On 12/12/2007, Auxence Sima <[EMAIL PROTECTED]> wrote:
>
> Hi everyone.
> I d like to have u guys input about my code. Im writing a perl script
> that would generate some primers. my input file calles " output.txt ) was
> generated from primer3.
> if u guys can take a look at my script and tell me what u detect that
> needs to be correcte/ or something that i missed to include. hope to hear
> from u all.
>
>
>
> #! /usr/bin/perl- w
> #programpro.pl
> use strict;
> use primer3;
>
> # initialize variables
>
> my %sequences;
> my $key;
> my $file = "output.txt";
>
> # Read a primer3 output file
>
> my $primer3 = primer3-> new ( -file=>"data/output.txt");
> # iterate over sequences
%sequences has no keys at this stage. You've declared %sequences but haven't
assigned anything to it so this loop will not happen.
Foreach should be foreach, perl is case senitive. You can declare my $key
here and drop it from above keeping it's scope within the block.
foreach my $key (keys %sequences) {
Foreach $key (keys (%sequences)) {
>
> # Search for primers
You've already declared $primer above. Are these meant to be separate
variables?
my $primer = primer3=>new ($key,
> $sequences {$key};
> print "$key\nLeft\t\t\tRight\n";
> while ($primer=>getNextpair ( )) {
> print $primer=> LeftOligo ( ) . "\t" .
> $primer=>RightOligo( ) . "\n" ;
> }
> Print "\n";
>
> }
I am not sure if it's you mail client but the are too many capitalised
words in what you have shown. What happens if you run it? I imagine that
with the perl -w you would get lots of warnings and errors.
