From b72ffb5d2c9fad56249faa0ed205651bca6c04d3 Mon Sep 17 00:00:00 2001 From: Tanushree Tunstall Date: Wed, 19 Jan 2022 18:57:04 +0000 Subject: [PATCH] just tested logo plot msa with embb after correcting the OMINOUS fasta file --- scripts/functions/tests/test_logo_plots.R | 5 +++-- scripts/gene_targets_names.txt | 6 +++--- scripts/plotting/logo_data_msa.R | 2 +- 3 files changed, 7 insertions(+), 6 deletions(-) diff --git a/scripts/functions/tests/test_logo_plots.R b/scripts/functions/tests/test_logo_plots.R index 6985373..f2df33b 100644 --- a/scripts/functions/tests/test_logo_plots.R +++ b/scripts/functions/tests/test_logo_plots.R @@ -1,5 +1,6 @@ -source("~/git/LSHTM_analysis/config/gid.R") +#source("~/git/LSHTM_analysis/config/gid.R") #source("~/git/LSHTM_analysis/config/pnca.R") # YES +source("~/git/LSHTM_analysis/config/embb.R") #--------------------------------------------------- # FIXME # source("~/git/LSHTM_analysis/config/alr.R") @@ -7,7 +8,7 @@ source("~/git/LSHTM_analysis/config/gid.R") # source("~/git/LSHTM_analysis/config/katg.R") # source("~/git/LSHTM_analysis/config/rpob.R") #--------------------------------------------------- -#source("~/git/LSHTM_analysis/scripts/plotting/get_plotting_dfs.R") +source("~/git/LSHTM_analysis/scripts/plotting/get_plotting_dfs.R") # # ################################ # # Logo plot with custom Y axis diff --git a/scripts/gene_targets_names.txt b/scripts/gene_targets_names.txt index 25c6e02..ee933c3 100644 --- a/scripts/gene_targets_names.txt +++ b/scripts/gene_targets_names.txt @@ -1,6 +1,6 @@ -rpob rifampicin +embb ethambutol alr cycloserine +gid streptomycin katg isoniazid pnca pyrazinamide -gid streptomycin -embb ethambutol +rpob rifampicin diff --git a/scripts/plotting/logo_data_msa.R b/scripts/plotting/logo_data_msa.R index 3aea505..4651477 100644 --- a/scripts/plotting/logo_data_msa.R +++ b/scripts/plotting/logo_data_msa.R @@ -39,7 +39,7 @@ head(msa_seq) #================ #in_filename_fasta = paste0(tolower(gene), ".1fasta") -in_filename_fasta = paste0(tolower(gene), "2.2fasta") # gid +in_filename_fasta = paste0(tolower(gene), "2_f2.fasta") # gid infile_fasta = paste0(indir, "/", in_filename_fasta) cat("\nInput fasta file for WT: ", infile_fasta, "\n")