94    THI11    YDL244W    THI11    YFL058W    THI11    YJR156C    THI1
+1    YNL332W
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Ouput data:

102      94    1    THI11    YDL244W    
103      94      2    THI11    YFL058W    
104      94      3    THI11    YJR156C    
105      94      4    THI11    YNL332W
[download]

something like this:


#!perl

use strict;
use warnings;

# open a file for reading in the current directory

open(FILEHANDLE,"< input_file.txt") or die $!;
open(OUTFILE,"+> outfile_file.txt") or die $!;

my $record_count = 0;

while (<FILEHANDLE>){

    my @data = split /\s+/;
    my $first = shift @data;
    $record_count++;
    for (my $i = 0; $i < @data; $i+=2) {
        print OUTFILE "$record_count\t$first\t", $i/2+1, "\t$data[$i] 
+",  $data[$i+1], "\n";
    }
}
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May be I've missed some details, but the way is correct
As for me, I prefer -n flag in such cases:

#!perl -lwn

my @data = split /\s+/;
my $first = shift @data;

for (my $i = 0; $i < @data; $i+=2) {
    print join "\t", $., $first, $i/2+1, $data[$i], $data[$i+1];
}
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usage:

this_script.pl input_file.txt >> output_file.txt

Here is the golf version of your program

#!perl -lawn

$f = shift @F;
$i = 1;
print join "\t", $., $f, $i++, shift @F, shift @F while @F;
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see perldoc perlrun, perldoc perlvar for details