On 13/05/11 17:11, John Francini wrote:
"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>
No, I'm quite sure pb (bp?) stands for base pairs, or nucleotides, the
units of DNA sequences. :)
"I have come to the conclusion that one useless man is called a disgrace; that two
are called a law firm; and that three or more become a Congress. And by God I have had
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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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