Hello lairel,

When I run your code with perl -c, I get the following output:

16:16 >perl -c 1583_SoPW.pl
Global symbol "$headerHash" requires explicit package name (did you fo
+rget to declare "my $headerHash"?) at 1583_SoPW.pl line 59.
1583_SoPW.pl had compilation errors (#1)
    (F) You've said "use strict" or "use strict vars", which indicates
    that all variables must either be lexically scoped (using "my" or 
+"state"),
    declared beforehand using "our", or explicitly qualified to say
    which package the global variable is in (using "::").

Uncaught exception from user code:
        Global symbol "$headerHash" requires explicit package name (di
+d you forget to declare "my $headerHash"?) at 1583_SoPW.pl line 59.
        1583_SoPW.pl had compilation errors.

16:16 >
[download]

What this is telling you is that the variable $headerHash is being used where it hasn’t been declared. That’s because a variable declaration with my (which produces what is called a lexical variable) has a scope which is limited to the block where it occurs (see e.g. the tutorials in Variables and Scoping). So in this code:

while (<INFILE>){
    chomp;
    my $line = $_;
    ...
    if ($line =~ /^>/){
        my $header = $line;
        if ($header =~ /(>gi.*)\[(.+)\](>gi.*)\[(.+)\]/){
            my $headerHash;                                 # A
            $headerHash{$1} = $2;
        }
        else{
            my $seq = $line;
            print OUTFILE $headerHash, "\n", $seq, "\n";    # B
        }
    }
}
[download]

the declaration at point A has gone out of scope by the time the variable is referenced at point B. To fix this, you need to give the variable a wider scope, by declaring it before you enter the if/else construct:

while (<INFILE>){
    chomp;
    my $line = $_;
    my $headerHash;
    ...
    if ($line =~ /^>/){
        my $header = $line;
        if ($header =~ /(>gi.*)\[(.+)\](>gi.*)\[(.+)\]/){
            $headerHash{$1} = $2;
        }
        else{
            my $seq = $line;
            print OUTFILE $headerHash, "\n", $seq, "\n";
        }
    }
}
[download]

But while this will remove the compile error, it doesn’t make a lot of sense: you print out the value of $headerHash only if its value has not been initialised! Perhaps you need to declare $headerHash before the while loop? In any case, a line such as:

print OUTFILE $headerHash ...
[download]

will only result in output like this:

16:17 >perl -wE "my $h = { a => 1, e => 2 }; print STDOUT $h;"
HASH(0x3ac320)
16:30 >
[download]

which is not what you want. Please supply a sample input file, together with the output you want to produce from that file (see How do I post a question effectively?). This will help the monks to understand what you’re really trying to achieve.

Update:

Until I read Marshall’s reply, I hadn’t noticed that %headerHash is already declared before the loop; I was reading the line $headerHash{$1} = $2; as though it were this: $headerHash->{$1} = $2; — i.e., treating $headerHash as a hash reference — which of course it isn’t. :-(

lairel, just to emphasise the point Marshall is making: in Perl, $headerHash, @headerHash, and %headerHash are separate, completely unrelated variables. $headerHash{$key} references one element of the hash %headerHash, and is unrelated to the scalar variable $headerHash.

Hope that helps,