added ed_pfm_data.R function and its corresponding test

scripts/functions/tests/test_ed_pfm_data.R

@@ -0,0 +1,36 @@
+# data msa: mut
+my_data = read.csv("/home/tanu/git/Misc/practice_plots/pnca_msa_eg2.csv", header = F) #15 cols only
+msaSeq_mut = my_data$V1
+msa_seq = msaSeq_mut
+
+# data msa: wt
+gene = "pncA"
+drug = "pyrazinamide"
+indir = paste0("~/git/Data/", drug , "/input/")
+
+in_filename_fasta = paste0(tolower(gene), "2_f2.fasta")
+infile_fasta = paste0(indir, in_filename_fasta)
+cat("\nInput fasta file for WT: ", infile_fasta, "\n")  
+
+msa2 = read.csv(infile_fasta, header = F)
+head(msa2)
+cat("\nLength of WT fasta:", nrow(msa2))
+wt_seq = msa2$V1
+head(wt_seq)  
+msaSeq_wt = msa2$V1
+wt_seq = msaSeq_wt
+
+################################
+# DataED_PFM():
+# script: ed_pfm_data.R
+source("~/git/LSHTM_analysis/scripts/functions/ed_pfm_data.R")
+################################
+
+data_ed = DataED_PFM(msa_seq, wt_seq)
+names(data_ed)
+
+#par(mfrow = c(2,1))
+logomaker(msa_seq, type = "EDLogo")
+ggseqlogo(data_ed[['combED_mutM']]
+          , method = "custom")
+