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Top Forums Shell Programming and Scripting Count specific characters at specific column positions Post 302739575 by thienxho on Tuesday 4th of December 2012 12:06:27 PM
Old 12-04-2012
Count specific characters at specific column positions

Hi all, I need help.

I have an input text file (input.txt) like this:

Code:
21	GTGCAACACCGTCTTGAGAGG	50
21	GACCGAGACAGAATGAAAATC	73
21	CGGGTCTGTAGTAGCAAACGC	108
21	CGAAAAATGAACCCCTTTATC	220
21	CGTGATCCTGTTGAAGGGTCG	259

Now I need to count A/T/G/C numbers at each character location in column 2, in this case is always 21 characters, but can be variable.

Output (output.txt) will need to be:

Code:
A	0	1	1	1	3	3	1	2	0	3	1	1	2	1	1	2	3	2	3	0	0
T	0	0	1	0	1	1	1	1	2	0	1	2	0	1	0	1	1	1	1	2	0
G	2	3	2	2	1	0	1	1	1	1	3	0	1	1	1	2	1	2	0	2	2
C	3	0	1	2	0	1	2	1	2	1	0	1	2	1	2	0	0	0	1	1	3

I can do this in Excel, but my file is way bigger than Excel can handle.

Thanks!

Last edited by Scott; 12-04-2012 at 01:07 PM.. Reason: Please use code tags
 

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Devel::Refcount(3pm)					User Contributed Perl Documentation				      Devel::Refcount(3pm)

NAME
"Devel::Refcount" - obtain the REFCNT value of a referent SYNOPSIS
use Devel::Refcount qw( refcount ); my $anon = []; print "Anon ARRAY $anon has " . refcount($anon) . " reference "; my $otherref = $anon; print "Anon ARRAY $anon now has " . refcount($anon) . " references "; DESCRIPTION
This module provides a single function which obtains the reference count of the object being pointed to by the passed reference value. FUNCTIONS
$count = refcount($ref) Returns the reference count of the object being pointed to by $ref. COMPARISON WITH SvREFCNT This function differs from "Devel::Peek::SvREFCNT" in that SvREFCNT() gives the reference count of the SV object itself that it is passed, whereas refcount() gives the count of the object being pointed to. This allows it to give the count of any referent (i.e. ARRAY, HASH, CODE, GLOB and Regexp types) as well. Consider the following example program: use Devel::Peek qw( SvREFCNT ); use Devel::Refcount qw( refcount ); sub printcount { my $name = shift; printf "%30s has SvREFCNT=%d, refcount=%d ", $name, SvREFCNT($_[0]), refcount($_[0]); } my $var = []; printcount 'Initially, $var', $var; my $othervar = $var; printcount 'Before CODE ref, $var', $var; printcount '$othervar', $othervar; my $code = sub { undef $var }; printcount 'After CODE ref, $var', $var; printcount '$othervar', $othervar; This produces the output Initially, $var has SvREFCNT=1, refcount=1 Before CODE ref, $var has SvREFCNT=1, refcount=2 $othervar has SvREFCNT=1, refcount=2 After CODE ref, $var has SvREFCNT=2, refcount=2 $othervar has SvREFCNT=1, refcount=2 Here, we see that SvREFCNT() counts the number of references to the SV object passed in as the scalar value - the $var or $othervar respectively, whereas refcount() counts the number of reference values that point to the referent object - the anonymous ARRAY in this case. Before the CODE reference is constructed, both $var and $othervar have SvREFCNT() of 1, as they exist only in the current lexical pad. The anonymous ARRAY has a refcount() of 2, because both $var and $othervar store a reference to it. After the CODE reference is constructed, the $var variable now has an SvREFCNT() of 2, because it also appears in the lexical pad for the new anonymous CODE block. PURE-PERL FALLBACK An XS implementation of this function is provided, and is used by default. If the XS library cannot be loaded, a fallback implementation in pure perl using the "B" module is used instead. This will behave identically, but is much slower. Rate pp xs pp 225985/s -- -66% xs 669570/s 196% -- SEE ALSO
o Test::Refcount - assert reference counts on objects AUTHOR
Paul Evans <leonerd@leonerd.org.uk> perl v5.14.2 2011-11-15 Devel::Refcount(3pm)
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