#! perl -w scipt

use strict;
use warnings;



# open a file for reading in the current directory

open(FILEHANDLE,"< input_file.txt");
open(OUTFILE,"+> outfile_file.txt");

my $record_count = 0;

while (<FILEHANDLE>){
  
  if ($_ =~ 
    /^(\d{1,5})\s+
     (?:([A-Z0-9()-]{2,15})\s+([A-Z0-9()-]{7})){1}
     (?:([A-Z0-9()-]{2,15})\s+([A-Z0-9()-]{7})){0,1}
     (?:([A-Z0-9()-]{2,15})\s+([A-Z0-9()-]{7})){0,1}
     (?:([A-Z0-9()-]{2,15})\s+([A-Z0-9()-]{7})){0,1}
     (?:([A-Z0-9()-]{2,15})\s+([A-Z0-9()-]{7})){0,1}
     (?:([A-Z0-9()-]{2,15})\s+([A-Z0-9()-]{7})){0,1}
     (?:([A-Z0-9()-]{2,15})\s+([A-Z0-9()-]{7})){0,1}
     (?:([A-Z0-9()-]{2,15})\s+([A-Z0-9()-]{7})){0,1}
     (?:([A-Z0-9()-]{2,15})\s+([A-Z0-9()-]{7})){0,1}
     (?:([A-Z0-9()-]{2,15})\s+([A-Z0-9()-]{7})){0,1}
     (?:([A-Z0-9()-]{2,15})\s+([A-Z0-9()-]{7})){0,1}
     (?:([A-Z0-9()-]{2,15})\s+([A-Z0-9()-]{7})){0,1}
     (?:([A-Z0-9()-]{2,15})\s+([A-Z0-9()-]{7})){0,1}
     (?:([A-Z0-9()-]{2,15})\s+([A-Z0-9()-]{7})){0,1}
     (?:([A-Z0-9()-]{2,15})\s+([A-Z0-9()-]{7})){0,1}
     (?:([A-Z0-9()-]{2,15})\s+([A-Z0-9()-]{7})){0,1}
     (?:([A-Z0-9()-]{2,15})\s+([A-Z0-9()-]{7})){0,1}
     (?:([A-Z0-9()-]{2,15})\s+([A-Z0-9()-]{7})){0,1}
     (?:([A-Z0-9()-]{2,15})\s+([A-Z0-9()-]{7})){0,1}
     (?:([A-Z0-9()-]{2,15})\s+([A-Z0-9()-]{7})){0,1}
     (?:([A-Z0-9()-]{2,15})\s+([A-Z0-9()-]{7})){0,1}
     (?:([A-Z0-9()-]{2,15})\s+([A-Z0-9()-]{7})){0,1}
     (?:([A-Z0-9()-]{2,15})\s+([A-Z0-9()-]{7})){0,1}
     (?:([A-Z0-9()-]{2,15})\s+([A-Z0-9()-]{7})){0,1}
     (?:([A-Z0-9()-]{2,15})\s+([A-Z0-9()-]{7})){0,1}
     (?:([A-Z0-9()-]{2,15})\s+([A-Z0-9()-]{7})){0,1}
     (?:([A-Z0-9()-]{2,15})\s+([A-Z0-9()-]{7})){0,1}
     (?:([A-Z0-9()-]{2,15})\s+([A-Z0-9()-]{7})){0,1}
     (?:([A-Z0-9()-]{2,15})\s+([A-Z0-9()-]{7})){0,1}
     (?:([A-Z0-9()-]{2,15})\s+([A-Z0-9()-]{7})){0,1}
     (?:([A-Z0-9()-]{2,15})\s+([A-Z0-9()-]{7})){0,1}
     (?:([A-Z0-9()-]{2,15})\s+([A-Z0-9()-]{7})){0,1}
     (?:([A-Z0-9()-]{2,15})\s+([A-Z0-9()-]{7})){0,1}
     (?:([A-Z0-9()-]{2,15})\s+([A-Z0-9()-]{7})){0,1}
     (?:([A-Z0-9()-]{2,15})\s+([A-Z0-9()-]{7})){0,1}
     (?:([A-Z0-9()-]{2,15})\s+([A-Z0-9()-]{7})){0,1}
     (?:([A-Z0-9()-]{2,15})\s+([A-Z0-9()-]{7})){0,1}
     (?:([A-Z0-9()-]{2,15})\s+([A-Z0-9()-]{7})){0,1}
     (?:([A-Z0-9()-]{2,15})\s+([A-Z0-9()-]{7})){0,1}
     (?:([A-Z0-9()-]{2,15})\s+([A-Z0-9()-]{7})){0,1}
     (?:([A-Z0-9()-]{2,15})\s+([A-Z0-9()-]{7})){0,1}
     (?:([A-Z0-9()-]{2,15})\s+([A-Z0-9()-]{7})){0,1}
     (?:([A-Z0-9()-]{2,15})\s+([A-Z0-9()-]{7})){0,1}
     (?:([A-Z0-9()-]{2,15})\s+([A-Z0-9()-]{7})){0,1}
     (?:([A-Z0-9()-]{2,15})\s+([A-Z0-9()-]{7})){0,1}
     (?:([A-Z0-9()-]{2,15})\s+([A-Z0-9()-]{7})){0,1}
     (?:([A-Z0-9()-]{2,15})\s+([A-Z0-9()-]{7})){0,1}
     $/gx){

      $record_count++;
      
      my $1st = $1;
      my $2st = $2;
      my $3st = $3;
      my $4st = $4;
      my $5st = $5;
      my $6st = $6;
      my $7st = $7;
      my $8st = $8;
      my $9st = $9;
      my $10st = $10;
      my $11st = $11;
      my $12st = $12;
      my $13st = $13;
      my $14st = $14;
      my $15st = $15;
      my $16st = $16;
      my $17st = $17;
      my $18st = $18;
      my $19st = $19;
      my $20st = $20;
      my $21st = $21;
      my $22st = $22;
      my $23st = $23;
      my $24st = $24;
      my $25st = $25;
      my $26st = $26;
      my $27st = $27;
      my $28st = $28;
      my $29st = $29;
      my $30st = $30;
      my $31st = $31;
      my $32st = $32;
      my $33st = $33;
      my $34st = $34;
      my $35st = $35;
      my $36st = $36;
      my $37st = $37;
      my $38st = $38;
      my $39st = $39;
      my $40st = $40;
      my $41st = $41;
      my $42st = $42;
      my $43st = $43;
      my $44st = $44;
      my $45st = $45;
      my $46st = $46;
      my $47st = $47;
      my $48st = $48;
      my $49st = $49;
      my $50st = $50;
      my $51st = $51;
      
      my @array_of_gene_records = ($2st, $3st, $4st, $5st, $6st, $7st,
+ $8st, $9st, $10st, $11st, $12st, $13st, $14st, $15st, $15, $16st, $1
+7st, $18st, $19st, $20st, $21st, $22st, $23st, $24st, $25st, $26st, $
+27st, $28st, $29st, $30st, $31st , $32st , $33st, $34st, $35st, $36st
+, $37st, $38st, $39st, $40st, $41st, $42st, $43st, $44st, $45st, $46s
+t, $47st, $48st, $49st, $50st, $51st);
      
      my $subrecord_id = 1;
      foreach (@array_of_gene_records){
    
    print OUTFILE "$record_count\t$1st\t$subrecord_id\t$_\n";
    $subrecord_id++;
    
      }
    }
}
[download]

Bareword found where operator expected at sc.pl line 70, near "$1st"
        (Missing operator before st?)
Bareword found where operator expected at sc.pl line 71, near "$2st"
        (Missing operator before st?)
Bareword found where operator expected at sc.pl line 72, near "$3st"
        (Missing operator before st?)
Bareword found where operator expected at sc.pl line 73, near "$4st"
        (Missing operator before st?)
Bareword found where operator expected at sc.pl line 74, near "$5st"
        (Missing operator before st?)
Can't use global $1 in "my" at sc.pl line 70, near "my $1"
syntax error at sc.pl line 70, near "$1st  "
Can't use global $2 in "my" at sc.pl line 71, near "my $2"
syntax error at sc.pl line 71, near "$2st "
Can't use global $3 in "my" at sc.pl line 72, near "my $3"
syntax error at sc.pl line 72, near "$3st "
Can't use global $4 in "my" at sc.pl line 73, near "my $4"
syntax error at sc.pl line 73, near "$4st "
Can't use global $5 in "my" at sc.pl line 74, near "my $5"
syntax error at sc.pl line 74, near "$5st "
sc.pl has too many errors.
[download]