tanu/LSHTM_analysis
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gidb_dev #1

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tanu wants to merge 386 commits from gidb_dev into master
pull from: gidb_dev
merge into: tanu:master
Conversation 3 Commits 386 Files changed 175 +9 -3
2 changed files with 9 additions and 3 deletions
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5
mcsm_analysis/pyrazinamide/scripts/combining_two_df.R
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@ -1,7 +1,7 @@
#########################################################
# TASK: To combine mcsm and meta data with af and or files
# Input csv files:
# 1) mcsm output formatted
# 1) mcsm normalised and struct params
# 2) gene associated meta_data_with_AFandOR
# Output:
@ -50,7 +50,8 @@ datadir = paste0('~/git/Data')
# infile1: mCSM data
#indir = '~/git/Data/pyrazinamide/input/processed/'
indir = paste0(datadir, '/', drug, '/', 'output') # revised {TODO: change in mcsm pipeline}
in_filename = 'mcsm_complex1_normalised.csv'
#in_filename = 'mcsm_complex1_normalised.csv'
in_filename = 'pnca_mcsm_struct_params.csv'
infile = paste0(indir, '/', in_filename)
cat(paste0('Reading infile1: mCSM output file', ' ', infile) )

7
mcsm_analysis/pyrazinamide/scripts/combining_two_df_lig.R
View file

@ -3,6 +3,10 @@
# by filtering for distance to ligand (<10Ang).
# This script doesn't output anything.
# This script is sourced from other .R scripts for plotting ligand plots
# Input csv files:
# 1) mcsm normalised and struct params
# 2) gene associated meta_data_with_AFandOR
#########################################################
getwd()
setwd('~/git/LSHTM_analysis/mcsm_analysis/pyrazinamide/scripts/')
@ -35,7 +39,8 @@ cat(gene_match)
# infile1: mCSM data
#indir = '~/git/Data/pyrazinamide/input/processed/'
indir = paste0('~/git/Data', '/', drug, '/', 'output') # revised {TODO: change in mcsm pipeline}
in_filename = 'mcsm_complex1_normalised.csv'
#in_filename = 'mcsm_complex1_normalised.csv'
in_filename = 'pnca_mcsm_struct_params.csv'
infile = paste0(indir, '/', in_filename)
cat(paste0('Reading infile1: mCSM output file', ' ', infile) )