Second You would probably better off storing your metadata keys in an array rather than a hash, because an array preserves the order of the data (and not a hash).

Third, a regex might be simpler than a split if you just want to remove the trailing comma:

while (my $line = <I1>) {
    chomp $line;
    if ($line =~ /##INFO=<ID=/) { 
        $line =~ s/,$//;
        # ...
}
[download]

Fifth, reading the file twice does not seem to be a very good idea. Can't you decide, based on the content, that you have finished reading the metadata and started to read the data?

Thank you very much for your answer :)

You are right about the csv format, I was thinking in a excel.

I thing that storing my metadata keys in an array rather than a hash it would be better, the problem is that I don't know how to asociate the metadata in the array with the values without doing it with a hash.

Your third and fifth points look like very interesting, but I am "noob" and i don't know how to do it :(

Hi,

in your inner loop you have to replace the last line

my ($string, $int) = (split(/\;/, $dat));
[download]

by the following

my @elements = split /;/, $data;
my %rowvalues;
foreach my $element (@elements) {
    my ($key, $value) = split /=/, $element;
    $rowvalues{$key} = $value;
}
foreach my $key (keys %info) {
   if(exists $rowvalue{$key}) {
       push @{$info{$key}}, $rowvalue{$key};
   }
   else {
       push @{$info{$key}}, 'NA';
   }
}
[download]

I hope that is it. I haven't tested. Please put code tags around your sample data so we can see the structure better.

Regards
McA

Thank you very much for your answer :)

I was trying something similar, but the problem is that at the end I obtain a hash of hashes, I don't know why. And it's imposible working with them.

Hi

I was wondering about your answer and therefore made this selfcontained snippet which should show the relevant elements.

#!/bin/env perl
use strict;
use warnings;
use 5.010;

my %info;
while (my $line = <DATA>) {
    chomp $line;
    if ($line =~ /##INFO=<ID=/) {
        my ($first, $second) = split /,/, $line;
        my ($firstsecond, $secondsecond) = split /ID=/, $first;
        $info{$secondsecond}=();
    }
    elsif ($line !~ /#/) {
        my ($numbers, $data) = split /\s+/, $line;
        foreach my $dat ($data){
            my @elements = split /;/, $data;
            my %rowvalues;
            foreach my $element (@elements) {
                my ($key, $value) = split /=/, $element;
                $rowvalues{$key} = $value;
            }
            foreach my $key (keys %info) {
               if(exists $rowvalues{$key}) {
                   push @{$info{$key}}, $rowvalues{$key};
               }
               else {
                   push @{$info{$key}}, 'NA';
               }
            }
        }
    }
    else {
        next;
    }
}
foreach my $header (sort keys %info) {
    say $header, ' => ', join(',', @{$info{$header}});
}

__DATA__
# First the headers
##INFO=<ID=AA,
##INFO=<ID=AB,
##INFO=<ID=AC,
# then the data
1   AA=1;AB=2;AC=3
2   AA=2;AB=2
3   AA=5;AB=1;AC=1
[download]

I hope this will clarify what was said before. I change one split from '\t' to '\s+' because of pasting this code herein would probably destroy tghe tab character.

Regards
McA

#!perl
use strict;
use Text::CSV;

my %info=();
my $line_count=0;
while (my $line = <DATA>){
  chomp($line);
  if ($line =~ /##INFO=<ID=([^,]+)/){
    $info{$1}=[];
  } else {
    my (undef,%hash) = split /[\t;=]/,$line;
    
    for (keys %info){
      push @{$info{$_}},$hash{$_} || 'NA';
    }
    ++$line_count;
  }
}

my $csv = Text::CSV->new ( {binary=>1, eol=>"\012"} )  
   or die "Cannot use CSV: ".Text::CSV->error_diag();
open my $fh,'>','output.csv' 
   or die "Could not open output.csv $!";

my @col_head = sort keys %info;
$csv->print($fh, \@col_head);
for my $i (1..$line_count){
  my @row = map { $info{$_}[$i-1] } @col_head;
  $csv->print($fh, \@row);
}

__DATA__
##INFO=<ID=AA,
##INFO=<ID=AB,
##INFO=<ID=AC,
1    AA=1;AB=2;AC=3
2    AA=2;AB=2
3    AA=5;AB=1;AC=1
[download]

Thank you very much for your answer :)

Your answer seems quite interesting but I don't know why but I obtain too many "NA".

With de first part of the script I obtain for example

AA=> NA, NA,1,2,5,NA,NA,NA,NA,NA

instead of

AA=> 1,2,5

Perhaps is related with

my (undef,%hash) = split /[\t;=]/,$line;

because you are spliting 3 times, I don't know.

The final csv is

AA => NA,NA,NA

AB => NA,NA,NA

AC => NA,NA,NA

Perhaps is because the problem with de "NA".

Do you have other lines in the file apart from those like
##INFO=<ID=AA, and 1 AA=1;AB=2;AC=3 ? Blank lines for example.

poj