Replacing Whitespace with Underscore

CPTQuesoXI has asked for the wisdom of the Perl Monks concerning the following question:

I am performing a phylogenetic tree from sequence alignments with a software that requires no whitespaces and no brackets/parentheses in the text file. I try to substitute my whitespaces with underscores and my brackets with whitespaces so that the file can be read without problem in the alignment software. My code runs without error warnings, but does not give any output whatsoever.

foreach my $line (<>) {
    chomp ($line);
    
    if ($line =~ m/^>/) {             #if line matches ">" at beginnin
+g
        
        if ($line =~ /\s/g) {                #if line matches whitespa
+ce globally
            
            $line =~ s/\]/\s/;
                        $line =~ s/\[/\s/;
                       
                         $line =~ s/\s /_/g;                #substitut
+e whitespace with underscore.
                        
        
}
        }
        }
[download]

Comment on Replacing Whitespace with Underscore Download Code

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Re: Replacing Whitespace with Underscore by pryrt (Abbot) on Apr 09, 2018 at 16:19 UTC
If that is your complete code, you are missing any output statements. You have edited the variable `$line`, which edits the string in memory... but then you do nothing with it. Given that you've `chomp`ed the line, I recommend something like `print "$line\n";` at the end of your `foreach` loop	[reply] [d/l] [select]
Re^2: Replacing Whitespace with Underscore by CPTQuesoXI (Novice) on Apr 09, 2018 at 16:47 UTC
I'm angry with myself for forgetting that. That ended up given me exactly what I needed. Thank you!	[reply]
Re: Replacing Whitespace with Underscore by jimpudar (Pilgrim) on Apr 09, 2018 at 16:24 UTC
You should turn on 'use strict' and 'use warnings', this will help lead you to a better solution. It seems your main problem might be that you are confusing the space character ' ' with the whitespace character class. In a regex, '\s' matches not only the space character, but ANY whitespace character. See Whitespace. Your substitutions like 's/\[/\s/' will fail because '\s' is only recognized as whitespace in a regex: `$ perl -wE 'my $str = "JA_PH"; $str =~ s/_/\s/; say $str' Unrecognized escape \s passed through at -e line 1. JAsPH $ perl -wE 'my $str = "JA_PH"; $str =~ s/_/ /; say $str' JA PH` [download] Also, your regex for substituting whitespace with underscore will only match a whitespace character followed by a space character. I don't think this is quite what you meant. `$ perl -wE 'my $str = "Some text with whitespace"; $str =~ s/\s /_/g; + say $str' Some text with_whitespace $ perl -wE 'my $str = "Some text with whitespace"; $str =~ s/\s/_/g; +say $str' Some_text_with__whitespace $ perl -wE 'my $str = "Some text with whitespace"; $str =~ s/\s+/_/g; + say $str' Some_text_with_whitespace` [download] Best, Jim	[reply] [d/l] [select]
Re^2: Replacing Whitespace with Underscore by CPTQuesoXI (Novice) on Apr 09, 2018 at 16:48 UTC
Thanks! It worked perfectly!	[reply]
Re: Replacing Whitespace with Underscore by Anonymous Monk on Apr 09, 2018 at 16:40 UTC
See perlrun for the meaning of -switches and Quote Like Operators for the transliteration operator. `$ perl -wpe 'tr/ []/_ /' < input.txt > output.txt` [download]	[reply] [d/l]


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