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1 #!/usr/bin/perl -w
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2 #Filename:
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3 #Author: Tian Dongmei
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4 #Email: tiandm@big.ac.cn
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5 #Date: 2009-05-06
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6 #Modified:
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7 #Description: ɾ³ýmatched reads
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8 my $version=1.00;
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9
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10 use strict;
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11 use Getopt::Long;
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12 use File::Basename;
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13
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14 my %opts;
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15 GetOptions(\%opts,"i=s","outdir=s","column1:i","mark1=s","depth1:i","depth2:i","column2:i","mark2=s","h");
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16 if (!(defined $opts{i} and defined $opts{outdir} and defined $opts{mark1} and defined $opts{mark2}) || defined $opts{h}) { #necessary arguments
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17 &usage;
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18 }
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19
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20 my $filein=$opts{'i'};
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21 my $outputdir=$opts{'outdir'};
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22 unless ($outputdir=~/\/$/) {$outputdir .="/";}
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23 my $column1=defined $opts{column1} ? $opts{column1} : 3;
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24 my $column2=defined $opts{column2} ? $opts{column2} : 4;
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25 my $mark1=$opts{mark1};
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26 my $mark2=$opts{mark2};
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27 my $fileout=$outputdir."degseq.R";
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28 my $log=$outputdir."LOG.txt";
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29
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30 open OUT,">$fileout"; #output file
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31 open LOG,">$log";
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32 print LOG "JOB start!\t";
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33 print LOG `date`;
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34 print LOG "\n";
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35 #my ($name,$dir);
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36 #$name=basename($filein);
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37 print OUT "library(DEGseq)\n";
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38 print OUT "geneExpFile <- system.file(package=\"DEGseq\")\n";
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39 print OUT "geneExpFile<-file.path(\"$filein\")\n";
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40 print OUT "layout(matrix(c(1,2,3,4,5,6), 3, 2, byrow=TRUE))\npar(mar=c(2, 2, 2,2))\n";
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41 print OUT "outputdir<-file.path(\"$outputdir\")\n";
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42 print OUT "geneExpMatrix1 <- readGeneExp(file=geneExpFile, geneCol=1, valCol=c($column1))\n";
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43 print OUT "geneExpMatrix2 <- readGeneExp(file=geneExpFile, geneCol=1, valCol=c($column2))\n";
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44 if(defined $opts{'depth1'} && defined $opts{'depth2'}){
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45 print OUT "DEGexp(geneExpMatrix1=geneExpMatrix1, geneCol1=1, expCol1=c(2), groupLabel1=\"$mark1\",geneExpMatrix2=geneExpMatrix2, geneCol2=1, expCol2=c(2), groupLabel2=\"$mark2\",depth1=$opts{depth1},depth2=$opts{depth2},outputDir=outputdir,method=\"MARS\")\n";
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46 }
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47 else{
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48 print OUT "DEGexp(geneExpMatrix1=geneExpMatrix1, geneCol1=1, expCol1=c(2), groupLabel1=\"$mark1\",geneExpMatrix2=geneExpMatrix2, geneCol2=1, expCol2=c(2), groupLabel2=\"$mark2\",outputDir=outputdir,method=\"MARS\")\n";
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49 }
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50 close OUT;
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51
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52 print LOG "Prepare for DEGseq!\t";
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53 print LOG `date`;
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54 print LOG "\n";
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55
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56 system("R CMD BATCH $fileout");
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57
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58 wait;
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59
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60 my $outfile=$outputdir."result.txt";
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61 open OUT ,">$outfile";
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62 my $deg=$outputdir."output_score.txt";
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63 open IN,"<$deg";
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64 my %hash;
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65 while (my $aline=<IN>) {
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66 chomp $aline;
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67 if($aline=~/^\"/){print OUT "#GeneID\tchromsome\tvalue1\tvalue2\ttag\n";next;}
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68 my @temp=split/\t/,$aline;
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69 #$hash{$temp[0].$temp[1].$temp[2]}=$temp[$#temp];
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70 #my @tmp=split/\|/,$temp[0];
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71 #my @tmp=split/\:/,$temp[0];
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72 #my @po=split/\-/,$tmp[1];
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73 print OUT $temp[0],"\t",$temp[1],"\t",$temp[2],"\t",$temp[-1],"\n";
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74 }
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75 close IN;
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76
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77 #open IN,"<$filein";
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78 #while (my $aline=<IN>) {
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79 # chomp $aline;
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80 # my @temp=split/\t/,$aline;
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81 # if (defined $hash{$temp[0].$temp[2].$temp[3]}) {print OUT $aline,"\t",$hash{$temp[0].$temp[2].$temp[3]},"\n";
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82 # }
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83 #}
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84
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85 print LOG "Finish all JOB !\t";
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86 print LOG `date`;
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87 print LOG "\n";
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88
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89 sub usage{
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90 print <<"USAGE";
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91 Version $version
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92 Usage:
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93 $0 -i -outdir -column1 -mark1 -column2 -mark2 -depth1 -depth2
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94 options:
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95 -i input file
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96 -outdir output file dir
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97 -column1 the first column for DEGseq
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98 -mark1 the name of the column1
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99 -depth1 depth for the first file,use for normalize
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100 -column2 the second column for DEGseq
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101 -mark2 the name of the column2
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102 -depth2 depth for the second file,use for normalize
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103
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104 -h help
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105 USAGE
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106 exit(1);
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107 }
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108
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