Shell Programming and Scripting

open INDEX,"49_unique_positions.txt" or die $!;
open WRITE,">hap.txt" or die $!;
@index = <INDEX>;
#print "$index[0]";
#while (<INDEX>)
#{

#}
@files = @ARGV;
foreach (@files){
print "file: $_ \t $index[0]\n";
$file = $_;
open F,$file or die $!;
while ($line=<F>){
chomp ($line);
@array = split(/\t/,$line);
print "$array[1] \n";
}
}

#! /bin/perl
open(IDX,"<Index") || die "Couldn't open index file";
@index=<IDX>;
close IDX;
$header{POSITION}="Position";
for($i=0;$i<$#ARGV+1;$i++)
{
$FH="F${i}";
open($FH,"< $ARGV[${i}]") || die "couldn't open $ARGV[${i}]";
$header{POSITION}="$header{POSITION} $ARGV[${i}]";
while(<$FH>){
chomp($_);
@array=split(/  */);
foreach $index (@index){
if($index==$array[1]){
chomp($index);
$hash{$index}="$hash{$index} $array[3] $array[5]";
}
}
}
close $FH;
}
print $header{POSITION}."\n";
foreach $item (keys %hash){
print "$item $hash{$item}"."\n";
}

perl anyname.pl file1 file2

Position 49_GB713_filtered.vcf 49_PO5X.4300_filtered.vcf
304  4 5 5 12
259  3 6 7 10
241  4 5 7 10
323  3 5 4 12
107  3 6 8 8
275  3 5 6 11
343  13 5
247  4 5 7 10
222  6 7

#!/bin/ksh
awk '
BEGIN { hdr2 = "Index" }
NF==1 { # WIth only one field, we have to be processing the index file.
        if(FNR == 1)
                # Print the headers since this is the first line.
                printf("%s\n%s\n", hdr1, hdr2)
        # Print the index entry.
        printf("%s", $1)
        # Print the reference and alternative values from each file.
        for(i = 1; i <= fc; i++)
                if(ref[i,$1] == "") printf("\t\t")
                else printf("\t%4d\t%4d", ref[i,$1], alt[i,$1])
        # Add the trailing <newline>.
        printf("\n")
        next
}
FNR==1 {# Print the file key entry for another file and update the header lines.
        printf("File%03d is %s\n", ++fc, FILENAME)
        hdr1 = sprintf("%s\t --File%03d--", hdr1, fc)
        hdr2 = sprintf("%s\t Ref\t Alt", hdr2)
}
{       # Store away the reference and alternate entries for this file.
        ref[fc,$2] = $4
        alt[fc,$2] = $6
}' *.vcf index