Add files via upload

sub/expression_filter.pl

@@ -0,0 +1,42 @@
+#!/usr/bin/perl-w
+# ******************** Software Information *******************
+# Version: TSNAD v1.1
+# File: expression_filter.pl
+# Perl Version: 5.18.2
+# Finish time: Octobor, 2018.
+# Developer: Jingcheng Wu, Zhan Zhou, Wenyi Zhao 
+# Copyright (C) 2018-2019 - College of Pharmaceutical Sciences, 
+#               Zhejiang University - All Rights Reserved 
+# *************************************************************
+use strict;
+
+my $in=$ARGV[0]; #input mutation file
+my $seq=$ARGV[1]; #gene expression file
+my $out=$ARGV[2]; # output mutation with expression
+
+open IN, "<$in" or die "cannot open $in:$!";
+open SEQ, "<$seq" or die "cannot open $seq:$!";
+open OUT, ">$out" or die "cannot open $out:$!";
+
+my %exp;
+while (<SEQ>){
+	chomp;
+	my @line=split/\t/,$_;
+	$exp{$line[0]."\t".$line[1]}=$line[7]."\t".$line[8];
+}
+
+while (<IN>){
+	chomp;
+	my @line=split/\t/,$_;
+	if ($_=~/##/){
+		print OUT"$_\n";
+	}
+	elsif($_=~/#/){
+		print OUT "$_\tRPKM\tTPM\n";
+	}
+	elsif($exp{$line[3]."\t".$line[17]}){
+		my $expression=$exp{$line[3]."\t".$line[17]};
+		my @expession=split/\t/,$expression;
+		print OUT"$_\t$expression\n" if ($expression>1);
+	}
+}