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Top Forums Shell Programming and Scripting Counting characters vertically Post 302629309 by Corona688 on Tuesday 24th of April 2012 01:04:13 PM
Old 04-24-2012
'best' as always is a thing open to interpretation. Here's one way:

Code:
$ cat vpos.awk

BEGIN { split("A T C G -", T); }

/^>/ { next }

{
        if((!LMAX) || (LMAX<length($0))) LMAX=length($0);
        for(N=1; N<=length($0); N++)    A[N,substr($0,N,1)]++;
}

END {   for(N=1; N<=LMAX; N++)
        {
                printf("%d", N);
                for(M=1; T[M]; M++)     printf("\t%s=%d", T[M], A[N,T[M]]);
                printf("\n");
        }
}

$ awk -f vpos.awk data

1       A=1     T=1     C=0     G=0     -=1
2       A=0     T=2     C=1     G=0     -=0
3       A=1     T=0     C=0     G=2     -=0
4       A=0     T=1     C=2     G=0     -=0
5       A=0     T=1     C=0     G=2     -=0
6       A=0     T=0     C=1     G=2     -=0

$

 

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IGAWK(1)							 Utility Commands							  IGAWK(1)

NAME
igawk - gawk with include files SYNOPSIS
igawk [ all gawk options ] -f program-file [ -- ] file ... igawk [ all gawk options ] [ -- ] program-text file ... DESCRIPTION
Igawk is a simple shell script that adds the ability to have ``include files'' to gawk(1). AWK programs for igawk are the same as for gawk, except that, in addition, you may have lines like @include getopt.awk in your program to include the file getopt.awk from either the current directory or one of the other directories in the search path. OPTIONS
See gawk(1) for a full description of the AWK language and the options that gawk supports. EXAMPLES
cat << EOF > test.awk @include getopt.awk BEGIN { while (getopt(ARGC, ARGV, "am:q") != -1) ... } EOF igawk -f test.awk SEE ALSO
gawk(1) Effective AWK Programming, Edition 1.0, published by the Free Software Foundation, 1995. AUTHOR
Arnold Robbins (arnold@skeeve.com). ATTRIBUTES
See attributes(5) for descriptions of the following attributes: +--------------------+-----------------+ | ATTRIBUTE TYPE | ATTRIBUTE VALUE | +--------------------+-----------------+ |Availability | SUNWgawk | +--------------------+-----------------+ |Interface Stability | Volatile | +--------------------+-----------------+ NOTES
Source for gawk is available on http://opensolaris.org. Free Software Foundation Nov 3 1999 IGAWK(1)
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