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split up FASTA into array....perl...any suggestions please?

P: 1
Okay,ive been working on this for a long time now and i cant seem to figure a way to make this code work.

I simply need to split a FASTA file that has no spaces into one with spoaces so i can input it into an array where i can read each character individually. I also have to shuffle the array but i cant even shuffle if i cant split the .txt file which contains the FASTA sequence.

Am i overlooking some small error here or is this just impossible?Below is where is a snippet of where i think the error is. thanks.

open (FILE, "sequencetoo.txt");
$data_file = "sequencetoo.txt";


$oldSequence = <FILE>;
chomp ($oldSequence);

@newSequence = split(//, $oldSequence);
close (FILE);

.....END CODE]
Mar 29 '10 #1
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