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1    SP_85(IS33, qqq), SP_155(IS33eee)    spr_111(ISyyy33, qqq), spr_1
+71(IS33eee)
2    SP_83(S3 , jgjg), SP_32(IS33, jhdjdjd)    spr_113(Stty3 , jgjg), 
+spr_1881(IS33, jhdjdjd)
3    SP_78(3jmdsjkdej), SP_66(IShbdhdhd33)    spr_115(3jmhhggggdsjkdej
+), spr_1551(IShbdhdjjjhd33), spr_88881(Iyt33ff), spr_145411(Iddd3ff)
4    SP_77(3jmdsjkdej), SP_1485(Idhd33ff)    spr_116(3jmdhhhhhsjkdej),
+ spr_17781(Idhdhhtytyt33ff)

1    SP_85(IS33, qqq)    spr_111(ISyyy33, qqq)
1    SP_155(IS33eee)    spr_171(IS33eee)
2    SP_83(S3 , jgjg)    spr_113(Stty3 , jgjg)
...
3     -     spr_145411(Iddd3ff)
4    SP_77(3jmdsjkdej)    spr_116(3jmdhhhhhsjkdej)
4    SP_1485(Idhd33ff)    spr_17781(Idhdhhtytyt33ff)

my $columnFile = q{re-organized.txt};
open my $columnFH, q{<}, $columnFile
   or die qq{open: < $columnFile: $!\n};
...
close $columnFH
   or die qq{close: < $columnFile: $!\n};