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For 2023 (and 2024 ...) - we are now fully retired from IT training.
We have made many, many friends over 25 years of teaching about Python, Tcl, Perl, PHP, Lua, Java, C and C++ - and MySQL, Linux and Solaris/SunOS too. Our training notes are now very much out of date, but due to upward compatability most of our examples remain operational and even relevant ad you are welcome to make us if them "as seen" and at your own risk.

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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.
Sar

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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