Can any Perl Monk help me to correct the mistake in counting motifs in a string in the perl program written by me?

[supriyoch_2008]

[Utilitarian]

This is a public message board, why would I send a solution to you without it being available to other monks to learn from? (and me to show off with of course)

From perldoc perlop and searching for transliteration we discover that

Because the transliteration table is built at compile time, neither th
+e SEARCHLIST nor the REPLACEMENTLIST 
are subjected to double quote interpolation.  That means that if you w
+ant to use variables, 
you must use an eval():

                   eval "tr/$oldlist/$newlist/";
                   die $@ if $@;

So that may be part of your issue, or at least it will be when you remove the g modifier which makes no sense with athe tr opperator

[marto]

Welcome to the Monastery. Please read and understand How do I compose an effective node title? and How do I post a question effectively?. Don't post your email address. Also consider using strictures: Use strict warnings and diagnostics.

[Corion]

Have you looked at line 38?

[supriyoch_2008]

Dear Sir,

I have seen the line 38. But I could not correct it because it is only 6 (six) days that I have been exposed to perl programming. I have read only chapter 3 and 4 of the book "Beginning Perl for Bioinformatics" by James Tisdall. But I failed to correct the mistake. I am learning it with my own efforts i.e. self study.

Chakraborty

[cdarke]

You have a space between the = and the ~ just before tr on line 38. The ~ is an operator on its own, so perl thinks you are doing an assignment.

That's only your first issue though...

[pvaldes]

not really sure what is a motif here, but this can't stop me to fail, of course XDD ... please, save the facepalms for the end, thanks ;-)

Only a draft, unworking and untested...but can give you some ideas

use 5.010;

my ($file, $motif) = @ARGV;

my $warn = <<'EOF';
     Number or arguments incorrect, Please run this program 
     with 2 arguments, a file and a motif to count the number 
     of letters between any two motifs: i.e. 
     perl script.pl myfile mymotif
EOF

if (scalar @ARGV != 2) {print $warn}

if (scalar @ARGV == 2){

open (my $DNAFILE, '<', $file) 
        or die "I need that you provide a file. Cannot open file $!";

## $DNAFILE = join( '', @DNA); 
## don't understand this line ... can you explain this?

$DNAFILE =~ s/\s//g;  # Remove whitespace, ok

if ( $DNAFILE =~ /$motif/ ) {
     print "\nI found it!\n";
      
       # Count number of nt between two motifs
 
my $string ="@DNA"; # same question, explain please, why do you need t
+his?
 ## mmmh... are you trying to say "\@DNA"?

     say "Lengths are:", $_ for map { sprintf("%d", length) } split /$
+motif/, $string;

# Count number of motifs

my $count=($string =~ m/$motif/g);

print "Number of motifs: $count.\n\n";

close DNAFILE;

} else { print "The motif: $motif was not found in the file $file.\n"}

} # first else block



__END__

Your turn

(Updated: problem with $warn fixed)