From c70170bffb311b0d59f4b2c8027897703743c8d8 Mon Sep 17 00:00:00 2001
From: Valentina Boeva <valeu@users.noreply.github.com>
Date: Fri, 24 Mar 2017 18:28:03 +0100
Subject: [PATCH] Delete getGCfromFasta.pl

---
 src/getGCfromFasta.pl | 62 -------------------------------------------
 1 file changed, 62 deletions(-)
 delete mode 100644 src/getGCfromFasta.pl

diff --git a/src/getGCfromFasta.pl b/src/getGCfromFasta.pl
deleted file mode 100644
index 0dcf7e2..0000000
--- a/src/getGCfromFasta.pl
+++ /dev/null
@@ -1,62 +0,0 @@
-# This file is part of ONCOCNV - a tool to detect copy number alterations in amplicon sequencing data
-# Copyright (C) 2014 OncoDNA
-
-# This program is free software: you can redistribute it and/or modify it
-# under the terms of the GNU General Public License as published by the Free
-# Software Foundation, either version 3 of the License, or (at your option)
-# any later version.
-# 
-# This program is distributed in the hope that it will be useful, but WITHOUT
-# ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
-# FOR A PARTICULAR PURPOSE.  See the GNU General Public License for more details.
-# 
-# You should have received a copy of the GNU General Public License
-# along with this program.  If not, see <http://www.gnu.org/licenses/>.
-
-#Author: Valentina BOEVA
-
-#!/usr/bin/perl -w
-use strict;
-use POSIX;
-
-my $usage = qq{    
-
-$0 getControlStats -f <fastaFile>
-	
-};
-
-my $filename = "";
-while(scalar(@ARGV) > 0){
-    my $this_arg = shift @ARGV; 
-    if ( $this_arg eq '-h') {print "$usage\n"; exit; }
-    elsif ( $this_arg eq '-f') {$filename = shift @ARGV;} 
-    elsif ( $this_arg =~ m/^-/ ) { print "unknown flag: $this_arg\n";}
-}
-print STDERR $usage if ($filename eq "");
-
-open FILE, "< $filename " || die "$filename : $!\n";
-
-print "region\tGC\n";
-
-my ($name,$GC);
-while(<FILE>){
-    chomp;
-    if (/>(.+)/) {
-	$name=$1;
-    } else {
-	my $len = length($_);
-	$GC=(tr/GCgc//) / ($len-(tr/nN//));
-	print "$name\t$GC\n";
-    }
-}
-close FILE;
-
-
-#------------------------------------------------------------------------------#
-#------------------------------------------------------------------------------#
-sub round {
-  my $number = shift || 0;
-  my $dec = 10 ** (shift || 0);
-  return int( $dec * $number + .5 * ($number <=> 0)) / $dec;
-}
-