From 873830c2727a2b8cbae126cf82bdfacac07e60d5 Mon Sep 17 00:00:00 2001
From: elserj <elserj@localhost>
Date: Thu, 10 Mar 2011 22:52:55 +0000
Subject: [PATCH] Added script that will take the list of protein coding genes
 and repeated genes from IPRscan and removes them from a fasta file

svn path=/; revision=89
---
 .../remove_transposable_elements.pl           | 66 +++++++++++++++++++
 1 file changed, 66 insertions(+)
 create mode 100755 interactome_scripts/remove_transposable_elements.pl

diff --git a/interactome_scripts/remove_transposable_elements.pl b/interactome_scripts/remove_transposable_elements.pl
new file mode 100755
index 0000000..9a4f51a
--- /dev/null
+++ b/interactome_scripts/remove_transposable_elements.pl
@@ -0,0 +1,66 @@
+#!/usr/bin/perl
+
+use strict;
+use warnings;
+
+if ($#ARGV != 3) {
+	print "usage: remove_transposable_elements.pl IPR_genes genes_to_remove fasta_file output_file\n";
+	exit;
+}
+
+my $ipr_file = $ARGV[0];
+my $remove_file = $ARGV[1];
+my $fasta_file = $ARGV[2];
+my $out_file = $ARGV[3];
+
+my %ipr_hash;
+open (ipr_file, $ipr_file);
+while(<ipr_file>) {
+	my $line = $_;
+	chomp $line;
+	$ipr_hash{$line} = $line;
+}
+close(ipr_file);
+
+my %remove_hash;
+
+open (remove_file, $remove_file);
+while(<remove_file>) {
+	my $line = $_;
+	chomp $line;
+	
+	$remove_hash{$line} = $line;
+}
+close(remove_file);
+
+open(fasta_file, $fasta_file);
+
+
+my %fasta_hash;
+my $gene_prev = "";
+while(<fasta_file>) {
+	my $line = $_;
+	
+	if ($line =~ /^>/) {
+		chomp $line;
+		$line =~ s/^>//g;
+		$line =~ s/_1//g;
+		$gene_prev=$line;
+	}else{
+		if(!defined($fasta_hash{$gene_prev})) {
+			$fasta_hash{$gene_prev} = $line;
+		}else{
+			$fasta_hash{$gene_prev} = $fasta_hash{$gene_prev} . $line;
+		}
+	}
+}
+close(fasta_file);
+
+open(out_file, ">$out_file");
+foreach my $gene (keys %fasta_hash) {
+	if(defined($ipr_hash{$gene}) && !defined($remove_hash{$gene})) {
+		print out_file ">$gene\n";
+		print out_file "$fasta_hash{$gene}";
+	}
+}
+close(out_file);
-- 
2.34.1