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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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5ac87e76c7
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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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bc03aab82d
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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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95147b577c
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saving work for today
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2020-04-09 16:40:45 +01:00 |
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f42b6f725f
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minor tweaks
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2020-04-08 18:27:09 +01:00 |
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e1e0313fe8
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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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6f545413bc
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correcting indendation
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2020-04-08 12:43:37 +01:00 |
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