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sequence file into a numeric file

Posted by sarish (sarish), 23 June 2005
Need some help!!!

I have a DNA sequence file and would like to convert each nucleotide (from the file) into some number (say I assign A=0, T=1, G=2, C=3). It sounds quite simple but since I am new to perl I need some assistance.
It is basically converting a sequence file into a numeric file and having that in a array format. Each cell having a number relating to a nucleotide.

just in case if you have any idea please let me know.

Thanks in advance.

Posted by admin (Graham Ellis), 23 June 2005
open (FH,"input.txt");
read (FH,$all,-s "input.txt");
$all =~ tr /ATGC/0123/;
open (FHO,">output.txt");
print FHO $all;
close FHO;

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