Interpolating a non-interpolated passed string inside a subroutine in Perl - perl

Question

I am looking to parse a tab delimited text file into a nested hash with a subroutine. Each file row will be keyed by a unique id from a uid column(s), with the header row as nested keys. Which column(s) is(are) to become the uid changes (as sometimes there isn't a unique column, so the uid has to be a combination of columns). My issue is with the $uid variable, which I pass as a non-interpolated string. When I try to use it inside the subroutine in an interpolated way, it will only give me the non-interpolated value:
use strict;
use warnings;
my $lofrow = tablehash($lof_file, '$row{gene}', "transcript", "ENST");
##sub to generate table hash from file w/ headers
##input values are file, uid, header starter, row starter, max column number
##returns hash reference (deref it)
sub tablehash {
my ($file, $uid, $headstart, $rowstart, $colnum) = #_;
if (!$colnum){ # takes care of a unknown number of columns
$colnum = 0;
}
open(INA, $file) or die "failed to open $file, $!\n";
my %table; # permanent hash table
my %row; # hash of column values for each row
my #names = (); # column headers
my #values = (); # line/row values
while (chomp(my $line = <INA>)){ # reading lines for lof info
if ($line =~ /^$headstart/){
#names = split(/\t/, $line, $colnum);
} elsif ($line =~ /^$rowstart/){ # splitting lof info columns into variables
#values = split(/\t/, $line, $colnum);
#row{#names} = #values;
print qq($uid\t$row{gene}\n); # problem: prints "$row{gene} ACB1"
$table{"$uid"} = { %row }; # puts row hash into permanent hash, but with $row{gene} key)
}
}
close INA;
return \%table;
}
I am out of ideas. I could put $table{$row{$uid}} and simply pass "gene", but in a couple of instances I want to have a $uid of "$row{gene}|$row{rsid}" producing $table{ACB1|123456}

Answer 1

Interpolation is a feature of the Perl parser. When you write something like
"foo $bar baz"
, Perl compiles it into something like
'foo ' . $bar . ' $baz'
It does not interpret data at runtime.
What you have is a string where one of the characters happens to be $ but that has no special effect.
There are at least two possible ways to do something like what you want. One of them is to use a function, not a string. (Which makes sense because interpolation really means concatenation at runtime, and the way to pass code around is to wrap it in a function.)
my $lofrow = tablehash($lof_file, sub { my ($row) = #_; $row->{gene} }, "transcript", "ENST");
sub tablehash {
my ($file, $mkuid, $headstart, $rowstart, $colnum) = #_;
...
my $uid = $mkuid->(\%row);
$table{$uid} = { %row };
Here $mkuid isn't a string but a reference to a function that (given a hash reference) returns a uid string. tablehash calls it, passing a reference to %row to it. You can then later change it to e.g.
my $lofrow = tablehash($lof_file, sub { my ($row) = #_; "$row->{gene}|$row->{rsid}" }, "transcript", "ENST");
Another solution is to use what amounts to a template string:
my $lofrow = tablehash($lof_file, "gene|rsid", "transcript", "ENST");
sub tablehash {
my ($file, $uid_template, $headstart, $rowstart, $colnum) = #_;
...
(my $uid = $uid_template) =~ s/(\w+)/$row{$1}/g;
$table{$uid} = { %row };
The s/// code goes through the template string and manually replaces every word by the corresponding value from %row.
Random notes:
Bonus points for using strict and warnings.
if (!$colnum) { $colnum = 0; } can be simplified to $colnum ||= 0;.
Use lexical variables instead of bareword filehandles. Barewords are effectively global variables (and syntactically awkward because they're not first-class citizens of the language).
Always use the 3-argument form of open to avoid unexpected interpretation of the second argument.
Include the name of your program in error messages (either explicitly with $0 or implicitly by omitting \n from die).
my #foo = (); my %bar = (); is redundant and can be simplified to my #foo; my %bar;. Arrays and hashes start out empty; overwriting them with an empty list is pointless.
chomp(my $line = <INA>) will throw a warning when you reach EOF (because you're trying to chomp a variable containing undef).
my %row; should probably be declared inside the loop. It looks like it's supposed to only contain values from the current line.
Suggestion:
open my $fh, '<', $file or die "$0: can't open $file: $!\n";
while (my $line = readline $fh) {
chomp $line;
...
}