Get_Make_bed_File.pl

#! /usr/bin/perl
use strict;
use warnings;

#First drafted up on July 8, 2019, last updated on July 16, 2019 by Dr. Jeff Chen
#Description: to get all 23andme SNP genotype files with all the successful conversion to prdocuce
# *.bed, *.bim, and *.fam files


    my $dir = '/m/CPHG/KING/xc3m/23andme_Run/'; # Where the binary files located, this is the data source directory
   
    opendir(DIR, $dir) or die $!;

    while (my $file = readdir(DIR)) {

	if ($file=~m/txt$/){     # Get the file name
       
       		my $bed=$dir.$file.".bed";  ## Make the *.bed file name with absolute directory path
       		my $bim =$dir.$file.".bim"; ## Make the *.bim file name with the absolute dirctory path
       		my $fam=$dir.$file.".fam";  ## Make the *.fam file name with the absolute directory path

       		# print "$file\n";          # Check the codes, the file and path to be correct

		if (-e $bed && -e $bim && -e $fam){ ## Only pick up data with all three files of *.bed, *.bim, and *.fam

		# Code checking with correctness

       			print "$file\n";
        		print "$bed\n";
        		print "$bim\n";

        		print "$fam\n";
	
		# Move selected files to new location for processing

		system ("mv $bed /m/CPHG/KING/xc3m/Good_Make_Bed_File/");
		system ("mv $bim /m/CPHG/KING/xc3m/Good_Make_Bed_File/");
		system ("mv $fam /m/CPHG/KING/xc3m/Good_Make_Bed_File/");

	}


}       

       	#my $stop = <STDIN>;  # Code checking ........

 	}

    closedir(DIR);

   print "\n******  Completed to Check make-bed file intergratity   *****\n";

   exit(0);