loop help

[tsbatth]

hi im writing this code to determine number of start codons after but I keep getting an error, this is the following code

RNAseq = split('', $RNA);
$nstart = 0; #number of start codons
$start = 'AUG';
for ($i=0; $i<$mlength -2; $i ++)
{
@codon = @RNAseq[$i, $i+1, $i+2];
$cod = join('', @codon);
if ($cod eq $start)
{
$start[$nstart]= $i;
$nstart ++;
}
}
print "\n Number of start codons is: $nstart";

I get an error saying name "Main:mlength" used only once and a possible typo at that line. Any help please?

 

[travs69]

yeah.. mlength was used only once. It isn't established anywhere.

~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Travis - Those who say it cannot be done are usually interrupted by someone else doing it; Give the wrong symptoms, get the wrong solutions;

 

[tsbatth]

how do i establish it?

 

[travs69]

well.. I don't really understand what your trying to do. Apparently you want to loop while $i < $mlength. Here do you plan on getting this mlength value from?

~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Travis - Those who say it cannot be done are usually interrupted by someone else doing it; Give the wrong symptoms, get the wrong solutions;

 

[tsbatth]

i am trying to find the start codon in a sequence, the start codon is a 3 letter sequence from rna 'AUG', i dont understand this mlength part, i got this piece of code from somewhere else. My guess would be that its supposed to be position of start codon?

 

[travs69]

So your just trying to see how many times AUG shows up in @RNAseq?

~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Travis - Those who say it cannot be done are usually interrupted by someone else doing it; Give the wrong symptoms, get the wrong solutions;

 

[tsbatth]

yea

 

[travs69]

$count = grep /AUG/, @RNAseq;
print "$count\n";

~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Travis - Those who say it cannot be done are usually interrupted by someone else doing it; Give the wrong symptoms, get the wrong solutions;

 

[tsbatth]

thanks, but i have to do it this way so i can get the position of the start codon, anyway i can make this work?

 

[tsbatth]

i set $mlength = @RNAseq but after it gives me the number of start codons, the program freezes well dos freezes and nothing more, i have to restart dos

 

[rharsh]

I think it's a fair assumption that most the people here don't know much about DNA/RNA sequences, or at least I don't.

If this isn't what you're looking for you might want to explain what you want with a more specific example.

use warnings;
use strict;

my $rna = 'GUCCAUGACUAGA';
my $start = 'AUG';
my $nstart;

if ($rna =~ m/^(.*?)$start/) {
	$nstart = length $1;
	print "Number of start codons is: $nstart\n";
} else {
	print "$start not found.\n";
}

Also, I'm not sure if 'AUG' is supposed to be included or not. In the example above, would you expect 4 or 7 to be printed? If $start is supposed to be included, move the right paren to the other side of $start.