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use strict;
use warnings;
...
1,4-alpha-glucan branching protein    NC_021192.1    NC_017522.1    NC
+_016934.1    NC_018078.1    NC_020089.1    NC_002755.2    NC_017524.1
+    NC_009565.1    NC_012943.1    NC_017523.1    NC_021740.1
1,4-dihydroxy-2-naphthoate octaprenyltransferase    NC_016934.1    NC_
+017026.1    NC_009525.1
1,4-dihydroxy-2-naphthoyl-CoA synthase    NC_018143.2    NC_009565.1  
+  NC_002755.2    NC_012943.1    NC_017523.1

$ perl fq_files.pl
(3R)-hydroxyacyl-ACP dehydratase                  0     0       0     
+  0       0       0       0       0       0       0       0       0  
+     0       0
...
1,4-alpha-glucan branching                        1     0       1     
+  1       0       1       0       1       1       1       0       1  
+     0       1
1,4-dihydroxy-2-naphthoate octaprenyltransferase  0     1       0     
+  0       0       1       1       0       0       0       0       0  
+     0       0
1,4-dihydroxy-2-naphthoyl-CoA synthase            1     0       1     
+  1       0       0       0       0       1       0       0       0  
+     1       0