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added active site indication for merged_dfs in count_vars_ML.R and also added 'gene_name' in combining_dfs.py

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Tanushree Tunstall 2022-06-15 18:36:28 +01:00
parent 1204f1faba
commit f355846dae
3 changed files with 59 additions and 15 deletions
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27
scripts/count_vars_ML.R
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@ -2,13 +2,33 @@
#source("~/git/LSHTM_analysis/config/alr.R")
#source("~/git/LSHTM_analysis/config/embb.R")
#source("~/git/LSHTM_analysis/config/gid.R")
##source("~/git/LSHTM_analysis/config/gid.R")
#source("~/git/LSHTM_analysis/config/katg.R")
#source("~/git/LSHTM_analysis/config/pnca.R")
#source("~/git/LSHTM_analysis/config/rpob.R")
source("~/git/LSHTM_analysis/config/rpob.R")
source("~/git/LSHTM_analysis/scripts/plotting/get_plotting_dfs.R")
################################################
# Add acticve site indication
###############################################
merged_df2$active_site = as.integer(merged_df2$position %in% active_aa_pos)
merged_df2_comp$active_site = as.integer(merged_df2_comp$position %in% active_aa_pos)
merged_df3$active_site = as.integer(merged_df3$position %in% active_aa_pos)
merged_df3_comp$active_site = as.integer(merged_df3_comp$position %in% active_aa_pos)
# sanity check
table(merged_df2$active_site)
table(merged_df3$active_site)
if( all(table(merged_df2$active_site) == table(as.integer(merged_df2$position %in% active_aa_pos))) &&
all(table(merged_df3$active_site) == table(as.integer(merged_df3$position %in% active_aa_pos)))
){
cat('\nActive site indications successfully applied to merged_dfs for gene:', tolower(gene))
}
gene
gene_match
@ -68,6 +88,9 @@ sum(table(merged_df3$drtype_mode_labels))
table(merged_df3$lineage)
sum(table(merged_df3$lineage_labels))
cat("\nWriting merged_df3 for:"
, "\nDrug:", drug
, "\nGene:", gene)
# write file
outfile_merged_df3 = paste0(outdir, '/', tolower(gene), '_merged_df3.csv')
outfile_merged_df3