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I have inherited an older script that uses hash references that I don't understand. It results in:
Can't use an undefined value as a HASH reference at
./make_quar_dbfile.pl line 65.
63 my $bucket = sprintf('%02x', $i);
64 my $file = sprintf('%s/%02x.db', $qdir, $i);
65 %{$hashes{$bucket}} ? 1 : next;
66 tie (my %hash, 'DB_File', $file, O_RDWR, 0600) || die "Can't open db file: $! \n ";
67 %hash = %{$hashes{$bucket}};
68 untie %hash;
The script reads through a number of gzipd emails to identify the sender/recip/subject/date etc., then writes that info to a DB_File hash.
This script used to work with older versions of Perl, but looks like it now is no longer compliant.
I'd really like to understand how this works, but I don't fully understand reference/dereference, why it's even necessary here, and the %{$var} notation. All of the references I've studied talk about hash references in terms of $hash_ref = \%author; not %hash_ref = %{$author}, for example.
Ideas on how to get this to work with hash references would be greatly appreciated.
#!/usr/bin/perl -w
use DB_File;
use File::Basename qw(basename);
use vars qw($verbose);
use strict;
use warnings;
sub DBG($);
$verbose = shift || 1;
my $qdir = '/var/spool/amavisd/qdb';
my $source_dir = '/var/spool/amavisd/quarantine';
my $uid = getpwnam('amavis');
my $gid = getgrnam('amavis');
my %hashes = ( );
my $me = basename($0);
my $version = '1.9';
my $steps = 100;
my $cnt = 0;
DBG("- Creating initial database files...");
for (my $i = 0; $i < 256; $i++) {
my $file = sprintf('%s/%02x.db', $qdir, $i);
unlink $file || DBG("Could not unlink $file to empty db: $! \n");
tie (my %hash, "DB_File", $file, O_CREAT, 0600) || die "Can't open db file: $! \n";
untie %hash;
chown($uid, $gid, $file) || die "Unable to set attributes on file: $! \n";
}
DBG("done\n");
opendir SOURCEDIR, $source_dir || die "Cannot open $source_dir: $! \n";
DBG("- Building hashes... ");
foreach my $f (sort readdir SOURCEDIR) {
next if ($f eq "." || $f eq "..");
if ($f =~ m/^(spam|virus)\-([^\-]+)\-([^\-]+)(\.gz)?/) {
my $type = $1;
my $key = $3;
my $bucket = substr($key, 0, 2);
my $d = $2;
my $subj = '';
my $to = '';
my $from = '';
my $size = '';
my $score = '0.0';
if (($cnt % $steps) == 0) { DBG(sprintf("\e[8D%-8d", $cnt)); } $cnt++;
if ($f =~ /\.gz$/ && open IN, "zcat $source_dir/$f |") {
while(<IN>) {
last if ($_ eq "\n");
$subj = $1 if (/^Subject:\s*(.*)$/);
$to = $1 if (/^To:\s*(.*)$/);
$from = $1 if (/^From:\s*(.*)$/);
$score = $1 if (/score=(\d{1,3}\.\d)/);
}
close IN;
$to =~ s/^.*\<(.*)\>.*$/$1/;
$from =~ s/^.*\<(.*)\>.*$/$1/;
$size = (stat("$source_dir/$f"))[7];
$hashes{$bucket}->{$f} = "$type\t$d\t$size\t$from\t$to\t$subj\t$score";
}
}
}
closedir SOURCEDIR;
DBG("...done\n\n- Populating database files...");
for (my $i = 0; $i < 256; $i++) {
my $bucket = sprintf('%02x', $i);
my $file = sprintf('%s/%02x.db', $qdir, $i);
%{$hashes{$bucket}} ? 1 : next;
tie (my %hash, 'DB_File', $file, O_RDWR, 0600) || die "Can't open db file: $! \n ";
%hash = %{$hashes{$bucket}};
untie %hash;
}
exit(0);
sub DBG($) { my $msg = shift; print $msg if ($verbose); }
What is $hash{$key}? A value associated with the (value of) $key, which must be a scalar. So we get the $value out of my %hash = ( $key => $value ).
That's a string, or a number. Or a filehandle. Or, an array reference, or a hash reference. (Or an object perhaps, normally a blessed hash reference.) They are all scalars, single-valued things, and as such are a legitimate value in a hash.
The syntax %{ ... } de-references a hash reference† so judged by %{ $hashes{$bucket} } that code expects there to be a hash reference. So the error says that there is actually nothing in %hashes for that value of a would-be key ($bucket), so it cannot "de-reference" it. There is either no key that is the value of $bucket at that point in the loop, or there is such a key but it has never been assigned anything.
So go debug it. Add printing statements through the loops so you can see what values are there and what they are, and which ones aren't even as they are assumed to be. Hard to tell what fails without running that program.
Then, the line %{$hashes{$bucket}} ? 1 : next; is a little silly. The condition of the ternary operator evaluates to a boolean, "true" (not undefined, not 0, not empty string '') or false. So it tests whether $hashes{$bucket} has a hashref with at least some keys, and if it does then it returns 1; so, the for loop continues. Otherwise it skips to the next iteration.
Well, then skip to next if there is not a (non-empty) hashref there:
next if not defined $hashes{$bucket} or not %{ $hashes{$bucket} };
Note how we first test whether there is such a key, and only then attempt to derefence it.
† Whatever expression may be inside the curlies must evaluate to a hash reference. (If it's else, like a number or a string, the code would still exit with an error but with a different one.)
So, in this code, the hash %hashes must have a key that is the value of $bucket at that point, and the value for that key must be a hash reference. Then, the ternary operator tests whether the hash obtained from that hash reference has any keys.
You need to understand references first, this is a kind of how-to :
#!/usr/bin/perl
use strict; use warnings;
use feature qw/say/;
use Data::Dumper;
my $var = {}; # I create a HASH ref explicitly
say "I created a HASH ref explicitly:";
say ref($var);
say "Now, let's add any type of content:";
say "Adding a ARRAY:";
push #{ $var->{arr} }, (0..5);
say Dumper $var;
say "Now, I add a new HASH";
$var->{new_hash} = {
foo => "value",
bar => "other"
};
say Dumper $var;
say 'To access the data in $var without Data::Dumper, we need to dereference what we want to retrieve';
say "to retrieve a HASH ref, we need to dereference with %:";
while (my ($key, $value) = each %{ $var->{new_hash} }) {
say "key=$key value=$value";
}
say "To retrieve the ARRAY ref:";
say join "\n", #{ $var->{arr} };
Output
I created a HASH ref explicitely:
HASH
Now, let's add any type of content:
Adding a ARRAY:
$VAR1 = {
'arr' => [
0,
1,
2,
3,
4,
5
]
};
Now, I add a new HASH
$VAR1 = {
'new_hash' => {
'foo' => 'value',
'bar' => 'other'
},
'arr' => [
0,
1,
2,
3,
4,
5
]
};
To access the data in $var without Data::Dumper, we need to dereference what we want to retrieve
to retrieve a HASH ref, we need to dereference with %:
key=foo value=value
key=bar value=other
To retrieve the ARRAY ref:
0
1
2
3
4
5
Now with your code, instead of
%{$hashes{$bucket}} ? 1 : next;
You should test the HASH ref first, because Perl say it's undefined, let's debug a bit:
use Data::Dumper;
print Dumper $hashes;
print "bucket=$bucket\n";
if (defined $hashes{$bucket}) {
print "Defined array\n";
}
else {
print "NOT defined array\n";
}
Related
I am currently writing a perl script where I have a reference to an array (students) of references. After adding the hash references to the array. Now I add the references to the array of students and then ask the user how to sort them. This is where it gets confusing. I do not know how to deference the sorted array. Using dumper I can get the sorted array but in a unorganized output. How can I deference the array of hash references after sorting?
#!bin/usr/perl
use strict;
use warnings;
use Data::Dumper;
use 5.010;
#reference to a var $r = \$var; Deferencing $$r
#reference to an array $r = \#var ; Deferencing #$r
#referenc to a hash $r = \%var ; deferencing %$r
my $filename = $ARGV[0];
my $students = [];
open ( INPUT_FILE , '<', "$filename" ) or die "Could not open to read \n ";
sub readLines{
while(my $currentLine = <INPUT_FILE>){
chomp($currentLine);
my #myLine = split(/\s+/,$currentLine);
my %temphash = (
name => "$myLine[0]",
age => "$myLine[1]",
GPA => "$myLine[2]",
MA => "$myLine[3]"
);
pushToStudents(\%temphash);
}
}
sub pushToStudents{
my $data = shift;
push $students ,$data;
}
sub printData{
my $COMMAND = shift;
if($COMMAND eq "sort up"){
my #sortup = sort{ $a->{name} cmp $b->{name} } #$students;
print Dumper #sortup;
}elsif($COMMAND eq "sort down"){
my #sortdown = sort{ $b->{name} cmp $a->{name} } #$students;
print Dumper #sortdown;
//find a way to deference so to make a more organize user friendly read.
}else{
print "\n quit";
}
}
readLines();
#Output in random, the ordering of each users data is random
printf"please choose display order : ";
my $response = <STDIN>;
chomp $response;
printData($response);
The problem here is that you're expected Dumper to provide an organised output. It doesn't. It dumps a data structure to make debugging easier. The key problem will be that hashes are explicitly unordered data structures - they're key-value mappings, they don't produce any output order.
With reference to perldata:
Note that just because a hash is initialized in that order doesn't mean that it comes out in that order.
And specifically the keys function:
Hash entries are returned in an apparently random order. The actual random order is specific to a given hash; the exact same series of operations on two hashes may result in a different order for each hash.
There is a whole section in perlsec which explains this in more detail, but suffice to say - hashes are random order, which means whilst you're sorting your students by name, the key value pairs for each student isn't sorted.
I would suggest instead of:
my #sortdown = sort{ $b->{name} cmp $a->{name} } #$students;
print Dumper #sortdown;
You'd be better off with using a slice:
my #field_order = qw ( name age GPA MA );
foreach my $student ( sort { $b -> {name} cmp $a -> {name} } #$students ) {
print #{$student}{#field_order}, "\n";
}
Arrays (#field_order) are explicitly ordered, so you will always print your student fields in the same sequence. (Haven't fully tested for your example I'm afraid, because I don't have your source data, but this approach works with a sample data snippet).
If you do need to print the keys as well, then you may need a foreach loop instead:
foreach my $field ( #field_order ) {
print "$field => ", $student->{$field},"\n";
}
Or perhaps the more terse:
print "$_ => ", $student -> {$_},"\n" for #field_order;
I'm not sure I like that as much though, but that's perhaps a matter of taste.
The essence of your mistake is to assume that hashes will have a specific ordering. As #Sobrique explains, that assumption is wrong.
I assume you are trying to learn Perl, and therefore, some guidance on the basics will be useful:
#!bin/usr/perl
Your shebang line is wrong: On Windows, or if you run your script with perl script.pl, it will not matter, but you want to make sure the interpreter that is specified in that line uses an absolute path.
Also, you may not always want to use the perl interpreter that came with the system, in which case #!/usr/bin/env perl maybe helpful for one-off scripts.
use strict;
use warnings;
use Data::Dumper;
use 5.010;
I tend to prefer version constraints before pragmata (except in the case of utf8). Data::Dumper is a debugging aid, not something you use for human readable reports.
my $filename = $ARGV[0];
You should check if you were indeed given an argument on the command line as in:
#ARGV or die "Need filename\n";
my $filename = $ARGV[0];
open ( INPUT_FILE , '<', "$filename" ) or die "Could not open to read \n ";
File handles such as INPUT_FILE are called bareword filehandles. These have package scope. Instead, use lexical filehandles whose scope you can restrict to the smallest appropriate block.
There is no need to interpolate $filename in the third argument to open.
Always include the name of the file and the error message when dying from an error in open. Surrounding the filename with ' ' helps you identify any otherwise hard to detect characters that might be causing the problem (e.g. a newline or a space).
open my $input_fh, '<', $filename
or die "Could not open '$filename' for reading: $!";
sub readLines{
This is reading into an array you defined in global scope. What if you want to use the same subroutine to read records from two different files into two separate arrays? readLines should receive a filename as an argument, and return an arrayref as its output (see below).
while(my $currentLine = <INPUT_FILE>){
chomp($currentLine);
In most cases, you want all trailing whitespace removed, not just the line terminator.
my #myLine = split(/\s+/,$currentLine);
split on /\s+/ is different than split ' '. In most cases, the latter is infinitely more useful. Read about the differences in perldoc -f split.
my %temphash = (
name => "$myLine[0]",
age => "$myLine[1]",
GPA => "$myLine[2]",
MA => "$myLine[3]"
);
Again with the useless interpolation. There is no need to interpolate those values into fresh strings (except maybe in the case where they might be objects which overloaded the stringification, but, in this case, you know they are just plain strings.
pushToStudents(\%temphash);
No need for the extra pushToStudents subroutine in this case, unless this is a stub for a method that will later be able to load the data to a database or something. Even in that case, it be better to provide a callback to the function.
sub pushToStudents{
my $data = shift;
push $students ,$data;
}
You are pushing data to a global variable. A program where there can only ever be a single array of student records is not useful.
sub printData{
my $COMMAND = shift;
if($COMMAND eq "sort up"){
Don't do this. Every subroutine should have one clear purpose.
Here is a revised version of your program.
#!/usr/bin/env perl
use 5.010;
use strict;
use warnings;
use Carp qw( croak );
run(\#ARGV);
sub run {
my $argv = $_[0];
#$argv
or die "Need name of student records file\n";
open my $input_fh, '<', $argv->[0]
or croak "Cannot open '$argv->[0]' for reading: $!";
print_records(
read_student_records($input_fh),
prompt_sort_order(),
);
return;
}
sub read_student_records {
my $fh = shift;
my #records;
while (my $line = <$fh>) {
last unless $line =~ /\S/;
my #fields = split ' ', $line;
push #records, {
name => $fields[0],
age => $fields[1],
gpa => $fields[2],
ma => $fields[3],
};
}
return \#records;
}
sub print_records {
my $records = shift;
my $sorter = shift;
if ($sorter) {
$records = [ sort $sorter #$records ];
}
say "#{ $_ }{ qw( age name gpa ma )}" for #$records;
return;
}
sub prompt_sort_order {
my #sorters = (
[ "Input order", undef ],
[ "by name in ascending order", sub { $a->{name} cmp $b->{name} } ],
[ "by name in descending order", sub { $b->{name} cmp $a->{name} } ],
[ "by GPA in ascending order", sub { $a->{gpa} <=> $b->{gpa} } ],
[ "by GPA in descending order", sub { $b->{gpa} <=> $a->{gpa} } ],
);
while (1) {
print "Please choose the order in which you want to print the records\n";
print "[ $_ ] $sorters[$_ - 1][0]\n" for 1 .. #sorters;
printf "\n\t(%s)\n", join('/', 1 .. #sorters);
my ($response) = (<STDIN> =~ /\A \s*? ([1-9][0-9]*?) \s+ \z/x);
if (
$response and
($response >= 1) and
($response <= #sorters)
) {
return $sorters[ $response - 1][1];
}
}
# should not be reached
return;
}
I am currently trying to implement a suffix tree using Perl, however, when I attempt to set the reference for the tree function, the reference location is not set, if I pass the address via a string then check the text in the string vs the location of the hash table and they are different. Any help is appreciated!
use strict;
use warnings;
use Data::Dumper;
my $count = 0;
my $str; # holds the complete string
my %root;
# takes in all lines of code
open(IN, '<:encoding(UTF-8)', $ARGV[0]) or die "Could not open file '$ARGV[0]' $!\n";
while (<IN>) {
chomp;
# concatinates with string
$str .= $_;
}
# closes input
close(IN);
#length of input string
my $l_size = length($str) - 1;
#recursively makes
sub tree {
#recursive root
my %treeRoot;
#checking incomming data
print "1 ".Dumper(\#_)."\n";
#checking incomming data
print "2 ".Dumper(\%root)."\n";
#attempts to set tree's refrence
\%treeRoot, $count = #_;
#checking incomming data
print "3 ".Dumper(\%root)."\n";
#checking incomming data
print "4 ".$count."\n";
#leaf for each node
my %leaf;
for (my $i = 0; $i < $l_size; $i++) {
#creates alphabet tree
$treeRoot { substr($str, $i, 1) } = %leaf;
}
#checking incomming data
print "5 ".Dumper(\%root)."\n";
while ($count > 0) {
#checking incomming data
print "loop 6 ".Dumper(\%root)."\n";
$count--;
#checking incomming data
print "loop 7 ".$count."\n";
#recursion not implamented yet
#tree(\$treeRoot{'a'}, $count);
}
}
tree(\%root, 2);
#print Dumper(\%root);
You need parentheses to disambiguate. This:
\%treeRoot, $count = #_;
means this:
\%treeRoot;
$count = #_;
Because the assignment operator = has higher precedence than the comma operator ,. The warning that you got from running that code tells you this: Useless use of reference constructor in void context.
To pass the arguments correctly, you need parentheses:
(\%treeRoot, $count) = #_;
Unfortunately, this does not work, because you cannot assign to a reference this way. The following error tells you that: Can't modify reference constructor in list assignment.
So what you need is to pass the reference to a scalar:
my ($href, $count) = #_;
print $href->{'value'};
I think this method is a bit backwards, though. Passing variables by reference is likely to become a source of bugs. A more natural solution is to use the return value of the subroutine to assign values:
sub foo {
my %hash;
$hash{'value'} = ....
....
return \%hash;
}
my $hashref = foo();
print $hashref->{'value'};
Your question isn't actually how to pass a hash reference, but how to receive it, as the following will not work:
\%treeRoot, $count = #_;
Basically, you need to assign your reference to a scalar like so:
use strict;
use warnings;
sub example_sub {
my ($hashref, $count) = #_;
# Add two values to the hash:
$hashref->{newkey} = 'val';
$hashref->{newkey2} = 'val2';
}
my %root;
example_sub(\%root, 2);
use Data::Dump;
dd \%root;
Outputs:
{ newkey => "val", newkey2 => "val2" }
If you don't want to modify your original hash, you can assign the values to a new hash within the sub:
my %newhash = %$hashref;
For more info on working with references, check out: perlref - Perl references and nested data structures
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I am trying to print values of range from #arr3 which are same and lie outside the range from #arr4 (not included in range of arr4) but I am not getting the desired output. Please suggest me the modifications in the following code to get the output as 1,2,8,13 (without repeating the values if any)
File 1: result
1..5
5..10
10..15
File 2: annotation
3..7
9..12
14..17
Code:
#!/usr/bin/perl
open($inp1, "<result") or die "not found";
open($inp2, "<annotation") or die "not found";
my #arr3 = <$inp1>;
my #arr4 = <$inp2>;
foreach my $line1 (#arr4) {
foreach my $line2 (#arr3) {
my ($from1, $to1) = split(/\.\./, $line1);
my ($from2, $to2) = split(/\.\./, $line2);
for (my $i = $from1 ; $i <= $to1 ; $i++) {
for (my $j = $from2 ; $j <= $to2 ; $j++) {
$res = grep(/$i/, #result); #to avoid repetition
if ($i != $j && $res == 0) {
print "$i \n";
push(#result, $i);
}
}
}
}
}
Try this:
#!/usr/bin/perl
use strict;
open (my $inp1,"<result.txt") or die "not found";
open (my $inp2,"<annotation.txt") or die "not found";
my #result;
my #annotation;
foreach my $line2 (<$inp2>) {
my ($from2,$to2)=split(/\.\./,$line2);
#annotation = (#annotation, $from2..$to2);
}
print join(",",#annotation),"\n";
my %in_range = map {$_=> 1} #annotation;
foreach my $line1 (<$inp1>) {
my ($from1,$to1)=split(/\.\./,$line1);
#result = (#result, $from1..$to1);
}
print join(",",#result),"\n";
my %tmp_hash = map {$_=> 1} #result;
my #unique = sort {$a <=> $b} keys %tmp_hash;
print join(",",#unique),"\n";
my #out_of_range = grep {!$in_range{$_}} #unique;
print join(",",#out_of_range),"\n";
The print statements are temporary, of course, to help show what's going on when you run this. The basic idea is you use one hash to eliminate duplicate numbers in your "result", and another hash to indicate which ones are in the "annotations".
If you used pattern-matching rather than split then I think it would be a little easier to make this ignore extra lines of input that aren't ranges of numbers, in case you ever have input files with a few "extra" lines that you need to skip over.
If the contents of the files is under your control, you can make use of eval for parsing them. On the other hand, if there might be something else than what you specified, the following is dangerous to use.
#!/usr/bin/perl
use strict;
use warnings;
use autodie;
use Data::Dumper;
open my $inc, '<', 'result';
open my $exc, '<', 'annotation';
my (%include, %exclude, #result);
while (<$inc>) { $include{$_} = 1 for eval $_ }
while (<$exc>) { $exclude{$_} = 1 for eval $_ }
for (sort {$a <=> $b} keys %include) {
push #result, $_ unless $exclude{$_}
}
print Dumper \#result;
Returns:
$VAR1 = [ 1, 2, 8, 13 ];
The only major tool you need is a %seen style hash as represented in perlfaq4 - How can I remove duplicate elements from a list or array?
The following opens filehandles to string references, but obviously these could be replaced with the appropriate file names:
use strict;
use warnings;
use autodie;
my %seen;
open my $fh_fltr, '<', \ "3..7\n9..12\n14..17\n";
while (<$fh_fltr>) {
my ($from, $to) = split /\.{2}/;
$seen{$_}++ for $from .. $to;
}
my #result;
open my $fh_src, '<', \ "1..5\n5..10\n10..15\n";
while (<$fh_src>) {
my ($from, $to) = split /\.{2}/;
push #result, $_ for grep {!$seen{$_}++} $from .. $to;
}
print "#result\n";
Outputs:
1 2 8 13
I would like to change variables stored in a hash, but I kept receiving the error:
"Can't use the string ("SCALAR(0x30f558)") as a SCALAR ref while "strict refs" in use at - line 14.
My simplified code is as follows:
#!/usr/bin/perl
use strict;
use warnings;
my $num = 1234;
my $a = 5;
my %hash = (\$num => "value");
foreach my $key (keys %{hash}){
print "Key: $key\n";
#OPTION1: $a = $$key;
}
my $ref = \$num ;
print "Ref: $ref\n";
#OPTION2: $a = $$ref ;
print $a;
Running this prints:
Key: SCALAR(0x30f558)
Ref: SCALAR(0x30f558)
5
showing that both $key and $ref are pointing to the same variable - $num
Also, the code on OPTION1 and OPTION2 are identical if $key and $ref are the same.
When I uncomment OPTION2, $a prints out as 1234.
When I uncomment OPTION1, however, I receive the error shown above.
QUESTION:
How do I change $a to $num using the hash as I tried to do in OPTION1? And why will this not work as is?
References:
http://cpansearch.perl.org/src/CHIPS/perl5.004_05/t/pragma/strict-refs
I followed this code closely:
use strict 'refs' ;
my $fred ;
my $b = \$fred ;
my $a = $$b ;
which posed no error until I introduced the hash.
Thank you for your help.
Original Code (doesn't work):
#User Defined - here are the defaults
my $a = 122160;
my $b = 122351;
my $c = 'string';
my $d = 15;
my $e = 123528;
#etc.
#Create variable/print statement hash
my %UserVariables = (
\$a => "A: (Default: $a): ",
\$b => "B: (Default: $b): ",
\$c => "C: (Default: $c): ",
\$d => "D: (Default: $d): ",
\$e => "E: (Default: $e): ",
);
#Allow user to change variables if desired
foreach (keys %UserVariables){
print $UserVariables{$_};
chomp (my $temp = <>);
print "$_\n";
$$_ = $temp unless ($temp eq '');
print "$temp\n" unless ($temp eq '');
};
Less efficient method that does work:
#Alternate Method without loops (not ideal)
my $temp;
print $UserVariables{\$a};
chomp ($temp = (<>));
$a= $temp unless ($temp eq '');
print $UserVariables{\$b};
chomp ($temp = (<>));
$b= $temp unless ($temp eq '');
print $UserVariables{\$c};
chomp ($temp = (<>));
$c= $temp unless ($temp eq '');
print $UserVariables{\$d};
chomp ($temp = (<>));
$d= $temp unless ($temp eq '');
print $UserVariables{\$e};
chomp ($temp = (<>));
$e= $temp unless ($temp eq '');
Perl hash keys can only be string. You don't have reference as key, but what your reference automatically stringified to: a verbatim string "SCALAR(0x30f558)" instead. Obviously, string won't work as reference.
You should rethink the way you store data and maybe explain in little more details what you want to do instead on focusing on how.
In your particular case illustrated by example just use plain hash for those values you want to be overridable:
my %config = (
a => 122160,
b => 122351,
c => 'string',
d => 15,
e => 123528,
);
...and then overwrite values in this hash.
I would like to change variables stored in a hash
Just like you can't store variables in a scalar, you can't store variables in hashes. You can store values (including references to variables) in hashes. (Such as the string value in your code.)
showing that both $key and $ref are pointing to the same variable - $num
No. It shows that the values of $key and $ref have the same stringification.
When I uncomment OPTION1, however, I receive the error shown above.
Hash table keys are necessarily strings, just like array keys are necessarily non-negative integers.
I followed this code closely:
No, the same with hashes works fine.
use strict 'refs' ;
my %hash = ( fred => undef );
my $b = \$hash{fred} ;
my $a = $$b ;
I can't provide a solution, because you didn't say what you are trying to do.
You keep saying in the comments that you want to modify variables passed through STDIN, however it is not clear what you mean by this. Are you passing command line arguments or requesting input from the user or piping the output of another program into yours, or something else entirely? The ideal approach will vary slightly depending on what you're trying to do.
To read command line arguments you access the #ARGV array:
$foo = $ARGV[0]; #read the first argument
To read a line off of STDIN:
print "Enter a number: ";
$foo = <STDIN>;
Given a set of genes and existing pair of genes, I want to generate new pairs of genes which are not already existing.
The genes file has the following format :
123
134
23455
3242
3423
...
...
The genes pairs file has the following format :
12,345
134,23455
23455,343
3242,464452
3423,7655
...
...
But I still get few common elements between known_interactions and new_pairs. I'm not sure where the error is.
For the arguments,
perl generate_random_pairs.pl entrez_genes_file known_interactions_file 250000
I got a common elements of 15880. The number 250000 is to tell how many random pairs I want the program to generate.
#! usr/bin/perl
use strict;
use warnings;
if (#ARGV != 3) {
die "Usage: generate_random_pairs.pl <entrez_genes> <known_interactions> <number_of_interactions>\n";
}
my ($e_file, $k_file, $interactions) = #ARGV;
open (IN, $e_file) or die "Error!! Cannot open $e_file\n";
open (IN2, $k_file) or die "Error!! Cannot open $k_file\n";
my #e_file = <IN>; s/\s+\z// for #e_file;
my #k_file = <IN2>; s/\s+\z// for #k_file;
my (%known_interactions);
my %entrez_genes;
$entrez_genes{$_}++ foreach #e_file;
foreach my $line (#k_file) {
my #array = split (/,/, $line);
$known_interactions{$array[0]} = $array[1];
}
my $count = 0;
foreach my $key1 (keys %entrez_genes) {
foreach my $key2 (keys %entrez_genes) {
if ($key1 != $key2) {
if (exists $known_interactions{$key1} && ($known_interactions{$key1} == $key2)) {next;}
if (exists $known_interactions{$key2} && ($known_interactions{$key2} == $key1)) {next;}
if ($key1 < $key2) { print "$key1,$key2\n"; $count++; }
else { print "$key2,$key1\n"; $count++; }
}
if ($count == $interactions) {
die "$count\n";
}
}
}
I can see nothing wrong with your code. I wonder if you have some whitespace in your data - either after the comma or at the end of the line? It would be safer to extract just the digit fields with, for instance
my #e_file = map /\d+/g, <IN>;
Also, you would be better off keeping both elements of the pair as the hash key, so that you can just check the existence of the element. And if you make sure the lower number is always first you don't need to do two lookups.
This example should work for you. It doesn't address the random selection part of your requirement, but that wasn't in your own code and wasn't your immediate problem
use strict;
use warnings;
#ARGV = qw/ entrez_genes.txt known_interactions.txt 9 /;
if (#ARGV != 3) {
die "Usage: generate_random_pairs.pl <entrez_genes> <known_interactions> <number_of_interactions>\n";
}
my ($e_file, $k_file, $interactions) = #ARGV;
open my $fh, '<', $e_file or die "Error!! Cannot open $e_file: $!";
my #e_file = sort { $a <=> $b } map /\d+/g, <$fh>;
open $fh, '<', $k_file or die "Error!! Cannot open $k_file: $!";
my %known_interactions;
while (<$fh>) {
my $pair = join ',', sort { $a <=> $b } /\d+/g;
$known_interactions{$pair}++;
}
close $fh;
my $count = 0;
PAIR:
for my $i (0 .. $#e_file-1) {
for my $j ($i+1 .. $#e_file) {
my $pair = join ',', #e_file[$i, $j];
unless ($known_interactions{$pair}) {
print $pair, "\n";
last PAIR if ++$count >= $interactions;
}
}
}
print "\nTotal of $count interactions\n";
first of all, you are not chomping (removing newlines) from your file of known interactions. That means that given a file like:
1111,2222
you will build this hash:
$known_interactions{1111} = "2222\n";
That is probably why you are getting duplicate entries. My guess is (can't be sure without your actual input files) that these loops should work ok:
map{
chomp;
$entrez_genes{$_}++ ;
}#e_file;
and
map {
chomp;
my #array = sort(split (/,/));
$known_interactions{$array[0]} = $array[1];
}#k_file;
Also, as a general rule, I find my life is easier if I sort the interacting pair (the joys of bioinformatics :) ). That way I know that 111,222 and 222,111 will be treated in the same way and I can avoid multiple if statements like you have in your code.
Your next loop would then be (which IMHO is more readable):
my #genes=keys(%entrez_genes);
for (my $i=0; $i<=$#genes;$i++) {
for (my $k=$n; $k<=$#genes;$k++) {
next if $genes[$n] == $genes[$k];
my #pp=sort($genes[$n],$genes[$k]);
next unless exists $known_interactions{$pp[0]};
next if $known_interactions{$pp[0]} == $pp[1];
print "$pp[0], $pp[1]\n";
$count++;
die "$count\n" if $count == $interactions;
}
}