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1 ##============ Sink warnings and errors to a file ==============
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2 ## use the sink() function to wrap all code within it.
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3 ##==============================================================
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4 zz = file('warnings_and_errors.txt')
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5 sink(zz)
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6 sink(zz, type = 'message')
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7
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8 #------------import libraries--------------------
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9 options(stringsAsFactors = FALSE)
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10
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11 library(getopt)
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12 library(rmarkdown)
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13 #------------------------------------------------
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14
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15
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16 #------------get arguments into R--------------------
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17 # library(dplyr)
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18 # getopt_specification_matrix(extract_short_flags('htseq_count.xml')) %>%
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19 # write.table(file = 'spec.txt', sep = ',', row.names = FALSE, col.names = TRUE, quote = FALSE)
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20
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21
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22 spec_matrix = as.matrix(
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23 data.frame(stringsAsFactors=FALSE,
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24 long_flags = c("X_e", "X_o", "X_d", "X_s", "X_t", "X_f", "X_r",
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25 "X_S", "X_a", "X_T", "X_i", "X_I", "X_m"),
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26 short_flags = c("e", "o", "d", "s", "t", "f", "r", "S", "a", "T",
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27 "i", "I", "m"),
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28 argument_mask_flags = c(1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L),
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29 data_type_flags = c("character", "character", "character", "character",
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30 "character", "character", "character",
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31 "character", "character", "character", "character",
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32 "character", "character")
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33 )
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34 )
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35 opt = getopt(spec_matrix)
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36 #----------------------------------------------------
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37
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38
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39 #-----------using passed arguments in R
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40 # to define system environment variables---
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41 do.call(Sys.setenv, opt[-1])
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42 #----------------------------------------------------
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43
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44 #---------- often used variables ----------------
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45 # OUTPUT_DIR: path to the output associated directory, which stores all outputs
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46 # TOOL_DIR: path to the tool installation directory
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47 OUTPUT_DIR = opt$X_d
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48 TOOL_DIR = opt$X_t
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49 RMD_NAME = 'htseq_count.Rmd'
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50 OUTPUT_REPORT = opt$X_o
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51
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52 # create the output associated directory to store all outputs
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53 dir.create(OUTPUT_DIR, recursive = TRUE)
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54
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55 #-----------------render Rmd--------------
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56 render(paste0(TOOL_DIR, '/', RMD_NAME), output_file = OUTPUT_REPORT)
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57 #------------------------------------------
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58
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59 #==============the end==============
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60
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61
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62 ##--------end of code rendering .Rmd templates----------------
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63 sink()
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64 ##=========== End of sinking output============================= |
