Question

I am using a perl package (Biomart), that includes a subroutine called addFilter(). That subroutine needs a couple of arguments, including one that needs to be of the format “nr:nr:nr”

If I use the subroutine as follows, it works fine:

$query->addFilter("chromosomal_region", ["1:1108138:1108138","1:1110294:1110294"]);

However, if I use it like this, it does not work:

my $string = '"1:1108138:1108138","1:1110294:1110294","1:1125105:1125105"';
$query->addFilter("chromosomal_region", ['$string']);

Since there are tens of thousands of those arguments that I construct in a for loop, I really need the second way to work… What could be causing this? I hope someone can help me out, many thanks in advance!

Answer 1

Because you seem to be trying to write in a language that’s not Perl. '"this","that","another"' isn’t an array, it’s a string. And '$string' doesn’t interpolate or include $string in any way because it uses single quotes. It just produces a string that starts with a dollar sign and ends with “string”.

Something more like what you intend would be:

my @things = ("1:1108138:1108138","1:1110294:1110294","1:1125105:1125105");
$query->addFilter("chromosomal_region", \@things);

-or-

$query->addFilter("chromosomal_region", [ @things ] );

And to build it up dynamically, you can simply do push @things, $value in a loop or whatever you need.