perl: simple one line replacement, simple error message!

pwd_pwd_omg_pwd · 11-18-2008, 05:24 AM

Just been trying out some simple perl to get me started, straight from a book and i keep getting back a syntax error back for the replacement line in:

Code:

sub translate {
	my ($mrna) = @_;
	my $pro = " ";
	while ($mrna =~s/(...)//){
		$pro = $pro . $codonMap{$1};
	}
	return $pro;
}

in the book ive got it shows the ~ as superscript but ive been assured that that key doesnt exist so not sure why it doesnt like it.

taylor_venable · 11-18-2008, 06:20 AM

Seeing the complete regex used in the substitution, along with the kinds of input the function is expected to take and the expected output, might help.

Telemachos · 11-18-2008, 07:33 AM

It wouldn't hurt to post the actual error message. As a general tip, try running the script with use diagnostics; in effect. You can put that up at the top of your script instead of use warnings; - it will give you more verbose error messages. Or you can run the script this way:

Code:

perl -Mdiagnostics script_name

chrism01 · 11-18-2008, 05:44 PM

Always use

use strict;
use warnings;

at the top of your programs it'll help a lot. BTW, an alternate for 'use warnings;' is to use the -w switch as in

#!/usr/bin/perl -w

as the first line of your code (adjust to match your env).
In this case,

use diagnostics;

as well is good for debugging. Showing us the exact error msg and the input data would really help.

pwd_pwd_omg_pwd · 11-19-2008, 08:55 AM

The error message reads as this:

Code:

syntax error at transprog.pl line 18, near "while ($mrna ~=s/("
  (Might be a runaway multi-line // string starting on line 10)
Global symbol "$pro" requires explicit package name at transprog.pl line 18.Global symbol "$pro" requires explicit package name at transprog.pl line 18.Execution of transprog.pl aborted due to compilation errors.

and it is still saying it after I have changed the replacement line, which i thought was the whole problem. the use warnings didnt say anything new than it was before and the -Mdiagnostics said: its probably a syntax error.

The script has a few other parts and subs to it, but essentially this sub will take an inputed mRNA seq AGCUAGUCGCUGCAGUCUGCAUGC... and look up each 3 letters to a data set at the end of the format:

Ala GCU, GCC, GCA, GCG
Leu UUA, UUG, CUU, CUC, CUA, CUG
Arg CGU, CGC, CGA, CGG, AGA, AGG
Lys AAA, AAG
etc.
and list the amino acids.
AlaLeuArgLys...

The first part of the code reads:

Quote:

#!/usr/bin/perl
use strict;
use diagnostics;
my %codonMap;

## translates DNA strings to RNA
sub transcribe {
my ($dna) = @_;
my $rna = scalar reverse $dna;
$rna =~tr/ACGT/UGCA; ##10
return $rna;
}

## translates mRNA strings to proteins
sub translate {
my ($mrna) = @_;
my $pro = " ";
while ($rna ~=s/(...)//){ ##18
$pro = $pro . $codonMap{$1};
}
return $pro;
}

(10 and 18 are the lines it mentions in the error btw)

thanks for the help guys.

Sergei Steshenko · 11-19-2008, 11:49 AM

Quote:

Originally Posted by pwd_pwd_omg_pwd

The error message reads as this:

Code:

syntax error at transprog.pl line 18, near "while ($mrna ~=s/("
  (Might be a runaway multi-line // string starting on line 10)
Global symbol "$pro" requires explicit package name at transprog.pl line 18.Global symbol "$pro" requires explicit package name at transprog.pl line 18.Execution of transprog.pl aborted due to compilation errors.

and it is still saying it after I have changed the replacement line, which i thought was the whole problem. the use warnings didnt say anything new than it was before and the -Mdiagnostics said: its probably a syntax error.

The script has a few other parts and subs to it, but essentially this sub will take an inputed mRNA seq AGCUAGUCGCUGCAGUCUGCAUGC... and look up each 3 letters to a data set at the end of the format:

Ala GCU, GCC, GCA, GCG
Leu UUA, UUG, CUU, CUC, CUA, CUG
Arg CGU, CGC, CGA, CGG, AGA, AGG
Lys AAA, AAG
etc.
and list the amino acids.
AlaLeuArgLys...

The first part of the code reads:

(10 and 18 are the lines it mentions in the error btw)

thanks for the help guys.

Try to make our lives easier - post the code processed by 'cat -n', so we'll be able to see line numbers and related them to the ones in error messages.

Sergei Steshenko · 11-19-2008, 11:53 AM

deleted by Sergei.

Sergei Steshenko · 11-19-2008, 11:57 AM

Quote:

Originally Posted by pwd_pwd_omg_pwd

The error message reads as this:

Code:

syntax error at transprog.pl line 18, near "while ($mrna ~=s/("
  (Might be a runaway multi-line // string starting on line 10)
Global symbol "$pro" requires explicit package name at transprog.pl line 18.Global symbol "$pro" requires explicit package name at transprog.pl line 18.Execution of transprog.pl aborted due to compilation errors.

and it is still saying it after I have changed the replacement line, which i thought was the whole problem. the use warnings didnt say anything new than it was before and the -Mdiagnostics said: its probably a syntax error.

The script has a few other parts and subs to it, but essentially this sub will take an inputed mRNA seq AGCUAGUCGCUGCAGUCUGCAUGC... and look up each 3 letters to a data set at the end of the format:

Ala GCU, GCC, GCA, GCG
Leu UUA, UUG, CUU, CUC, CUA, CUG
Arg CGU, CGC, CGA, CGG, AGA, AGG
Lys AAA, AAG
etc.
and list the amino acids.
AlaLeuArgLys...

The first part of the code reads:

(10 and 18 are the lines it mentions in the error btw)

thanks for the help guys.

You apparently have missing trailing '/' here:

$rna =~tr/ACGT/UGCA;

, i.e. I think it should be

$rna =~tr/ACGT/UGCA/;

Telemachos · 11-19-2008, 12:53 PM

Two other problems that I can see: on line 18 (1) you've written ~= instead of =~ and (2) you're using $rna in a subroutine where it isn't visible. Did you mean $mrna there (from line 16) or did you want $rna to be available to both subroutines?

As a general rule, the line number of the error from Perl is where the error gets caught. You will need to backtrack up from there, since the real problem is (often) somewhere earlier. Here's a quick example:

Code:

#!/usr/bin/perl
use strict;
use warnings;

my $foobar

print "$foobar\n";

The problem is the missing semicolon in line five, but Perl will tell me that the error was caught at the print statement in line 7 (even though the print statement itself is fine).