"200 pb" -- does pb mean petabytes?
If so, those aren't going to fit in memory; you're going to have to read the
file line by line, accumulating totals and ratios as you go.
J
--
John Francini <franc...@mac.com>
"I have come to the conclusion that one useless man is called a disgrace; that
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On May 13, 2011, at 11:46, Nathalie Conte <n...@sanger.ac.uk> wrote:
> 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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