I'm creating an array of hash in perl 5.34.0:
#!/usr/bin/env perl
use strict;
use warnings FATAL => 'all';
use autodie ':default';
use DDP;
my (#a1, #a2);
my %h = ('a' => 1);
push #a1, \%h; # make #a1 a hash of array with 'a' defined
$h{b} = 2; # define b within the hash, but don't write to #a1
push #a2, \%h; # push `a` and `b` onto #a2, but *not* #a1
p #a1; # DDP gives "p" which pretty-prints
p #a2;
and this outputs:
[
[0] {
a 1,
b 2
}
]
[
[0] {
a 1,
b 2
}
]
the problem is that the b key is showing up in #a1, yet $h{b} didn't exist when data was being written to #a1.
I don't want b to show up in #a1 and, it shouldn't.
How can I modify %h so that it doesn't magically appear in different arrays?
That code adds a reference to an existing (named) hash,
push #a1, \%h;
so when that is later queried you see whatever you'd see in the hash at that time. The array only carries a pointer of sorts with the address of the data, also referred to by the hash; it's an alias of sorts. So if the hash got written to in the meanwhile then that's what you'll see via #a1.†
Add it again and, even if the hash changed, you just add the same old reference.
What you want is to make a data copy and add a reference to that -- an anonymous hash
push #a1, { %h }; # but may need deep copy instead
Now the hash data gets copied in order to populate an anonymous hash constructed by {} and we have independent data that can be changed only by writing to it via its reference in #a1.
But note that if values in that hash themselves are references then those references get copied and we have the same problem! In that case you need a deep copy, and this is best done with libraries; Storable::dclone is a good one
use Storable qw(dclone);
push #a1, dclone \%h;
Now all of the actual data is copied, for (a reference to) an independent data copy on #a1
An important exception, which is frequently used
foreach my $elem (#ary) {
my %h;
# ... code that does its work and populates the hash ...
push #res, \%h;
}
Now this is OK, because the hash %h gets created anew at every iteration, being declared inside the loop. So what happens with the data created at the previous iteration?
Since its reference was added to an array the data itself is kept, being referred to by that reference in the array, and only by that. Precisely what you want, lone data accessible only via the array.
In such a case this is preferred to push #res, { %h }, which also works, since a data copy is avoided while the data is kept by, so to say, merely changing its ownership.
† And ff data is changed via #a1, like $a1[0]->{key} = 'val';, then that new value is seen via $h{key} as well.
Related
Lets say I have a large hash and I want to iterate over the contents of it contents. The standard idiom would be something like this:
while(($key, $value) = each(%{$hash_ref})){
///do something
}
However, if I understand my perl correctly this is actually doing two things. First the
%{$hash_ref}
is translating the ref into list context. Thus returning something like
(key1, value1, key2, value2, key3, value3 etc)
which will be stored in my stacks memory. Then the each method will run, eating the first two values in memory (key1 & value1) and returning them to my while loop to process.
If my understanding of this is right that means that I have effectively copied my entire hash into my stacks memory only to iterate over the new copy, which could be expensive for a large hash, due to the expense of iterating over the array twice, but also due to potential cache hits if both hashes can't be held in memory at once. It seems pretty inefficient. I'm wondering if this is what really happens, or if I'm either misunderstanding the actual behavior or the compiler optimizes away the inefficiency for me?
Follow up questions, assuming I am correct about the standard behavior.
Is there a syntax to avoid copying of the hash by iterating over it values in the original hash? If not for a hash is there one for the simpler array?
Does this mean that in the above example I could get inconsistent values between the copy of my hash and my actual hash if I modify the hash_ref content within my loop; resulting in $value having a different value then $hash_ref->($key)?
No, the syntax you quote does not create a copy.
This expression:
%{$hash_ref}
is exactly equivalent to:
%$hash_ref
and assuming the $hash_ref scalar variable does indeed contain a reference to a hash, then adding the % on the front is simply 'dereferencing' the reference - i.e. it resolves to a value that represents the underlying hash (the thing that $hash_ref was pointing to).
If you look at the documentation for the each function, you'll see that it expects a hash as an argument. Putting the % on the front is how you provide a hash when what you have is a hashref.
If you wrote your own subroutine and passed a hash to it like this:
my_sub(%$hash_ref);
then on some level you could say that the hash had been 'copied', since inside the subroutine the special #_ array would contain a list of all the key/value pairs from the hash. However even in that case, the elements of #_ are actually aliases for the keys and values. You'd only actually get a copy if you did something like: my #args = #_.
Perl's builtin each function is declared with the prototype '+' which effectively coerces a hash (or array) argument into a reference to the underlying data structure.
As an aside, starting with version 5.14, the each function can also take a reference to a hash. So instead of:
($key, $value) = each(%{$hash_ref})
You can simply say:
($key, $value) = each($hash_ref)
No copy is created by each (though you do copy the returned values into $key and $value through assignment). The hash itself is passed to each.
each is a little special. It supports the following syntaxes:
each HASH
each ARRAY
As you can see, it doesn't accept an arbitrary expression. (That would be each EXPR or each LIST). The reason for that is to allow each(%foo) to pass the hash %foo itself to each rather than evaluating it in list context. each can do that because it's an operator, and operators can have their own parsing rules. However, you can do something similar with the \% prototype.
use Data::Dumper;
sub f { print(Dumper(#_)); }
sub g(\%) { print(Dumper(#_)); } # Similar to each
my %h = (a=>1, b=>2);
f(%h); # Evaluates %h in list context.
print("\n");
g(%h); # Passes a reference to %h.
Output:
$VAR1 = 'a'; # 4 args, the keys and values of the hash
$VAR2 = 1;
$VAR3 = 'b';
$VAR4 = 2;
$VAR1 = { # 1 arg, a reference to the hash
'a' => 1,
'b' => 2
};
%{$h_ref} is the same as %h, so all of the above applies to %{$h_ref} too.
Note that the hash isn't copied even if it is flattened. The keys are "copied", but the values are returned directly.
use Data::Dumper;
my %h = (abc=>"def", ghi=>"jkl");
print(Dumper(\%h));
$_ = uc($_) for %h;
print(Dumper(\%h));
Output:
$VAR1 = {
'abc' => 'def',
'ghi' => 'jkl'
};
$VAR1 = {
'abc' => 'DEF',
'ghi' => 'JKL'
};
You can read more about this here.
Suppose you have a very large hash (lots of keys), and have a function that potentially deletes many of those keys, e.g.:
while ( each %in ) {
push #out, $_;
functionThatDeletesOneOrMoreKeys($_, \%in);
}
I believe each in this case is an efficient way to pull a single key from the hash, but the documentation says each should not be used when deleting keys from the hash.
Otherwise I could use while (%in) { $_ = (keys(%in))[0] .... but that seems horribly inefficient for a very large hash.
Is there a better way to do this?
This seems to be a horrible thing to do, and it would be better if you explained what you were trying to achieve
However the problem with deleting hash elements while iterating using each is that each holds a state value for the hash that depends on the hash remaining unchanged
You can clear that state by calling keys (or values) on the same hash.
Here's an example which deletes the three elements with the given key and those before and after it in an attempt to emulate what your function_that_deletes_one_or_more_keys (which is what it should be called) might do
use strict;
use warnings 'all';
use feature 'say';
my %h = map +( $_ => 1), 0 .. 9;
while ( my $key = each %h ) {
say $key;
delete #h{$key-1, $key, $key+1};
keys %h; # Reset "each" state
}
I recommend that you don't use the global $_ variable for this
output
2
9
4
6
0
General advice without knowing details of the complexity to which you refer:
Change the function lines that delete keys to instead store the keys to be deleted in an array or hash (or file). After the first loop completes, loop through that array or hash (or file) and delete those keys from the first hash.
my #in_keys = keys %in;
for (#in_keys) {
if (exists $in{$_}) {
...
}
}
Or do as Borodin shows, resetting the iterator each time you know you've deleted at least one element.
Here's some perl pseudo code for what I'm asking:
my %x;
# initialize %x
my $ref = whateverSyntacticSugarIsNeeded( $x{this}{hash}{is}{deep} );
# ...
# make use of $ref multiple times
# ...
delete $ref; # ideally, this would delete $x{this}{hash}{is}{deep}
... where the idea is to avoid use of $x{this}{hash}{is}{deep} more than is absolutely necessary.
I'm fairly sure this isn't possible and the least uses possible is 2 (the initial ref/copy of the value, then to delete the key/value pair from %x). However, if I'm mistaken then feel free to correct me.
It's not clear what you want exactly. If
%x = ( very => { deep => { hash => { is => "here" } } } );
and you assign
$y = $x{very}{deep}{hash}{is}
then is's like writing
$y = 'here'
so you can't delete $y. You can, though,
$z = $x{very}{deep}{hash};
delete $z->{is};
The easiest thing is just to reference the hash one level up.
This is especially true if you give the variable a semantically appropriate name (something other than ref):
my %x;
# initialize %x
my $ref = $x{this}{hash}{is};
# ...
# make use of $ref multiple times
# ...
delete $ref->{deep};
Perl tracks whether or not a piece of memory is used by using a count to that piece of memory. If I did this:
my $ref->{this}->{is}->{a}->{deep} = "hash";
undef $ref; # Note I use "undef" and not "delete"
I free up all of that memory. All of the hash references and the actual scalar that those hash references point to. That's because I have no further way of accessing that memory.
If I do something a bit simpler:
my %hash = ( one => 1, two => 2, ref => { three => 3, four => 4 }, five => 5 );
Note that $hash{ref} is a reference to another hash. If I did this:
my $ref = $hash{ref};
I now have two variables that can access that piece of memory. Doing this:
delete $hash{ref};
does not free up that memory because $ref still points to it. However, that hash reference is no longer in my %hash hash.
If I didn't delete $hash{ref}, but did this:
$ref->{seven} = 7;
I have changed %hash because $ref and $hash{ref} point to the same piece of memory: That same hash reference. Doing this:
delete $hash{ref}->{four};
or
delete $ref->{four};
will both delete a particular entry in that hash reference.
We don't have to do something that complex either:
my %hash = ( one => 1, two => 2, three => 3 );
my $ref = \%hash; #Creating a reference to that hash
delete $ref->{three};
This will delete $hash{three} since both are pointing to the same hash in memory. However,
undef $ref;
will not undefine $hash too.
I hope this covers your question. As long as there's another way to refer to a memory location, it's not freed in Perl. However, if you point a reference to a data structure, manipulating that data structure through the reference will manipulate that data structure referenced through an array or hash variable.
I need to create multi-dimensional hash.
for example I have done:
$hash{gene} = $mrna;
if (exists ($exon)){
$hash{gene}{$mrna} = $exon;
}
if (exists ($cds)){
$hash{gene}{$mrna} = $cds;
}
where $gene, $mrna, $exon, $cds are unique ids.
But, my issue is that I want some properties of $gene and $mrna to be included in the hash.
for example:
$hash{$gene}{'start_loc'} = $start;
$hash{gene}{mrna}{'start_loc'} = $start;
etc. But, is that a feasible way of declaring a hash? If I call $hash{$gene} both $mrna and start_loc will be printed. What could be the solution?
How would I add multiple values for the same key $gene and $mrna being the keys in this case.
Any suggestions will be appreciated.
What you need to do is to read the Perl Reference Tutorial.
Simple answer to your question:
Perl hashes can only take a single value to a key. However, that single value can be a reference to a memory location of another hash.
my %hash1 = ( foo => "bar", fu => "bur" }; #First hash
my %hash2;
my $hash{some_key} = \%hash1; #Reference to %hash1
And, there's nothing stopping that first hash from containing a reference to another hash. It's turtles all the way down!.
So yes, you can have a complex and convoluted structure as you like with as many sub-hashes as you want. Or mix in some arrays too.
For various reasons, I prefer the -> syntax when using these complex structures. I find that for more complex structures, it makes it easier to read. However, the main this is it makes you remember these are references and not actual multidimensional structures.
For example:
$hash{gene}->{mrna}->{start_loc} = $start; #Quote not needed in string if key name qualifies as a valid variable name.
The best thing to do is to think of your hash as a structure. For example:
my $person_ref = {}; #Person is a hash reference.
my $person->{NAME}->{FIRST} = "Bob";
my $person->{NAME}->{LAST} = "Rogers";
my $person->{PHONE}->{WORK}->[0] = "555-1234"; An Array Ref. Might have > 1
my $person->{PHONE}->{WORK}->[1] = "555-4444";
my $person->{PHONE}->{CELL}->[0] = "555-4321";
...
my #people;
push #people, $person_ref;
Now, I can load up my #people array with all my people, or maybe use a hash:
my %person;
$person{$bobs_ssn} = $person; #Now, all of Bob's info is index by his SSN.
So, the first thing you need to do is to think of what your structure should look like. What are the fields in your structure? What are the sub-fields? Figure out what your structure should look like, and then setup your hash of hashes to look like that. Figure out exactly how it will be stored and keyed.
Remember, this hash contains references to your genes (or whatever), so you want to choose your keys wisely.
Read the tutorial. Then, try your hand at it. It's not all that complicated to understand. However, it can be a bear to maintain.
When you say use strict;, you give yourself some protection:
my $foo = "bar";
say $Foo; #This won't work!
This won't work because you didn't declare $Foo, you declared $foo. The use stict; can catch variable names that are mistyped, but:
my %var;
$var{foo} = "bar";
say $var{Foo}; #Whoops!
This will not be caught (except maybe that $var{Foo} has not been initialized. The use strict; pragma can't detect mistakes in typing in your keys.
The next step, after you've grown comfortable with references is to move onto object oriented Perl. There's a Tutorial for that too.
All Object Oriented Perl does is to take your hash references, and turns them into objects. Then, it creates subroutines that will help you keep track of manipulating objects. For example:
sub last_name {
my $person = shift; #Don't worry about this for now..
my $last_name = shift;
if ( exists $last_name ) {
my $person->{NAME}->{LAST} = $last_name;
}
return $person->{NAME}->{LAST};
}
When I set my last name using this subroutine ...I mean method, I guarantee that the key will be $person->{NAME}->{LAST} and not $person->{LAST}->{NAME} or $person->{LAST}->{NMAE}. or $person->{last}->{name}.
The main problem isn't learning the mechanisms, but learning to apply them. So, think about exactly how you want to represent your items. This about what fields you want, and how you're going to pull up that information.
You could try pushing each value onto a hash of arrays:
my (#gene, #mrna, #exon, #cds);
my %hash;
push #{ $hash{$gene[$_]} }, [$mrna[$_], $exon[$_], $cds[$_] ] for 0 .. $#gene;
This way gene is the key, with multiple values ($mrna, $exon, $cds) associated with it.
Iterate over keys/values as follows:
for my $key (sort keys %hash) {
print "Gene: $key\t";
for my $value (#{ $hash{$key} } ) {
my ($mrna, $exon, $cds) = #$value; # De-references the array
print "Values: [$mrna], [$exon], [$cds]\n";
}
}
The answer to a question I've asked previously might be of help (Can a hash key have multiple 'subvalues' in perl?).
I noticed the other day that - while altering values in a hash - that when you dereference a hash in Perl, you actually are making a copy of that hash. To confirm I wrote this quick little script:
#! perl
use warnings;
use strict;
my %h = ();
my $hRef = \%h;
my %h2 = %{$hRef};
my $h2Ref = \%h2;
if($hRef eq $h2Ref) {
print "\n\tThey're the same $hRef $h2Ref";
}
else {
print "\n\tThey're NOT the same $hRef $h2Ref";
}
print "\n\n";
The output:
They're NOT the same HASH(0x10ff6848) HASH(0x10fede18)
This leads me to realize that there could be spots in some of my scripts where they aren't behaving as expected. Why is it even like this in the first place? If you're passing or returning a hash, it would be more natural to assume that dereferencing the hash would allow me to alter the values of the hash being dereferenced. Instead I'm just making copies all over the place without any real need/reason to beyond making syntax a little more obvious.
I realize the fact that I hadn't even noticed this until now shows its probably not that big of a deal (in terms of the need to go fix in all of my scripts - but important going forward). I think its going to be pretty rare to see noticeable performance differences out of this, but that doesn't alter the fact that I'm still confused.
Is this by design in perl? Is there some explicit reason I don't know about for this; or is this just known and you - as the programmer - expected to know and write scripts accordingly?
The problem is that you are making a copy of the hash to work with in this line:
my %h2 = %{$hRef};
And that is understandable, since many posts here on SO use that idiom to make a local name for a hash, without explaining that it is actually making a copy.
In Perl, a hash is a plural value, just like an array. This means that in list context (such as you get when assigning to a hash) the aggregate is taken apart into a list of its contents. This list of pairs is then assembled into a new hash as shown.
What you want to do is work with the reference directly.
for (keys %$hRef) {...}
for (values %$href) {...}
my $x = $href->{some_key};
# or
my $x = $$href{some_key};
$$href{new_key} = 'new_value';
When working with a normal hash, you have the sigil which is either a % when talking about the entire hash, a $ when talking about a single element, and # when talking about a slice. Each of these sigils is then followed by an identifier.
%hash # whole hash
$hash{key} # element
#hash{qw(a b)} # slice
To work with a reference named $href simply replace the string hash in the above code with $href. In other words, $href is the complete name of the identifier:
%$href # whole hash
$$href{key} # element
#$href{qw(a b)} # slice
Each of these could be written in a more verbose form as:
%{$href}
${$href}{key}
#{$href}{qw(a b)}
Which is again a substitution of the string '$href' for 'hash' as the name of the identifier.
%{hash}
${hash}{key}
#{hash}{qw(a b)}
You can also use a dereferencing arrow when working with an element:
$hash->{key} # exactly the same as $$hash{key}
But I prefer the doubled sigil syntax since it is similar to the whole aggregate and slice syntax, as well as the normal non-reference syntax.
So to sum up, any time you write something like this:
my #array = #$array_ref;
my %hash = %$hash_ref;
You will be making a copy of the first level of each aggregate. When using the dereferencing syntax directly, you will be working on the actual values, and not a copy.
If you want a REAL local name for a hash, but want to work on the same hash, you can use the local keyword to create an alias.
sub some_sub {
my $hash_ref = shift;
our %hash; # declare a lexical name for the global %{__PACKAGE__::hash}
local *hash = \%$hash_ref;
# install the hash ref into the glob
# the `\%` bit ensures we have a hash ref
# use %hash here, all changes will be made to $hash_ref
} # local unwinds here, restoring the global to its previous value if any
That is the pure Perl way of aliasing. If you want to use a my variable to hold the alias, you can use the module Data::Alias
You are confusing the actions of dereferencing, which does not inherently create a copy, and using a hash in list context and assigning that list, which does. $hashref->{'a'} is a dereference, but most certainly does affect the original hash. This is true for $#$arrayref or values(%$hashref) also.
Without the assignment, just the list context %$hashref is a mixed beast; the resulting list contains copies of the hash keys but aliases to the actual hash values. You can see this in action:
$ perl -wle'$x={"a".."f"}; for (%$x) { $_=chr(ord($_)+10) }; print %$x'
epcnal
vs.
$ perl -wle'$x={"a".."f"}; %y=%$x; for (%y) { $_=chr(ord($_)+10) }; print %$x; print %y'
efcdab
epcnal
but %$hashref isn't acting any differently than %hash here.
No, dereferencing does not create a copy of the referent. It's my that creates a new variable.
$ perl -E'
my %h1; my $h1 = \%h1;
my %h2; my $h2 = \%h2;
say $h1;
say $h2;
say $h1 == $h2 ?1:0;
'
HASH(0x83b62e0)
HASH(0x83b6340)
0
$ perl -E'
my %h;
my $h1 = \%h;
my $h2 = \%h;
say $h1;
say $h2;
say $h1 == $h2 ?1:0;
'
HASH(0x9eae2d8)
HASH(0x9eae2d8)
1
No, $#{$someArrayHashRef} does not create a new array.
If perl did what you suggest, then variables would get aliased very easily, which would be far more confusing. As it is, you can alias variables with globbing, but you need to do so explicitly.