#!/usr/local/bin/perl
### freec_to_spc.pl #########################################################################
#
### HISTORY #######################################################################################
# Version Date Coder Comments
# 1.0 2012/04/11 sgovind Versioning start point
### INCLUDES ######################################################################################
use warnings;
use strict;
use File::Basename;
### Global Variables ##############################################################################
my $input_file_path;
my $input_file_name;
my $output_directory;
my $output_file_name;
my $INPUT_FILE;
my $OUTPUT_FILE;
my $path;
my $suffix;
my $line;
my @line_data;
my $chr;
my $number;
my $copy_number;
### Sub-Methods ###################################################################################
### Main ##########################################################################################
my $ARGC = @ARGV;
if($ARGC != 2){
die "ERROR: $ARGC arguments were provided, exactly 2 are expected\n";
}
$input_file_path = $ARGV[0];
$output_directory = $ARGV[1];
( $input_file_name, $path, $suffix ) = fileparse( $input_file_path, "\.[^.]*");
$output_file_name = $output_directory.$input_file_name.".spc";
print "$output_file_name\n";
open ($INPUT_FILE, "<", $input_file_path) or die "ERROR: could not open file at path $input_file_path\n";
open ($OUTPUT_FILE, ">", $output_file_name) or die "ERROR could not open file at path $output_file_name\n";
print $OUTPUT_FILE "#chr\tstart\tend\tnumber\tquality";
while(!(eof($INPUT_FILE))){
$line = <$INPUT_FILE>;
@line_data = split(' ',$line);
if(!($line_data[0] =~ m/^(chr)?(.*)/)){
warn "ERROR chr entry was invalid\n";
}
$chr = $2;
if($line_data[3] == 2){
warn "ERROR: FOUND a 2\n";
next;
}
$number = $line_data[3];
print $OUTPUT_FILE "\n";
print $OUTPUT_FILE $chr;
print $OUTPUT_FILE "\t";
print $OUTPUT_FILE $line_data[1];
print $OUTPUT_FILE "\t";
print $OUTPUT_FILE $line_data[2];
print $OUTPUT_FILE "\t";
print $OUTPUT_FILE $number;
print $OUTPUT_FILE "\t";
print $OUTPUT_FILE ".";
}