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Full Discussion: Uppercase/lowercase comparison of one character per line with awk??
Top Forums Shell Programming and Scripting Uppercase/lowercase comparison of one character per line with awk?? Post 302385062 by ivpz on Thursday 7th of January 2010 04:27:05 AM
Old 01-07-2010
Quote:
Originally Posted by durden_tyler
Why column 5 ? If A, C, G, T are in columns 2, 3, 4, 5, then shouldn't "a" be in column 6 ?
Sorry, my mistake. Yes, it should be column 6.


Quote:
Originally Posted by durden_tyler
... Hence, shouldn't line 8 be followed by "-" because count of uppercase characters < count of lowercase characters ?
Each Uppercase A should be compared with the lowercase a only; in essence:

compare col2 and col6; if col2>col6, add + else - to a new col. If both col2 and col6 are 0 then compare col3 and col7 ...

---------- Post updated at 04:27 AM ---------- Previous update was at 04:20 AM ----------

Alister, thanks for your help. Can I ask you, what is the function of a, in the last line of the script?

Quote:
Originally Posted by alister

Code:
$ cat dna.awk 
{
    for (i=2; i<=5; i++) {
        if ($i || $(i+4)) {
            print $0, ($i>$(i+4) ? "+" : "-")
            getline
        }
    }
    print $0, (split($0, a, /\./) > split($0, a, /,/) ? "+" : "-")
}

Also, when I ran this script, most of the comparisons seems to be correct but I got a few which are obviously incorrect and one extra line was added at the end:

Code:
,,.$.,..,....,.G,g,T.gG..Gg.,,,........,g,.....,g...,^F. 0 0 3 1 0 0 5 0 +
,,.$.,..,....,.G,g,T.gG..Gg.,,,........,g,.....,g...,^F. 0 0 3 1 0 0 5 0 +
,,.$.,..,....,.G,g,T.gG..Gg.,,,........,g,.....,g...,^F. 0 0 3 1 0 0 5 0 -

should be
,,.$.,..,....,.G,g,T.gG..Gg.,,,........,g,.....,g...,^F. 0 0 3 1 0 0 5 0 -
,,.$.,..,....,.G,g,T.gG..Gg.,,,........,g,.....,g...,^F. 0 0 3 1 0 0 5 0 +
,,.$.,..,....,.G,g,T.gG..Gg.,,,........,g,.....,g...,^F. 0 0 3 1 0 0 5 0 +

Another example:
Code:
...,.,,,..,c,...$..,,...,.cgA,,.GG,...........,,,,.G,,.Ng,,.G.,. 1 0 4 0 0 2 2 0 +
...,.,,,..,c,...$..,,...,.cgA,,.GG,...........,,,,.G,,.Ng,,.G.,. 1 0 4 0 0 2 2 0 +
...,.,,,..,c,...$..,,...,.cgA,,.GG,...........,,,,.G,,.Ng,,.G.,. 1 0 4 0 0 2 2 0 -
...,.,,,..,c,...$..,,...,.cgA,,.GG,...........,,,,.G,,.Ng,,.G.,. 1 0 4 0 0 2 2 0 +

should be:
...,.,,,..,c,...$..,,...,.cgA,,.GG,...........,,,,.G,,.Ng,,.G.,. 1 0 4 0 0 2 2 0 +
...,.,,,..,c,...$..,,...,.cgA,,.GG,...........,,,,.G,,.Ng,,.G.,. 1 0 4 0 0 2 2 0 -
...,.,,,..,c,...$..,,...,.cgA,,.GG,...........,,,,.G,,.Ng,,.G.,. 1 0 4 0 0 2 2 0 +
...,.,,,..,c,...$..,,...,.cgA,,.GG,...........,,,,.G,,.Ng,,.G.,. 1 0 4 0 0 2 2 0 +

Although some of the lines contains characters other than the 4 ACGT, they should be ignored.
Last edited by ivpz; 01-07-2010 at 05:25 AM..
 

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