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comparison DEGseq.pl @ 44:0c4e11018934 draft

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author big-tiandm
date Thu, 30 Oct 2014 21:29:19 -0400
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43:4c0b1a94b882 44:0c4e11018934
1 #!/usr/bin/perl -w
2 #Filename:
3 #Author: Tian Dongmei
4 #Email: tiandm@big.ac.cn
5 #Date: 2009-05-06
6 #Modified:
7 #Description:
8 my $version=1.00;
9
10 use strict;
11 use Getopt::Long;
12 use File::Basename;
13
14 my %opts;
15 GetOptions(\%opts,"i=s","outdir=s","column1:i","mark1=s","depth1:i","depth2:i","column2:i","mark2=s","h");
16 if (!(defined $opts{i} and defined $opts{outdir} and defined $opts{mark1} and defined $opts{mark2}) || defined $opts{h}) { #necessary arguments
17 &usage;
18 }
19
20 my $filein=$opts{'i'};
21 my $outputdir=$opts{'outdir'};
22 unless ($outputdir=~/\/$/) {$outputdir .="/";}
23 my $column1=defined $opts{column1} ? $opts{column1} : 3;
24 my $column2=defined $opts{column2} ? $opts{column2} : 4;
25 my $mark1=$opts{mark1};
26 my $mark2=$opts{mark2};
27 my $fileout=$outputdir."degseq.R";
28
29 open OUT,">$fileout"; #output file
30
31 print OUT "library(DEGseq)\n";
32 print OUT "geneExpFile <- system.file(package=\"DEGseq\")\n";
33 print OUT "geneExpFile<-file.path(\"$filein\")\n";
34 print OUT "layout(matrix(c(1,2,3,4,5,6), 3, 2, byrow=TRUE))\npar(mar=c(2, 2, 2,2))\n";
35 print OUT "outputdir<-file.path(\"$outputdir\")\n";
36 print OUT "geneExpMatrix1 <- readGeneExp(file=geneExpFile, geneCol=1, valCol=c($column1))\n";
37 print OUT "geneExpMatrix2 <- readGeneExp(file=geneExpFile, geneCol=1, valCol=c($column2))\n";
38 if(defined $opts{'depth1'} && defined $opts{'depth2'}){
39 print OUT "DEGexp(geneExpMatrix1=geneExpMatrix1, geneCol1=1, expCol1=c(2), groupLabel1=\"$mark1\",geneExpMatrix2=geneExpMatrix2, geneCol2=1, expCol2=c(2), groupLabel2=\"$mark2\",depth1=$opts{depth1},depth2=$opts{depth2},outputDir=outputdir,method=\"MARS\")\n";
40 }
41 else{
42 print OUT "DEGexp(geneExpMatrix1=geneExpMatrix1, geneCol1=1, expCol1=c(2), groupLabel1=\"$mark1\",geneExpMatrix2=geneExpMatrix2, geneCol2=1, expCol2=c(2), groupLabel2=\"$mark2\",outputDir=outputdir,method=\"MARS\")\n";
43 }
44 close OUT;
45
46 system("R CMD BATCH $fileout");
47
48 sub usage{
49 print <<"USAGE";
50 Version $version
51 Usage:
52 $0 -i -outdir -column1 -mark1 -column2 -mark2 -depth1 -depth2
53 options:
54 -i input file
55 -outdir output file dir
56 -column1 the first column for DEGseq
57 -mark1 the name of the column1
58 -depth1 depth for the first file,use for normalize
59 -column2 the second column for DEGseq
60 -mark2 the name of the column2
61 -depth2 depth for the second file,use for normalize
62
63 -h help
64 USAGE
65 exit(1);
66 }
67