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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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Excel::Template::Plus::TT(3pm)				User Contributed Perl Documentation			    Excel::Template::Plus::TT(3pm)

NAME
Excel::Template::Plus::TT - Extension of Excel::Template to use TT SYNOPSIS
use Excel::Template::Plus::TT; # this is most commonly used through # the Excel::Template::Plus factory my $template = Excel::Template::Plus::TT->new( template => 'greeting.tmpl', config => { INCLUDE => [ '/templates' ] }, params => { greeting => 'Hello' } ); $template->param(location => 'World'); $template->write_file('greeting.xls'); DESCRIPTION
This is an engine for Excel::Template::Plus which replaces the standard Excel::Template template features with TT. See the Excel::Template::Plus docs for more information. METHODS
Accessors config template template_class params Excel::Template compat methods params ($name | $name = $value)> This provides access to getting and setting the parameters, it behaves exactly like the standard CGI.pm-style param method. output Returns the generated excel file. write_file ($filename) Writes the generated excel file to $filename. Housekeeping DEMOLISH This will cleanup any temp files generated in the process. meta Returns the metaclass. BUGS
All complex software has bugs lurking in it, and this module is no exception. If you find a bug please either email me, or add the bug to cpan-RT. ACKNOWLEDGEMENTS
This module was inspired by Excel::Template::TT. AUTHOR
Stevan Little <stevan@iinteractive.com> COPYRIGHT AND LICENSE
Copyright 2007-2010 by Infinity Interactive, Inc. <http://www.iinteractive.com> This library is free software; you can redistribute it and/or modify it under the same terms as Perl itself. perl v5.14.2 2012-05-06 Excel::Template::Plus::TT(3pm)
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