On 2011-05-13 17:46, Nathalie Conte wrote:
ATGGATAGATA\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...
perl -MData::Dumper -wle '
my %pos;
my $s = $ARGV[0];
push @{ $pos{ substr $s, $_, 2 } }, $_
On Fri, May 13, 2011 at 11:46, Nathalie Conte wrote:
> 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 po
On 13/05/2011 16:46, Nathalie Conte wrote:
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
Does your data look like this? With 10, 11, or 12 characters per line?
I'm afraid I don't know what a pb is, are yo
Hi Nathalie
I'm absolute newbie in terms of Perl but take into account the use of PDL
that will help you better manage vectors, matrix and number crunch
calculations.
cheers,
Luca
--
---
Luca Cappelletti
http://developerinfodomestic.blogspot.com
"...Together we stand, divided we
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
No, I'm quite sure pb (bp?) stands for base pairs, or nucl
"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
"I have come to the conclusion that one useless man is called a disgrace; that
two are called a law
