TargetPerla.pl

#!/usr/bin/perl

use warnings;
use Pod::Usage;
use Getopt::Long;
use strict;
use Cwd 'abs_path';
use File::Path;
use File::Basename;
	
######################################################################
#
#	Variables initialization with default values
#
######################################################################

our ($record,@words,@unlinkfiles);

our ($Assembly,$Window,$Target_File_Out);

our ($Program_Folder_Path,$Target_File_Path,$Target_Name,$Source_Data);

our ($Path_2_Wig,$Path_2_fasta);

our ($verbose,$help,$man);

our $Target_Filt_Path;

######################################################################
#
#	Defining options
#
######################################################################

GetOptions('verbose|v'=>\$verbose,'help|h'=>\$help,'man|m'=>\$man,) or pod2usage ();

$help and pod2usage (-verbose=>1, -exitval=>1, -output=>\*STDOUT);
$man and pod2usage (-verbose=>2, -exitval=>1, -output=>\*STDOUT);
@ARGV or pod2usage (-verbose=>0, -exitval=>1, -output=>\*STDOUT);
@ARGV == 5 or pod2usage ("Syntax error");
	
######################################################################
#
#	Defining system variables
#
######################################################################

my ($myscriptname,$myscript,$workingfolder,$L1,$L2);

$myscript = abs_path($0);
$Program_Folder_Path= dirname $myscript;

print "Program folder is: $Program_Folder_Path\n";

$Source_Data=$ARGV[0];
$Target_File_Path=$ARGV[1];
$Target_Name=$ARGV[2];
$Window=$ARGV[3];
$Assembly=$ARGV[4];

$Target_Filt_Path="$Program_Folder_Path/data/targets/$Assembly/$Target_Name";




######################################################################
#
#	Removing empty lines from source file
#	and creating support temporary files
#
######################################################################

my $range=99999;
my $ID=int(rand($range));
my $filename="source.$ID";

if(-e $filename){ 
	$ID=$ID+100000;
}

system qq(awk NF $Source_Data > source.$ID);

######################################################################
#
#	Reading source file
#
######################################################################

open(CHECKBOOK,"source.$ID") || die "Couldn't open the source file!";

while($record=<CHECKBOOK>){
	chomp($record);
	@words=split(' ',$record);
	
	$Path_2_Wig=$words[0];
	$Path_2_fasta=$words[1];
			
######################################################################
#
#	Checking target file format
#
######################################################################

print "Checking target file format...\n";
system qq(rm -f ErrorTarget.out);
system qq(head -1 $Target_File_Path | awk '{if (\$3<\$2) print "Exon #1 end value is smaller than start value. Please check target file format. Exons start (end) must be in column 2 (3)." > "ErrorTarget.out"; else print "Target file seems properly formatted."}');

if(-e "ErrorTarget.out"){
	print "Exiting: target seems to be uncorrectly formatted. Please check ErrorTarget.out!\n";
	exit;
}

######################################################################
#
#	Target initialization
#
######################################################################

print "Filtering target from $Target_File_Path...\n";
system qq(R --slave --args $Target_File_Path,$Program_Folder_Path,$Target_Name,$Assembly,$Window < $Program_Folder_Path/lib/R/FilterTarget.R);


$Target_File_Out="$Program_Folder_Path/data/targets/$Assembly/$Target_Name/Filtered.txt";
print "Calculating Mappability and GC content...\n";
system qq($Program_Folder_Path/lib/bash/./TargetCreate.sh $Path_2_Wig $Target_File_Out $Program_Folder_Path $Assembly $Target_Name $Path_2_fasta);
print "...done!\n";

}


close(CHECKBOOK);
@unlinkfiles=("source.$ID");
unlink @unlinkfiles;

######################################################################
#
#	Documentation
#
######################################################################

=head1 SYNOPSIS 

 perl TargetPerla.pl [arguments] [options]

 Options:

       -h, --help                   Print help message.
       -m, --man                    Print complete documentation.
       -v, --verbose                Use verbose output.

 Function:
 
TargetPerla.pl initialises target files for further data processing with the EXCAVATOR2 package. It requires 5 arguments (one source files - with space-delimited paths to source data for mappability and GC-content calculations), path to target file, target name, window size and assembly to run properly. A sub-folder with the specified target name will be created under "EXCAVATOR2/data/targets/hgXX". Target input file (.bed, .txt or any plain text file) must be tab-delimited. 

 Example: 
 
 EXCAVATOR2> perl TargetPerla.pl SourceTarget.txt /Users/.../MyTarget.bed TargetName 50000  hg19
 
=head1 OPTIONS

=over 8

=item B<--help>

Print a brief usage message and detailed explanation of options.

=item B<--man>

Print the complete manual of the script.

=item B<--verbose>

Use verbose output.


=back

=head1 DESCRIPTION

TargetPerla.pl is a Perl script which is part of the EXCAVATOR2 package. It includes all of the first step operations of the EXCAVATOR2 package. It filters a target file and calculates, for a specific assembly, GC content and mappability.

It requires, as arguments, the path to a source file (the default source file is "SourceTarget.txt" which is placed in the main EXCAVATOR2 folder) containing the paths to source data (for the calculations of mappability and GC-content), the path to the target input file, a "target name", the window size and the assembly. Target input file (.bed, .txt or any plain text file) must be tab-delimited. Setting the target name as "MyTarget", all data calculated will be saved in the "MyTarget" folder in (if you are using the hg19 assembly) EXCAVATOR2/data/targets/hg19/MyTarget.

The allowed assemblies are hg19 and hg38.

EXCAVATOR2 is freely available to the community for non-commercial use. For questions or comments, please contact "romina.daurizio@gmail.com".

=cut