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Merge_bed_File.pl
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Merge_bed_File.pl
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#! /usr/bin/perl
use strict;
use warnings;
#First draft on July 8, 2019, last updated on July 10, 2019 by Dr. Jeff Chen
#Description: This script mege the openSNP datasets of *.bed, *.bim, *.fam files processed produced by plink.
my $dir = '/m/CPHG/KING/xc3m/Good_Make_Bed_File/'; ## Get indiviual *.bed file.
my $First_File="23andme01"; ## As first seed file for data merge.
my $File_Name="23andme";
my $bed="bed";
my $bim="bim";
my $fam="fam";
my $i=1;
my $j=$i;
my $k=$i;
my $merge01="merge";
my $merge02="merge";
my $merge03="merge";
my $master_file="Master";
my $missnp="merge-merge.missnp";
my $missnp02="2ndmissnp_file";
my $run="comand";
opendir(DIR, $dir) or die $!;
while (my $file = readdir(DIR)) {
if ($file=~m/bed$/){
$File_Name=$file;
$File_Name=~s/bed$//; ## Get the filename for reformating to get absolutely directory of *.bed, *.bim, and *.fam files.
#print "****** $File_Name\n";
my $bed=$dir.$File_Name."bed";
my $bim =$dir.$File_Name."bim";
my $fam=$dir.$File_Name."fam";
#print "**** $bed\n";
$merge01="merge".$j;
if($i==1){
print "\n******* working on $i ******\n";
$run="/home/xc3m/openSNP/plink -bfile $First_File -bmerge $bed $bim $fam -make-bed -out $merge01";
print "******=====>$run\n\n-------------------------------------------------------------------\n\n";
system ("$run"); #Run first two files merging.
}else{
print "\n******* Working on $i of $bed **********\n\n";
$master_file=$merge01.".bed"; #Merged BIG master *.bed data file.
#print "****master file ===> $merge01******\n";
if(-e $master_file){
$run="/home/xc3m/openSNP/plink -bfile $merge01 -bmerge $bed $bim $fam -make-bed -out $merge02";
print "******=====>$run\n---------------------------------------------------------------------\n\n";
system ("$run"); #Run the rest file merging.
}
#### Checking whether plink run successfully, this check is data dependent, eventually could put a while or for loop
#### to replace the below copy-and-paste block.
$missnp=$merge01."-merge.missnp"; # For merge-merge.missnp file checking, this was unsuccessful plink run.
#print "\n?????Founding $missnp?????\n";
if(-e $missnp){
print "\n*******Founding $missnp *******\n";
print "\n****master file ===> $merge03******\n";
### Handling missnp bad files #######
$missnp02=$merge03."-merge.missnp";
# Multiple random *.missnp files may be produced, need to figure out total how many sequential failed runs in the dataset.
if(-e $missnp02){ # 1 bad file
$k=$k-1; $merge03="merge".$k; $missnp02=$merge03."-merge.missnp";}
if(-e $missnp02){ # 2 bad file
$k=$k-1; $merge03="merge".$k; $missnp02=$merge03."-merge.missnp";}
if(-e $missnp02){ # 3 bad file
$k=$k-1; $merge03="merge".$k; $missnp02=$merge03."-merge.missnp";}
if(-e $missnp02){ # 4 bad file
$k=$k-1; $merge03="merge".$k; $missnp02=$merge03."-merge.missnp";}
if(-e $missnp02){ # 5 bad file
$k=$k-1; $merge03="merge".$k; $missnp02=$merge03."-merge.missnp";}
if(-e $missnp02){ # 6 bad file
$k=$k-1; $merge03="merge".$k; $missnp02=$merge03."-merge.missnp";}
if(-e $missnp02){ # 7 bad file
$k=$k-1; $merge03="merge".$k; $missnp02=$merge03."-merge.missnp";}
if(-e $missnp02){ # 8 bad file
$k=$k-1; $merge03="merge".$k; $missnp02=$merge03."-merge.missnp";}
if(-e $missnp02){ # 9 bad file
$k=$k-1; $merge03="merge".$k; $missnp02=$merge03."-merge.missnp";}
if(-e $missnp02){ # 10 bad file
$k=$k-1; $merge03="merge".$k; $missnp02=$merge03."-merge.missnp";}
if(-e $missnp02){ # 11 bad file
$k=$k-1; $merge03="merge".$k; $missnp02=$merge03."-merge.missnp";}
if(-e $missnp02){ # 12 bad file
$k=$k-1; $merge03="merge".$k; $missnp02=$merge03."-merge.missnp";}
if(-e $missnp02){ # 13 bad file
$k=$k-1; $merge03="merge".$k; $missnp02=$merge03."-merge.missnp";}
if(-e $missnp02){ # 14 bad file
$k=$k-1; $merge03="merge".$k; $missnp02=$merge03."-merge.missnp";}
if(-e $missnp02){ # 15 bad file
$k=$k-1; $merge03="merge".$k; $missnp02=$merge03."-merge.missnp";}
if(-e $missnp02){ # 16 bad file
$k=$k-1; $merge03="merge".$k; $missnp02=$merge03."-merge.missnp";}
if(-e $missnp02){ # 17 bad file
$k=$k-1; $merge03="merge".$k; $missnp02=$merge03."-merge.missnp";}
if(-e $missnp02){ # 18 bad file
$k=$k-1; $merge03="merge".$k; $missnp02=$merge03."-merge.missnp";}
if(-e $missnp02){ # 19 bad file
$k=$k-1; $merge03="merge".$k; $missnp02=$merge03."-merge.missnp";}
if(-e $missnp02){ # 19 bad file
$k=$k-1; $merge03="merge".$k; $missnp02=$merge03."-merge.missnp";}
if(-e $missnp02){ # 20 bad file
$k=$k-1; $merge03="merge".$k; $missnp02=$merge03."-merge.missnp";}
if(-e $missnp02){ # 21 bad file
$k=$k-1; $merge03="merge".$k; $missnp02=$merge03."-merge.missnp";}
if(-e $missnp02){ # 22 bad file
$k=$k-1; $merge03="merge".$k; $missnp02=$merge03."-merge.missnp";}
if(-e $missnp02){ # 23 bad file
$k=$k-1; $merge03="merge".$k; $missnp02=$merge03."-merge.missnp";}
if(-e $missnp02){ # 24 bad file
$k=$k-1; $merge03="merge".$k; $missnp02=$merge03."-merge.missnp";}
if(-e $missnp02){ # 25 bad file
$k=$k-1; $merge03="merge".$k; $missnp02=$merge03."-merge.missnp";}
if(-e $missnp02){ # 26 bad file
$k=$k-1; $merge03="merge".$k; $missnp02=$merge03."-merge.missnp";}
if(-e $missnp02){ # 27 bad file
$k=$k-1; $merge03="merge".$k; $missnp02=$merge03."-merge.missnp";}
if(-e $missnp02){ # 28 bad file
$k=$k-1; $merge03="merge".$k; $missnp02=$merge03."-merge.missnp";}
if(-e $missnp02){ # 29 bad file
$k=$k-1; $merge03="merge".$k; $missnp02=$merge03."-merge.missnp";}
if(-e $missnp02){ # 30 bad file
$k=$k-1; $merge03="merge".$k; $missnp02=$merge03."-merge.missnp";}
## Pick the latest sucessuful run, and merge the new files into it.
print "******** merge02 ====> $merge02 ********\n";
print "******** merge03 ====> $merge03 ********\n";
$run="/home/xc3m/openSNP/plink -bfile $merge03 -bmerge $bed $bim $fam -make-bed -out $merge02";
print "******=====>$run\n";
system ("$run");
#sleep(5);
}
}
$i++; $j=$i-1;$k=$i-2;
$merge02="merge".$i; $merge03="merge".$k;
# Move the successful run files to Done directory
system ("mv $bed /m/CPHG/KING/xc3m/Done_Merge/");
system ("mv $bim /m/CPHG/KING/xc3m/Done_Merge/");
system ("mv $fam /m/CPHG/KING/xc3m/Done_Merge/");
} # end of if
my $stop = <STDIN>;
} # end of while
closedir(DIR);
print "\n**** A total of $i files merged *****\n";
print "\n****** Completed to make the BIG make-bed file *****\n";
exit(0);