in reply to Adding missing values into a hash

Try 
#!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]
poj

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Re^2: Adding missing values into a hash
by Biopolete (Initiate) on Jun 19, 2014 at 14:32 UTC

    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".

[reply]
[d/l]

      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
[reply]
[d/l]
[select]

        No, I don't have any other lines in the file :(

        I have the same problem if I use your complete script with:

        __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

        I only obtain "NA" values in CVS file

[reply]

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