RNA seq analysis - Aminata NDIAYE

analysis.01/FilterPval.pl

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+#!/usr/bin/perl
+###################
+#
+# Written by Aminata NDIAYE 
+# 		This script take as input a tab separated matrix wich contains results from DESeq analysis. 
+#		It filters the input matrix and outputs a file with tab separated columns describing gene deferentially expressed with p-adj < 0.01 
+# 		
+#
+####################
+
+
+if (scalar @ARGV < 2)
+{
+	print "\n\nUsage : perl FilterPval.pl input_matrix_file output_file \n\n";
+	exit;
+}
+
+#~~~~~~~~Arguments settings
+my $input_matrix_file = $ARGV[0];
+my $output_file = $ARGV[1];
+
+
+#~~~~~~~~Opening output file for writing in .txt format
+open OUTPUT, '>', "$output_file.txt" or die "Cannot open $output_file\n";
+
+#~~~~~~~~Set output file headers. 
+printf OUTPUT ("%-20s %-20s\n", "Gene", "P-adj"); 
+
+#~~~~~~~~Opening input file for reading then filter according to p-adj and output result in a .txt format
+open my $file, '<', $input_matrix_file or die "Cannot open $input_matrix_file\n";
+my @list_lines;
+while (my $line = <$file>)
+{
+	chomp $line;
+	next if($line =~ m/^"base"/);
+	push @list_lines, $line;
+}
+
+foreach my $list_line (@list_lines)
+{
+		my @attributes = split(/ /,$list_line);
+		my $padj = $attributes[6];
+		if (($padj < 0.01) and ($padj ne "NA"))
+		{
+			printf OUTPUT ("%-20s %-20s\n", "$attributes[0]", "$attributes[6]");
+		}
+}
+
+close(OUTPUT);
+close($file);