Mercurial > repos > pmac > normalizemediannegcntrl
changeset 0:087ab474dfa4 draft default tip
Uploaded
author | pmac |
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date | Wed, 01 Jun 2016 03:52:52 -0400 |
parents | |
children | |
files | normalizeMedianNegCntrl.pl normalizeMedianNegCntrl.xml test-data/150615-HR-12015-01A.linear test-data/normalized_using_median.tabular test-data/plate_config.txt |
diffstat | 5 files changed, 993 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/normalizeMedianNegCntrl.pl Wed Jun 01 03:52:52 2016 -0400 @@ -0,0 +1,87 @@ +############################################################################### +# In summary this script normalizes each plate of input data to each of its negative +# controls. +# +# Args: +# input.data.frame contains one or more columns of plate data. The first column +# must contain the well annotation ie A01, A02 etc. Each subsequent column represents +# a plate of data where the column name is the plate name. +# +# plate.conf.data.frame is a file of the following format: +# well, type (syntax must be either "poscontr" or "negcontr" or "empty"), name (name of control) +# +# Returns: +# plate values normalized to each negative control type per plate. +# +# Author: kate gould +############################################################################### + +use strict; +use warnings; +use IO::Handle; +use File::Temp qw/ tempfile tempdir /; +my $tdir = tempdir( CLEANUP => 0 ); + +# check to make sure having correct input and output files +my $usage = "usage: normalizeMedianNegCntrl.pl [TABULAR.in] [TABULAR.in] [TABULAR.out] \n"; +die $usage unless @ARGV == 3; + +#get the input arguments +my $plateData = $ARGV[0]; +my $plateConfig = $ARGV[1]; +my $normMedNeg = $ARGV[2]; + +#open the input files +open (INPUT1, "<", $plateData) || die("Could not open file $plateData \n"); +open (INPUT2, "<", $plateConfig) || die("Could not open file $plateConfig \n"); +open (OUTPUT1, ">", $normMedNeg) || die("Could not open file $normMedNeg \n"); + +#variable to store the name of the R script file +my $r_script; + +# R script to implement the calcualtion of q-values based on multiple simultaneous tests p-values +# construct an R script file and save it in a temp directory +chdir $tdir; +$r_script = "normalizeMedianNegCntrl.r"; + +open(Rcmd,">", $r_script) or die "Cannot open $r_script \n\n"; +print Rcmd " + #options(show.error.messages = FALSE); + header <- read.table(\"$plateData\", head=F, sep=\"\\t\", comment=\"\", nrows=1); + input.data.frame <- read.table(\"$plateData\", head=F, sep=\"\\t\", skip=1); + plate.conf.data.frame <- read.table(\"$plateConfig\", head=T, sep=\"\\t\", comment=\"\"); + + normalise <- function(x, y){if (!is.na(x)) return (x/y) else (return (NA))} + + # assumed second column is type ie negcontr and third column is name of control + negative.controls.list <- unique(plate.conf.data.frame[which (plate.conf.data.frame[,2] == \"negcontr\"),][,3]); + + normalized.data.frame <- data.frame(well=input.data.frame[,1], stringsAsFactors=FALSE); + column.name.list <- c(); + for (negative.control in negative.controls.list){ + negative.control.wells <- plate.conf.data.frame[which (plate.conf.data.frame[3] == negative.control),][,1]; + + for (i in 2:length(colnames(input.data.frame))){ + column.name <- paste(colnames(input.data.frame)[i], \".normalised.to.\", negative.control, sep=\"\"); + column.name.list <- append(column.name.list, column.name); + + negative.control.values <- input.data.frame[((input.data.frame[,1] %in% negative.control.wells)&(!(is.na(input.data.frame[,i])))),][,i]; + median.negative.value <- median(negative.control.values); + + normalised.to.median.negative.control.value <- round(sapply(input.data.frame[,i], FUN=normalise, median.negative.value), 2); + normalized.data.frame <- cbind(normalized.data.frame, normalised.to.median.negative.control.value); + } + } + header <- c(header[1], column.name.list) + write.table(header, file=\"$normMedNeg\", quote=F, sep=\"\\t\", row.names=F, col.names=F); + write.table(normalized.data.frame, file=\"$normMedNeg\", quote=F, sep=\"\\t\", row.names=F, col.names=F, append=T); + #eof\n"; + +close Rcmd; + +system("R --no-restore --no-save --no-readline < $r_script > $r_script.out"); + +#close the input and output files +close(OUTPUT1); +close(INPUT1); +close(INPUT2);
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/normalizeMedianNegCntrl.xml Wed Jun 01 03:52:52 2016 -0400 @@ -0,0 +1,135 @@ +<tool id="normalizeMedianNegCntrl" name="Normalize Using Median Negative Controls" version="1.0.0"> + + <command interpreter="perl"> + normalizeMedianNegCntrl.pl $inputFile1 $inputFile2 $outputFile1 + </command> + + <inputs> + <param format="tabular" name="inputFile1" type="data" label="Select the linear plates file"/> + <param format="tabular" name="inputFile2" type="data" label="Select the plate configuration file"/> + </inputs> + + <outputs> + <data format="tabular" name="outputFile1"/> + </outputs> + + <tests> + <test> + <param name="inputFile1" value="150615-HR-12015-01A.linear"/> + <param name="inputFile2" value="plate_config.txt"/> + <output name="outputFile1" file="normalized_using_median.tabular"/> + </test> + </tests> + + <help> + +.. class:: infomark + +**What it does** + +This program takes a linear plate table and a plate config file as input and then normalizes each plate in the table to the negative controls in the config. +The plate config file **must** contain the columns Well, Type and Name in that order. Further the data in column Type must be **exclude**, **negcontr** or **poscontr**. + +**Example** + +If the plates table consisted of:: + + #Well Table_1 Table_2 A01 1654 6 A02 1719 8 A03 1624 19 A04 1518 6 A05 1587 12 A06 1517 8 A07 1638 9 A08 1733 7 A09 1617 6 A10 1722 8 ... + P14 1630 6 P15 1576 6 P16 1740 7 P17 1578 6 P18 1544 6 P19 1692 6 P20 1560 6 P21 1552 6 P22 1790 7 P23 1537 6 P24 NA NA + +and the plates config was:: + + #Well Type Name A02 negcontr NT2 + B02 negcontr NT2 + C02 poscontr ASCIZ + D02 poscontr PARP + E02 negcontr NT2 + F02 poscontr ASCIZ + G02 poscontr PARP + H02 negcontr NT2 + I02 poscontr ASCIZ + J02 poscontr PARP + K02 negcontr NT2 + L02 poscontr ASCIZ + M02 poscontr PARP + N02 negcontr NT2 + O02 poscontr ASCIZ + P02 negcontr NT2 + A23 negcontr NT2 + B23 negcontr NT2 + C23 poscontr ASCIZ + D23 poscontr PARP + E23 negcontr NT2 + F23 poscontr ASCIZ + G23 poscontr PARP + H23 negcontr NT2 + I23 poscontr ASCIZ + J23 poscontr PARP + K23 negcontr NT2 + L23 poscontr ASCIZ + M23 poscontr PARP + N23 negcontr NT2 + O23 poscontr ASCIZ + P23 negcontr NT2 + A01 exclude exclude + A24 exclude exclude + B01 exclude exclude + B24 exclude exclude + C01 exclude exclude + C24 exclude exclude + D01 exclude exclude + D24 exclude exclude + E01 exclude exclude + E24 exclude exclude + F01 exclude exclude + F24 exclude exclude + G01 exclude exclude + G24 exclude exclude + H01 exclude exclude + H24 exclude exclude + I01 exclude exclude + I24 exclude exclude + J01 exclude exclude + J24 exclude exclude + K01 exclude exclude + K24 exclude exclude + L01 exclude exclude + L24 exclude exclude + M01 exclude exclude + M24 exclude exclude + N01 exclude exclude + N24 exclude exclude + O01 exclude exclude + O24 exclude exclude + P01 exclude exclude + P24 exclude exclude + +Running the program will give the following output:: + + #Well Table_1 Table_2 + A01 1.03 0.75 + A02 1.07 1 + A03 1.02 2.38 + A04 0.95 0.75 + A05 0.99 1.5 + A06 0.95 1 + A07 1.02 1.12 + A08 1.08 0.88 + A09 1.01 0.75 + A10 1.08 1 + ... + P14 1.02 0.75 + P15 0.99 0.75 + P16 1.09 0.88 + P17 0.99 0.75 + P18 0.97 0.75 + P19 1.06 0.75 + P20 0.98 0.75 + P21 0.97 0.75 + P22 1.12 0.88 + P23 0.96 0.75 + P24 NA NA + + </help> + +</tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/150615-HR-12015-01A.linear Wed Jun 01 03:52:52 2016 -0400 @@ -0,0 +1,385 @@ +#Well Table_1 Table_2 Table_3 Table_4 Table_5 Table_6 +A01 2215 8.88 55.62 2.57 2.91 78.76 +A02 2811 8.61 57.35 1.07 2.03 63.32 +A03 2226 10.96 70.4 0.54 2.41 79.41 +A04 2528 9.35 61.59 1.66 2.14 74.9 +A05 1827 11.87 73.78 0.66 2.27 79.31 +A06 2337 8.69 58.49 1.07 1.87 62.34 +A07 2233 9.7 63.41 1.07 2.32 77.48 +A08 2462 8.48 57.39 1.06 2.07 67.32 +A09 2790 9.5 62.83 1.65 2.52 80.57 +A10 2792 9.19 60.67 1.9 2.38 73.6 +A11 2547 9.51 61.76 1.33 2.8 84.6 +A12 2629 9.47 60.94 2.09 2.42 72.34 +A13 1655 11.8 71.24 0.85 2.3 71.88 +A14 2647 8.27 52.13 2.15 2.37 72.76 +A15 2300 11.5 72.17 0.57 2.68 86.26 +A16 2030 11.71 71.63 0.74 2.66 89.03 +A17 2124 9.78 63.89 1.13 2.45 81.13 +A18 2461 9.14 59.65 1.83 2.3 77.14 +A19 2273 8.68 57.85 0.97 2.32 69.57 +A20 2281 10.62 70.58 0.7 1.98 65.3 +A21 2412 10.49 69.86 0.46 2.07 70.27 +A22 1331 10.72 69.65 0.68 1.97 61.54 +A23 2245 9.88 66.24 0.4 2.17 66.33 +A24 2037 8.13 53.26 1.42 2.06 70.05 +B01 2184 10.31 65.29 0.87 2.33 72.4 +B02 2104 9.33 57.94 3.09 2.44 79.26 +B03 1639 11.13 69.68 0.55 2.03 67.42 +B04 2467 9.84 64.33 0.77 2.03 67.95 +B05 1818 11.75 75.25 0.66 1.97 68.96 +B06 1769 9.08 57.32 2.43 2.29 69.18 +B07 1654 12.22 75.7 0.6 2.14 75.29 +B08 2199 10.04 68.58 0.73 2.43 73.55 +B09 2043 8.74 59.03 1.22 1.96 57.65 +B10 1329 11.6 73.06 0.68 2.04 58.75 +B11 2533 7.31 47.06 3.83 3.01 95.3 +B12 2712 9.31 61.98 2.06 2.49 75.2 +B13 1824 10.83 68.42 1.54 2.45 80.09 +B14 2718 7.68 49.74 4.01 2.54 81.37 +B15 2443 10.4 68.81 1.02 2.64 91.33 +B16 2061 11.82 77.1 0.39 2.53 87.74 +B17 2088 10.83 70.69 0.62 2.22 74.12 +B18 2730 10.36 70.4 0.81 2.39 78.69 +B19 2279 8.09 54.28 1.14 1.98 61.28 +B20 2371 12.37 78.28 0.25 2.23 78.36 +B21 2114 10.49 71.85 0.85 2.32 73.66 +B22 2355 9.84 66.71 0.72 2.04 64.63 +B23 1154 11.75 72.1 0.35 2.35 65.16 +B24 1646 7.49 50.12 1.82 2.11 64.74 +C01 2356 9.67 64.43 1.02 2.07 61.55 +C02 2680 10.27 67.57 0.82 2.03 60.64 +C03 2305 8.51 55.88 1.56 1.87 56.38 +C04 2510 9.55 63.55 1 2.02 58.22 +C05 2650 10.23 67.96 0.3 1.95 59.48 +C06 2918 9.76 64.98 0.69 2.21 65.35 +C07 2618 8.28 55.39 1.26 2.42 68.98 +C08 2654 9.56 65.3 1.09 2.52 75.17 +C09 2828 8.44 57.39 1.34 2.21 63.59 +C10 2877 9.48 64.75 1.32 2.59 77.38 +C11 2441 9.78 65.38 1.47 2.38 73.63 +C12 2870 7.1 47.04 3.69 2.87 88.54 +C13 3202 9.02 59.93 1.72 2.43 78.2 +C14 2619 8.63 57.43 2.1 2.93 95.11 +C15 2716 8.82 58.73 1.18 2.46 78.45 +C16 2413 10.72 71.07 0.33 2.62 84.52 +C17 2893 8.18 56.14 1.52 2.8 83.32 +C18 2669 9.82 66.62 0.67 2.26 70.88 +C19 2272 10.81 71.79 0.79 2.1 68.8 +C20 2161 9.42 63.4 1.2 2.79 79.7 +C21 2677 8.75 59.62 0.78 2.04 62.52 +C22 2406 9.91 65 0.71 2.08 68.61 +C23 2494 7.54 49.44 2.33 2.25 63.14 +C24 1760 7.85 51.99 1.82 2.15 66.92 +D01 2206 7.2 45.01 2.77 1.41 36.44 +D02 1033 10.08 62.25 1.84 2.61 77.42 +D03 1744 7.58 49.14 3.04 2.4 70.59 +D04 2579 8.78 59.83 1.2 2.12 62.68 +D05 1921 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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/plate_config.txt Wed Jun 01 03:52:52 2016 -0400 @@ -0,0 +1,1 @@ +well type name geneID B02 poscontr Hamp 57817 C02 negcontr OTP -1 D02 poscontr PLK 5347 E02 poscontr TOX -1 F02 negcontr OTP -1 G02 poscontr MPEG1 17476 H02 poscontr TOX -1 I02 poscontr PLK 5347 J02 negcontr OTP -1 K02 poscontr TOX -1 L02 poscontr Hamp 57817 M02 negcontr OTP -1 N02 poscontr PLK 5347 O02 negcontr mock -1 B23 poscontr PLK 5347 C23 negcontr OTP -1 D23 poscontr TOX -1 E23 negcontr OTP -1 F23 poscontr PLK 5347 G23 poscontr MPEG1 17476 H23 poscontr TOX -1 I23 negcontr OTP -1 J23 poscontr PLK 5347 K23 poscontr Hamp 57817 L23 negcontr OTP -1 M23 poscontr MPEG1 17476 N23 negcontr OTP -1 O23 negcontr mock -1 \ No newline at end of file