Hi

I' m trying to convert a column to a csv file.

My data looks like:

##INFO=<ID=AA,

##INFO=<ID=AB,

##INFO=<ID=AC,

Num Data

1 AA=1;AB=2;AC=3

2 AA=2;AB=2

3 AA=5;AB=1;AC=1

And I want a csv like this:

AC AB AC

1 2 3

2 2 NA

5 1 1

First of all I do a hash obtaining the keys from the metadata (##)

open(I1,$ARGV[0]); 
my %info;
while (my $line = <I1>) {
    if ($line =~ /##INFO=<ID=/) {    
    my ($first,$second) = (split(/\,/, $line));
    my ($firstsecond,$secondsecond) = (split(/ID=/, $first));
    $info{$secondsecond}=();
    }
}

[download]

Now I have my hash “info” with my keys (AA, AB, AC)

Then I want to introduce the values.

I start with:

while (my $line = <I1>) {
    if ($line !~ /#/) {    
    my ($numbers,$data) = (split(/\t/, $line));    
    foreach my $dat ($data){
    my ($string, $int) = (split(/\;/, $dat));

[download]

That is because I want to eliminate “\t” and “;”

But I don't know how to introduce the missing values (NA)

I want something like this:

AA => 1,2,5

AB => 2,2,1

AC => 3,NA,1

Anyone knows how to introduce the “NA” string in its correct position?? (my real file is much bigger with a lot of “NA”)

Thank you very much.

In reply to Adding missing values into a hash by Biopolete

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