I can't even get this to run. I get the following run-time error:

Argument "╛¡¡╛ª╫╧ç╬₧M-^]╩&#9
+556;Ö╟╓" isn't numeric in numeric ne (!=) at checkme.pl l
+i
ne 29, <INPUT> line 2.
[download]

So I rewrote it a bit:

#!/usr/bin/perl -w
use strict;

my $ex_line = q(perl -ne "if (/(\d{6})_/g){ chomp;print qq($1,),(split
+/;/,$_)[-1],qq(\n)};" input.dat);
my $stuff = `$ex_line`;
 my %hash;
for (split /\n/, $stuff) {
  my @arr = split/,/,$_;
  push @{$hash{$arr[0]}} , $arr[1];
}

foreach (keys %hash) {
 print "$_\t" . join / /, @{$hash{$_}} , qq(\n);
}

1;
[download]

With the following data:

>probe:ATH1-121501:244901_at:594:703;Interrogation_Position=56;Antisen
+se;TTGCTGCTATTCTATCTATTTGTGC
    Times 11
    >probe:ATH1121501:244902_at:522:511;Interrogation_Position=153;Ant
+isense;GGTATTTTCCGTTTCTTCGGATGAT
    Times 11
    >probe:ATH1121501:244902_at:522:511;Interrogation_Position=153;Ant
+isense;GGTATTTTCCGTTTCTTCGGATGAT
    Times 11
    >probe:ATH1121501:244902_at:522:511;Interrogation_Position=153;Ant
+isense;GGTATTTrCCGTTTCTTCGGATGAT
    Times 11
    >probe:ATH1121501:244902_at:522:511;Interrogation_Position=153;Ant
+isense;GGTATTfTCCGTTTCTTCGGATGAT
    Times 11
    >probe:ATH1121501:244902_at:522:511;Interrogation_Position=153;Ant
+isense;GGTATTTnCCGTTTCTTCGGATGAT
    Times 11
    >probe:ATH1121501:244902_at:522:511;Interrogation_Position=153;Ant
+isense;GGTATTTTCCGuTTCTTCGGATGAT
    Times 11
    >probe:ATH1121501:244902_at:522:511;Interrogation_Position=153;Ant
+isense;GGTATTTTiCGTTTCTTCGGATGAT
    Times 11
[download]

And I get:

244901  TTGCTGCTATTCTATCTATTTGTGC
244902  GGTATTTTCCGTTTCTTCGGATGATGGTATTTTCCGTTTCTTCGGATGATGGTATTTrCCGT
+TTCTTCGGAT
GATGGTATTfTCCGTTTCTTCGGATGATGGTATTTnCCGTTTCTTCGGATGATGGTATTTTCCGuTTCTT
+CGGATGATGG
TATTTTiCGTTTCTTCGGATGAT
[download]

I also get a nasty little warning about my ``. Something is not escaped :( You should probably rewrite that inside of the body of the code anyway.

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