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Top Forums Shell Programming and Scripting Counting characters at each position Post 302768189 by amits22 on Friday 8th of February 2013 06:18:11 AM
Old 02-08-2013
Counting characters at each position

Hi All, here's a question from newbie

I have a data like this, which set of small DNA sequences separated by new line

HTML Code:
GAATCCGGAAACAGCAACTTCAAANCA
GTNATTCGGGCCAAACTGTCGAA
TTNGGCAACTGTTAGAGCTCATGCGACA
CCTGCTAAACGAGTTCGAGTTGAANGA
TTNCGGAAGTGGTCGCTGGCACGG
ACNTGCATGTACGGAGTGACGAAACC
I usually have to count frequency of each character in whole data, which I do with
Code:
awk -F "" '{ for ( i=1; i<=NF; i++) freq[$i]++} END {for (a in freq) print a, freq[a]}'

Now I am almost clueless when I need to count frequency of characters at each position, I am trying to present example with subset of data below
HTML Code:
GAATCCGGAAACAGCAACTTCAAANCA
GTNATTCGGGCCAAACTGTCGAA
TTNGGCAACTGTTAGAGCTCATGCGACA
CCTGCTAAACGAGTTCGAGTTGAANGA
TTNCGGAAGTGGTCGCTGGCACGG
         
1st position G = 1
T = 2
C =1
 A =1 
2nd position 
T=3
C=2 
so on
Any ideas, help is most appreciated. Please tell me if I am not clearly stating the problem.

Thank you,

Amit
 

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HTML::Filter(3) 					User Contributed Perl Documentation					   HTML::Filter(3)

NAME
HTML::Filter - Filter HTML text through the parser NOTE
This module is deprecated. The "HTML::Parser" now provides the functionally of "HTML::Filter" much more efficiently with the the "default" handler. SYNOPSIS
require HTML::Filter; $p = HTML::Filter->new->parse_file("index.html"); DESCRIPTION
"HTML::Filter" is an HTML parser that by default prints the original text of each HTML element (a slow version of cat(1) basically). The callback methods may be overridden to modify the filtering for some HTML elements and you can override output() method which is called to print the HTML text. "HTML::Filter" is a subclass of "HTML::Parser". This means that the document should be given to the parser by calling the $p->parse() or $p->parse_file() methods. EXAMPLES
The first example is a filter that will remove all comments from an HTML file. This is achieved by simply overriding the comment method to do nothing. package CommentStripper; require HTML::Filter; @ISA=qw(HTML::Filter); sub comment { } # ignore comments The second example shows a filter that will remove any <TABLE>s found in the HTML file. We specialize the start() and end() methods to count table tags and then make output not happen when inside a table. package TableStripper; require HTML::Filter; @ISA=qw(HTML::Filter); sub start { my $self = shift; $self->{table_seen}++ if $_[0] eq "table"; $self->SUPER::start(@_); } sub end { my $self = shift; $self->SUPER::end(@_); $self->{table_seen}-- if $_[0] eq "table"; } sub output { my $self = shift; unless ($self->{table_seen}) { $self->SUPER::output(@_); } } If you want to collect the parsed text internally you might want to do something like this: package FilterIntoString; require HTML::Filter; @ISA=qw(HTML::Filter); sub output { push(@{$_[0]->{fhtml}}, $_[1]) } sub filtered_html { join("", @{$_[0]->{fhtml}}) } SEE ALSO
HTML::Parser COPYRIGHT
Copyright 1997-1999 Gisle Aas. This library is free software; you can redistribute it and/or modify it under the same terms as Perl itself. perl v5.16.3 2013-03-25 HTML::Filter(3)
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