diff DEGseq_2.pl @ 18:22d79320085c draft

Uploaded

--- a/DEGseq_2.pl	Wed Oct 29 05:03:38 2014 -0400
+++ b/DEGseq_2.pl	Thu Oct 30 21:31:55 2014 -0400
@@ -25,13 +25,8 @@
 my $mark1=$opts{mark1};
 my $mark2=$opts{mark2};
 my $fileout=$outputdir."degseq.R";
-my $log=$outputdir."LOG.txt";
 
 open OUT,">$fileout"; #output file  
-open LOG,">$log";
-print LOG "JOB start!\t";
-print LOG `date`;
-print LOG "\n";
 #my ($name,$dir);
 #$name=basename($filein);
 print OUT "library(DEGseq)\n";
@@ -49,42 +44,12 @@
 }
 close OUT;
 
-print LOG "Prepare for DEGseq!\t";
-print LOG `date`;
-print LOG "\n";
 
 system("R CMD BATCH $fileout");
 
 wait;
 
-my $outfile=$outputdir."result.txt";
-open OUT ,">$outfile";
-my $deg=$outputdir."output_score.txt";
-open IN,"<$deg";
-my %hash;
-while (my $aline=<IN>) {
-	chomp $aline;
-	if($aline=~/^\"/){print OUT "#GeneID\tchromsome\tvalue1\tvalue2\ttag\n";next;}
-	my @temp=split/\t/,$aline;
-	#$hash{$temp[0].$temp[1].$temp[2]}=$temp[$#temp];
-	#my @tmp=split/\|/,$temp[0];
-	#my @tmp=split/\:/,$temp[0];
-	#my @po=split/\-/,$tmp[1];
-	print OUT $temp[0],"\t",$temp[1],"\t",$temp[2],"\t",$temp[-1],"\n";
-}
-close IN;
 
-#open IN,"<$filein";
-#while (my $aline=<IN>) {
-#	chomp $aline;
-#	my @temp=split/\t/,$aline;
-#	if (defined $hash{$temp[0].$temp[2].$temp[3]}) {print OUT $aline,"\t",$hash{$temp[0].$temp[2].$temp[3]},"\n";
-#	}
-#}
-
-print LOG "Finish all JOB !\t";
-print LOG `date`;
-print LOG "\n";
 
 sub usage{
 print <<"USAGE";