Mercurial > repos > iuc > join_files_by_id

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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 17:44:39 -0400
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ada3968ebf26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/join_files_by_id commit a835a0b20127f485a6af4b466bb29d58d63541ea
iuc
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diff changeset
1 # libraries
ada3968ebf26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/join_files_by_id commit a835a0b20127f485a6af4b466bb29d58d63541ea
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2 library(data.table)
ada3968ebf26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/join_files_by_id commit a835a0b20127f485a6af4b466bb29d58d63541ea
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3 library(parallel)
ada3968ebf26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/join_files_by_id commit a835a0b20127f485a6af4b466bb29d58d63541ea
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4
ada3968ebf26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/join_files_by_id commit a835a0b20127f485a6af4b466bb29d58d63541ea
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5 # inputs
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6 args <- commandArgs()
ada3968ebf26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/join_files_by_id commit a835a0b20127f485a6af4b466bb29d58d63541ea
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7
ada3968ebf26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/join_files_by_id commit a835a0b20127f485a6af4b466bb29d58d63541ea
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8 input <- gsub("--in=", "", args[grepl("--in=", args)])
ada3968ebf26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/join_files_by_id commit a835a0b20127f485a6af4b466bb29d58d63541ea
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9 header <- as.integer(gsub("--he=", "", args[grepl("--he=", args)]))
ada3968ebf26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/join_files_by_id commit a835a0b20127f485a6af4b466bb29d58d63541ea
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10 join_col <- gsub("--jc=", "", args[grepl("--jc=", args)])
ada3968ebf26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/join_files_by_id commit a835a0b20127f485a6af4b466bb29d58d63541ea
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11 separator <- gsub("--sep=", "", args[grepl("--sep=", args)])
ada3968ebf26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/join_files_by_id commit a835a0b20127f485a6af4b466bb29d58d63541ea
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12 null_char <- gsub("--nc=", "", args[grepl("--nc=", args)])
ada3968ebf26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/join_files_by_id commit a835a0b20127f485a6af4b466bb29d58d63541ea
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13 output <- gsub("--out=", "", args[grepl("--out=", args)])
ada3968ebf26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/join_files_by_id commit a835a0b20127f485a6af4b466bb29d58d63541ea
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ada3968ebf26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/join_files_by_id commit a835a0b20127f485a6af4b466bb29d58d63541ea
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15 # test VARS
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16 # input <- list("test-data/df1.txt", "test-data/df2.txt", "test-data/df3.txt")
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17 #
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18 # input <- list("test-data/df_big_1.txt", "test-data/df_big_2.txt", "test-data/df_big_3.txt",
ada3968ebf26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/join_files_by_id commit a835a0b20127f485a6af4b466bb29d58d63541ea
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19 # "test-data/df_big_4.txt", "test-data/df_big_5.txt", "test-data/df_big_6.txt",
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20 # "test-data/df_big_7.txt", "test-data/df_big_8.txt", "test-data/df_big_9.txt",
ada3968ebf26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/join_files_by_id commit a835a0b20127f485a6af4b466bb29d58d63541ea
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21 # "test-data/df_big_10.txt")
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22 # header <- 1
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23 # join_col <- 1
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24 # separator <- "ta"
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25 # null_char <- 0
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26 # output <- "out"
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27
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28 if(header > 0){
ada3968ebf26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/join_files_by_id commit a835a0b20127f485a6af4b466bb29d58d63541ea
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29 header <- TRUE
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30 }else{
ada3968ebf26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/join_files_by_id commit a835a0b20127f485a6af4b466bb29d58d63541ea
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31 header <- FALSE
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32 }
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33 join_col <- as.integer(join_col)
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35 # read files into list
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36 df_list <- lapply(input, function(x){as.data.frame(fread(x))})
ada3968ebf26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/join_files_by_id commit a835a0b20127f485a6af4b466bb29d58d63541ea
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ada3968ebf26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/join_files_by_id commit a835a0b20127f485a6af4b466bb29d58d63541ea
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39 #### fix the ids name for all read in tables
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40 df_list <- lapply(df_list, function(x){
ada3968ebf26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/join_files_by_id commit a835a0b20127f485a6af4b466bb29d58d63541ea
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41 names_x <- names(x)
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42 names_x[names_x == "ids"] <- "id" # to join correctly
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43 names_x[join_col] <- "ids"
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44 names(x) <- names_x
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45 x
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46 })
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47
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48 # generate unique ids string
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49 df0 <- lapply(df_list, function(x){
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50 x[join_col]
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51 })
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52
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53 df0 <- data.frame(ids=unique(do.call(rbind, df0)))
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54 df_list <- append(df0, df_list)
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55 df_list[[1]] <- data.frame(ids=df_list[[1]])
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58
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59 ids <- df_list[[1]]
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60 ids <- data.frame(ids = ids[order(ids$ids), "ids" ])
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61 merged_df <- mclapply(2:length(df_list), function(x){
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62 merged_sub <- merge(x = ids, y = df_list[[x]], by = "ids", all.x = T, sort = F)
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63 merged_sub <- merged_sub[order(merged_sub$ids), ]
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64 merged_sub[-1]
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65 }, mc.cores=4)
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66
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67 df <- cbind(ids, do.call(cbind, merged_df))
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68
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69 # benchmarking
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70 # library(microbenchmark)
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71 # microbenchmark(
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72 # df1 <- lapply(2:length(df_list), function(x){
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73 # merge(df_list[[1]], df_list[[x]], by = "ids", all.x = T)[-1]
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74 # }),
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75 # merged_df <- mclapply(2:length(df_list), function(x){
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76 # merge(x = ids, y = df_list[[x]], by = "ids", all.x = T, sort = F)[-1]}, mc.cores=7)
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77 # ,times = 4
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78 # )
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79
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80 # change null_char
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81 df[is.na(df)] <- null_char
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82 # separator <- "ta"
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83 # print(separator)
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84 delim <- list(ta = "\t", do = ".", co = ",", un = "_", da = "-", sp = " ")
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85 # print(separator)
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86 separator <- delim[[separator]]
ada3968ebf26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/join_files_by_id commit a835a0b20127f485a6af4b466bb29d58d63541ea
iuc
parents:
diff changeset
87 # write data.frame to file
ada3968ebf26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/join_files_by_id commit a835a0b20127f485a6af4b466bb29d58d63541ea
iuc
parents:
diff changeset
88 write.table(df, file = output, sep = separator, row.names = F, quote = F, col.names = header)