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

The standard way to deal with this kind of problem is utilising command-line options, not gathering input from STDIN. Getopt::Long comes with Perl and is servicable:

use strict; use warnings FATAL => 'all';
use Getopt::Long qw(GetOptions);
my %opt;
GetOptions(\%opt, 'qseq=s', 'barcode=s') or die;
die <<"USAGE" unless exists $opt{qseq} and $opt{qseq} =~ /^sample\d[.]qseq$/ and exists $opt{barcode} and $opt{barcode} =~ /^barcode.*\.txt$/;
Usage: $0 --qseq sample1.qseq --barcode barcode.txt
       $0 -q sample1.qseq -b barcode.txt
USAGE
printf "q==<%s> b==<%s>\n", $opt{qseq}, $opt{barcode};

The shell will deal with any extraneous whitespace, try it and see. You need to do the validation of the file names, I made up something with regex in the example. Employ Pod::Usage for a fancier way to output helpful documentation to your users who are likely to get the invocation wrong.

There are dozens of more advanced Getopt modules on CPAN.

Answer 2

You'll need to trim spaces before handling the filename data in your routine, you could check the file extension with yet another regular expression, as nicely described in Is there a regular expression in Perl to find a file's extension?. If it's the actual type of file that matters to you, then it might be more worthwile to check for that instead with File::LibMagicType.

Answer 3

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.

Answer 4

While I think your design is a little iffy, the following will work?

my @fileNames = split(',', $filenames);
foreach my $fileName (@fileNames) {
  if($fileName =~ /\s/) {
    print STDERR "Invalid filename.";
    exit -1;
  }
}
my ($qsec, $barcode) = @fileNames;

Answer 5

And here is one more way you could do it with regex (if you are reading the input from STDIN):

# read a line from STDIN
my $filenames = <STDIN>;

# parse the line with a regex or die with an error message
my ($qseq_filename, $barcode) = $filenames =~ /^\s*(\S.*?)\s*,\s*(\S.*?)\s*$/
    or die "invalid input '$filenames'";