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1 ###############################################################################
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2 # This script converts plate data from linear to tabular format.
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3 #
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4 # Args:
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5 # input file:
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6 # a text file containing a set of linear data in either 384/96 well format,
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7 #
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8 # Returns:
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9 # For each input file, a tabular version of the data is returned
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10 # in the same format typically generated from synergy or cellomics software.
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11 #
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12 # Author: jason ellul
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13 ###############################################################################
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14
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15 use strict;
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16 use warnings;
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17 use IO::Handle;
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18 use File::Temp qw/ tempfile tempdir /;
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19 my $tdir = tempdir( CLEANUP => 0 );
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20
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21 # check to make sure having correct input and output files
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22 my $usage = "usage: reformatPlatesTabularToLinear.pl [TABULAR.in] [TABULAR.out] \n";
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23 die $usage unless @ARGV == 2;
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24
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25 #get the input arguments
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26 my $linearPlateTable = $ARGV[0];
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27 my $tabularPlateTable = $ARGV[1];
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28
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29 #open the input files
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30 open (INPUT, "<", $linearPlateTable) || die("Could not open file $linearPlateTable \n");
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31 open (OUTPUT1, ">", $tabularPlateTable) || die("Could not open file $tabularPlateTable \n");
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32
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33 #variable to store the name of the R script file
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34 my $r_script;
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35
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36 # R script to implement the calcualtion of q-values based on multiple simultaneous tests p-values
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37 # construct an R script file and save it in a temp directory
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38 chdir $tdir;
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39 $r_script = "reformatPlatesLinearToTabular.r";
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40
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41 open(Rcmd,">", $r_script) or die "Cannot open $r_script \n\n";
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42 print Rcmd "
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43 #options(show.error.messages = FALSE);
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44
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45 #read the plates table
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46 #tables <- read.table(\"$linearPlateTable\", sep=\"\\t\", head=T, comment=\"\");
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47 tablesTMP <- scan(\"$linearPlateTable\", sep=\"\\n\", what=\"character\", quiet = TRUE);
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48 tmp <- strsplit(tablesTMP[1], \"\t\")[[1]];
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49 tables <- matrix(\"\", nrow=length(tablesTMP)-1, ncol=length(tmp))
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50 colnames(tables) <- tmp;
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51 for(i in 2:length(tablesTMP)) {
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52 tmp <- strsplit(tablesTMP[i], \"\t\")[[1]];
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53 if(length(tmp) > ncol(tables)) stop(paste(\"Error: Row\", i, \"has more columns than the header\"));
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54 tables[i-1, 1:length(tmp)] <- tmp;
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55 }
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56 tables <- as.data.frame(tables, stringsAsFactors=F);
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57
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58 if(ncol(tables) < 2) {
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59 stop(\"The first column of the table must contain the well ID from A01 to either H12 or P24 depending on the number of wells.\")
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60 }
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61
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62 # check if the plate is in 96 or 384 well format
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63 if(nrow(tables) == 96) {
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64 nc <- 12;
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65 nr <- 8;
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66 } else if(nrow(tables) == 384) {
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67 nc <- 24;
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68 nr <- 16;
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69 } else {
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70 stop(\"Table is not for a 96 or 384 well plate. Please ensure you either have 96 or 384 rows plus a header.\")
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71 }
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72
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73 # for each table
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74 for(i in 2:ncol(tables)) {
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75 # write the name of the table
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76 write(paste(colnames(tables)[i], sep=\"\"), file=\"$tabularPlateTable\", append=T);
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77 write(\"\", file=\"$tabularPlateTable\", append=T);
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78 # the column header
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79 write(paste(\"\\t\", paste(1:nc, collapse=\"\\t\"), sep=\"\"), file=\"$tabularPlateTable\", append=T);
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80 # replace any NAs with blank
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81 if(any(is.na(tables[,i]))) tables[which(is.na(tables[,i])),i] <- \"\";
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82 # for each row print the values
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83 curr <- 0;
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84 for(j in LETTERS[1:nr]) {
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85 write(paste(j, \"\\t\", paste(tables[(curr+1):(curr+nc), i], collapse=\"\\t\"), sep=\"\"), file=\"$tabularPlateTable\", append=T);
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86 curr <- curr + nc;
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87 }
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88 # if we are at the last table do not add an extra line
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89 if(i != ncol(tables)) write(\"\", file=\"$tabularPlateTable\", append=T);
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90 }
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91 #eof\n";
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92
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93 close Rcmd;
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94
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95 system("R --no-restore --no-save --no-readline < $r_script > $r_script.out");
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96
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97 #close the input and output files
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98 close(OUTPUT1);
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99 close(INPUT);
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