diff pre_process_protein_name_set.R @ 21:9e0a894d2676 draft

Uploaded

--- a/pre_process_protein_name_set.R	Thu Nov 19 13:31:59 2015 -0500
+++ b/pre_process_protein_name_set.R	Thu Nov 19 13:38:20 2015 -0500
@@ -26,7 +26,7 @@
 library(VennDiagram)
 #####
 #data
-main <- function(peptides_file) {
+main <- function(peptides_file, db_path) {
 	peptides_file = read.delim(peptides_file,header=TRUE,stringsAsFactors=FALSE,fill=TRUE)
   peptides_txt = peptides_file
 	intensity_columns = names(peptides_txt[,str_detect(names(peptides_txt),"Intensity\\.*")]) #Pulls out all lines with Intensity in them.
@@ -36,7 +36,7 @@
 	peptides_txt_mapped = subset(peptides_txt_mapped,!is.na(Uniprot)) #removes reverse sequences and any that didn't match a uniprot accession
 	columns_comb = c("Uniprot", intensity_columns) 
 	peptides_mapped_intensity = subset(peptides_txt_mapped, select = columns_comb) #Subsets out only the needed cloumns for Tukeys (Uniprot IDS and baited intensities)
-	swissprot_fasta = scan("/home/philip/galaxy/tools/Moffitt_Tools/uniprot_names.txt",what="character")
+	swissprot_fasta = scan(db_path, what="character")
 	peptides_txt_mapped_log2 = peptides_mapped_intensity
   # Takes the log2 of the intensities. 
 	for (i in intensity_columns) { 
@@ -95,4 +95,4 @@
 }
 
 args <- commandArgs(trailingOnly = TRUE)
-main(args[1])
+main(args[1], args[2])