here is what I have and as I said it didn't work with the data format I am working with:
#!/usr/bin/perl
use strict;
use integer;
my $input = shift @ARGV || 'Data.txt';
my $output = shift @ARGV || 'Output.txt';
print $input, "\n";
open(DATA,"$input") || die "cannot open $input for reading";
open(OUT, ">$output") || die "cannot open $output for writing"
+;
my @newcols=();
my ($genome, $id, $abd);
my %phage=();
my @pg=();
my @id=();
while (my $line=<DATA>){
chomp $line;
#$line =~ s/"//g;
if($line =~ m/#/){
$genome = $line;
push(@pg, $genome);}
elsif($line !=~ m/#/){ my @cols = split(/\t/, $line);
$id = $cols[0];
$abd = $cols[1];
push(@id, $id);
$phage{$id}{$genome}=$abd;}
#print OUT "$genome $id, $abd\n";
}
my %hash = map { $_ => 1 } @id;
my @unique = keys %hash;
my @sorted_id = sort { ( $a <=> $b) } @unique;
print OUT "\t";
for my $phagegenome(@pg){
print OUT $phagegenome, "\t";
}
print OUT "\n";
for my $sorted_id(@sorted_id){
print OUT $sorted_id, "\t";
for my $pg(@pg){
print OUT "$phage{$sorted_id}{$pg}\t";
}
print OUT "\n";
}
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