HI,
I have a file with sequences each sequence is 200 pb long and I have 30K
lines
ATGGATAGATA\n
TTCGATTCATT\n
GCCTAGACAT\n
TTGCATAGACTA\n
I want to calculate the AT ratio of each base based on their position
(3/4) for the 1st position, 3/4 on the second, (0/4) on the 3rd...
I am beginner so please excuse my perl thinking!
my plan was to put everything in arrays, split on the digit and then
for each line put the 1st digit in another array,
my $fh ="./txt" ;
unless (open(REGIONS, $fh)){
print "Cannot open file \n";
}
my @list = <REGIONS>;
close REGIONS;
foreach my $line (@list){
chomp $line;
my @pb = split(/\d/, $line);
my @position = $pb[0]; for the fisrt position
$line++;
do that in a loop 200 times ( as we have 200 pb per sequence) which will
create 200 arrays with 30K digits in them. I would need an array of all
arrays at that point???
from them use a condition loop assessing the A or T compo for each
array in the big array , count them with a counter and divide by the
size of each array.
Could you please help me with this?
Thanks
Nat
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