That big if/elsif/elsif/else block is broken, here is why/how 

$ perl -e " use strict; use warnings; if( 0 ){ my $foo = 1; } else { $
+foo = 2; } "
Global symbol "$foo" requires explicit package name at -e line 1.
Execution of -e aborted due to compilation errors.

$ perl -e " use strict; use warnings; if( 1 ){ my $foo = 1; } else { $
+foo = 2; } "
Global symbol "$foo" requires explicit package name at -e line 1.
Execution of -e aborted due to compilation errors.

[download]

The  my $foo only exists inside that first if-block, all the other $foo refer to the undeclared global variable $foo

somebody told you to use strict, and you gave it a shot, but since you did not understand the benefits, you eventually turned it off , and now your program is broken

The shortest fix to satisfy strict is to move  my $foo outside the if/else/block, as in 

$ perl -e " use strict; use warnings; my $foo; if( 0 ){ $foo = 1; } el
+se { $foo = 2; } "

[download]

More on scope/strict in Lexical scoping like a fox, Read this if you want to cut your development time in half! and understand that  strict itself confers no benefits; The benefits come from avoidance of the bad practices forbidden by  strict :)

My second piece of advice, is turn that if/else block into a function, maybe like so 

    my( $Flag1, $Flag2 ) = ProtsFlags( $Subj_id, \%proph_prots, \%euk_
+prots, \%vir_prots );

    $HoFlg1{$Query_id}{$Subj_id}{$bits} = $Flag1;
    $HoFlg2{$Query_id}{$Subj_id}{$bits} = $Flag2;

[download]

In reply to Re: help with hash or arrays or hash references by Anonymous Monk
in thread help with hash or arrays or hash references by AWallBuilder

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