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

Dear all

I have a text file and some of the lines contain a trailing asterisk (they are protein sequences and * stands for a stop codon). I was trying to write a short perl script to remove (substitute with empty string) them, but I got some results I found weird. Hopefully someone could help me.

I tried this code, but it does not work. The * are still there.

while(my $line = <$in>){
    $line =~ s/\*$//;
    print $line;
    }

[download]

When I tried this code, it suddenly worked. 

while(my $line = <$in>){
    $line =~ s/\*\s$//;
    print $line;
}

[download]

I think the previous code worked because every line contains a newline character (\n). But when I replace \s with \n the code stopped working. That made me confused and made me wonder these three things:

Thanks in advance.

Replies are listed 'Best First'.
Re: Removing trailing asterisk from lines with regex
by AnomalousMonk (Archbishop) on Apr 14, 2017 at 22:16 UTC

    Just another set of examples to drive home the point that, whatever else may happen (i.e., with the newlines), the  * (asterisk) is always gone: 

    c:\@Work\Perl\monks>perl -wMstrict -le
"my $s = qq{AAA*\n};
 ;;
 my $t = $s;
 print qq{A1: '$t'};
 $t =~ s/\*$//;
 print qq{A2: '$t'};
 ;;
 $t = $s;
 print qq{B1: '$t'};
 $t =~ s/\*\s$//;
 print qq{B2: '$t'};
 ;;
 $t = $s;
 print qq{C1: '$t'};
 $t =~ s/\*[\n]$//;
 print qq{C2: '$t'};
"
A1: 'AAA*
'
A2: 'AAA
'
B1: 'AAA*
'
B2: 'AAA'
C1: 'AAA*
'
C2: 'AAA'

    [download]
    Note that:  \n is a member of the  \s (whitespace) set;  [\n] is the same as  \n (newline) alone. Please see perlre, perlretut, and perlrequick.

    Update:

    Does perl let you print $line as a literal string with \n etc.?
    Some questions can be answered by simple experimentation. What happens when you print the strings "foobar", "foo\nbar", "foo\n\n\nbar", "foobar\n", "foobar\n\n\n", etc?

    Give a man a fish:  <%-{-{-{-<

[reply]
[d/l]
[select]
Re: Removing trailing asterisk from lines with regex
by Anonymous Monk on Apr 14, 2017 at 21:03 UTC
    $ matches at the end of line *or* just before the \n at the end of the line. Use Data::Dumper to look at $line, sounds like there is extra whitespace on the end
[reply]
Re: Removing trailing asterisk from lines with regex
by Anonymous Monk on Apr 14, 2017 at 21:17 UTC 
    my @lines = ("foo*\n", "foo* \n", "foo*  \n");
for my $line (@lines) {
   $line =~ s/\*\s$//;
   print "($line)\n";
}

    [download]
    For the first input, the * and newline are removed. For the second input, the * and trailing space are removed, but the newline is left there. For the third input, nothing is removed. You might want to use this substitution instead: 
       $line =~ s/\*\s*$//;

    [download]
[reply]
[d/l]
[select]

Back to Seekers of Perl Wisdom