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#!/usr/bin/perl -w                 
...
close (REP);
close (OUT);

SEQ:
...
REP:
1    116.68    116.68    48.2199996709824    26.8999993801117    21.17
+99994111061    ENST00000379802_141    [201 - 8954] cdna:known chromos
+ome:GRCh37:6:7541808:7586950:1 gene:ENSG00000096696 gene_biotype:prot
+ein_coding transcript_biotype:protein_coding            2    99.00000
+09536743    AELIVQPELK            -5.64623987884261E-05    1138.65991
+210938    570.3372    1138.65979003906    570.337158203125    2    14
+    2.1.1.3480.1    1    0.7224    -1    -1

#!/usr/bin/perl -w                 
use strict;
...
close (SEQ);
close (REP);
close (OUT);