#!/usr/local/bin/perl
### gasv_to_spt.pl #########################################################################
#
### HISTORY #######################################################################################
# Version Date Coder Comments
# 1.0 2012/10/12 sgovind Versioning start point
### INCLUDES ######################################################################################
use strict;
### 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 @startend;
### 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.".spt";
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 "#chr1\tstart\tend\tchr2\tstart\tend\tquality";
#read header
$line = <$INPUT_FILE>;
while(!(eof($INPUT_FILE))){
$line = <$INPUT_FILE>;
@line_data = split(' ',$line);
#Check if localization score is -1
if($line_data[6] eq -1){
next;
}
@startend = split(',',$line_data[2]);
#Test for size of translocation [5]
if(abs($startend[1]-$startend[0]) < 70 ){
next;
}
if($line_data[7] eq "T" || $line_data[7] eq "TR" || $line_data[7] eq "TNR+" || $line_data[7] eq "TNR-"){
print $OUTPUT_FILE "\n";
print $OUTPUT_FILE $line_data[1];
print $OUTPUT_FILE "\t";
print $OUTPUT_FILE $startend[0];
print $OUTPUT_FILE "\t";
print $OUTPUT_FILE $startend[1];
print $OUTPUT_FILE "\t";
print $OUTPUT_FILE $line_data[3];
print $OUTPUT_FILE "\t";
@startend = split(',',$line_data[4]);
print $OUTPUT_FILE $startend[0];
print $OUTPUT_FILE "\t";
print $OUTPUT_FILE $startend[1];
print $OUTPUT_FILE "\t";
print $OUTPUT_FILE ".";
}
}
close($INPUT_FILE);
close($OUTPUT_FILE);