Regex: How to remove extra spaces between strings in Perl

Question

I am working on a program that take user input for two file names. Unfortunately, the program can easily break if the user does not follow the specified format of the input.

Answer 1

First, put use strict; at the top of your code and declare your variables.

Second, this:

# remove the ',' and put the files into an array separated by spaces; indexes the files
push @filename, join(' ', split(',', $filenames))

Is not going to do what you want. split() takes a string and turns it into an array. Join takes a list of items and returns a string. You just want to split:

my @filenames = split(',', $filenames);

That will create an array like you expect.

This function will safely trim white space from the beginning and end of a string:

sub trim {
    my $string = shift;
    $string =~ s/^\s+//;
    $string =~ s/\s+$//;
    return $string;
}

Access it like this:

my $file = trim(shift @filenames);

Depending on your script, it might be easier to pass the strings as command line arguments. You can access them through the @ARGV array but I prefer to use GetOpt::Long:

use strict;
use Getopt::Long;
Getopt::Long::Configure("bundling");

my ($qseq_filename, $barcode);

GetOptions (
    'q|qseq=s' => \$qseq_filename,
    'b|bar=s'  => \$barcode,
);

You can then call this as:

./script.pl -q sample1.qseq -b barcode.txt

And the variables will be properly populated without a need to worry about trimming white space.