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comparison join_files.R @ 0:d212d12aee5e draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/join_files_by_id commit a835a0b20127f485a6af4b466bb29d58d63541ea
author iuc
date Wed, 09 Aug 2017 17:44:54 -0400
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-1:000000000000 0:d212d12aee5e
1 # libraries
2 library(data.table)
3 library(parallel)
4
5 # inputs
6 args <- commandArgs()
7
8 input <- gsub("--in=", "", args[grepl("--in=", args)])
9 header <- as.integer(gsub("--he=", "", args[grepl("--he=", args)]))
10 join_col <- gsub("--jc=", "", args[grepl("--jc=", args)])
11 separator <- gsub("--sep=", "", args[grepl("--sep=", args)])
12 null_char <- gsub("--nc=", "", args[grepl("--nc=", args)])
13 output <- gsub("--out=", "", args[grepl("--out=", args)])
14
15 # test VARS
16 # input <- list("test-data/df1.txt", "test-data/df2.txt", "test-data/df3.txt")
17 #
18 # input <- list("test-data/df_big_1.txt", "test-data/df_big_2.txt", "test-data/df_big_3.txt",
19 # "test-data/df_big_4.txt", "test-data/df_big_5.txt", "test-data/df_big_6.txt",
20 # "test-data/df_big_7.txt", "test-data/df_big_8.txt", "test-data/df_big_9.txt",
21 # "test-data/df_big_10.txt")
22 # header <- 1
23 # join_col <- 1
24 # separator <- "ta"
25 # null_char <- 0
26 # output <- "out"
27
28 if(header > 0){
29 header <- TRUE
30 }else{
31 header <- FALSE
32 }
33 join_col <- as.integer(join_col)
34
35 # read files into list
36 df_list <- lapply(input, function(x){as.data.frame(fread(x))})
37
38
39 #### fix the ids name for all read in tables
40 df_list <- lapply(df_list, function(x){
41 names_x <- names(x)
42 names_x[names_x == "ids"] <- "id" # to join correctly
43 names_x[join_col] <- "ids"
44 names(x) <- names_x
45 x
46 })
47
48 # generate unique ids string
49 df0 <- lapply(df_list, function(x){
50 x[join_col]
51 })
52
53 df0 <- data.frame(ids=unique(do.call(rbind, df0)))
54 df_list <- append(df0, df_list)
55 df_list[[1]] <- data.frame(ids=df_list[[1]])
56
57
58
59 ids <- df_list[[1]]
60 ids <- data.frame(ids = ids[order(ids$ids), "ids" ])
61 merged_df <- mclapply(2:length(df_list), function(x){
62 merged_sub <- merge(x = ids, y = df_list[[x]], by = "ids", all.x = T, sort = F)
63 merged_sub <- merged_sub[order(merged_sub$ids), ]
64 merged_sub[-1]
65 }, mc.cores=4)
66
67 df <- cbind(ids, do.call(cbind, merged_df))
68
69 # benchmarking
70 # library(microbenchmark)
71 # microbenchmark(
72 # df1 <- lapply(2:length(df_list), function(x){
73 # merge(df_list[[1]], df_list[[x]], by = "ids", all.x = T)[-1]
74 # }),
75 # merged_df <- mclapply(2:length(df_list), function(x){
76 # merge(x = ids, y = df_list[[x]], by = "ids", all.x = T, sort = F)[-1]}, mc.cores=7)
77 # ,times = 4
78 # )
79
80 # change null_char
81 df[is.na(df)] <- null_char
82 # separator <- "ta"
83 # print(separator)
84 delim <- list(ta = "\t", do = ".", co = ",", un = "_", da = "-", sp = " ")
85 # print(separator)
86 separator <- delim[[separator]]
87 # write data.frame to file
88 write.table(df, file = output, sep = separator, row.names = F, quote = F, col.names = header)