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Uppercase/lowercase comparison of one character per line with awk??

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Top Forums Shell Programming and Scripting Uppercase/lowercase comparison of one character per line with awk??
# 8  
Old 01-07-2010
Hey, ivpz:

a is an array which holds the results of the split operation. It isn't used for anything except that split() requires a place to put the fields it creates. I'm only interested in the return value which indicates how many elements are in the array, which tells me if there are more commas or more periods.

Regarding the errors in the script's output, it may well be related to those lines which should be ignored. You didn't mention any "rogues" in your original post. The code's logic assumes that the file is well-formed, i.e. every line will be used and that they number exactly as required for the number of comparisons to be made.

Could you please provide an example or two of the "rogue" lines which should be ignored? Do they occur between sets of dupes or embedded within them? A minimal data sample with these special cases would help me help you. I assume when you mean that they include letters outside AaCcGgTt that doesn't include the '^F' I'm seeing in your sample data. Is that a form-feed control character in the data or is it a literal caret ("^") followed by a literal upper case eff ("F")?



alister
Last edited by alister; 01-07-2010 at 10:34 AM..
# 9  
Old 01-07-2010
Hi Alister,

I don't think any of those characters cause the error. Many of the lines have them too and the the output results are ok. When I took out those lines with incorrect output and reran them with the script the results were fine. Looking at the lines before I came to realise that there are some lines with no duplication, i.e. they are unique with no . or ,

Correct me if I'm wrong, the last line of your script will always look for duplicate since it is an array statement? Any suggestion how to modify this line?

Below is the example I'm talking about:

Code:
ccCCcc$c$cCC$CC$ccccCc$CCCccccCcccccCCCcCCcCccCccCCCCCCCcCcCCcCCCcccCCCCCC 0 37 0 0 0 32 0 0
ggGGgGGgggGGGGggggGgggggGGGgGGgGggGggGGGGGGGgGgGGgGGGgggGGGGGGg 0 0 35 0 0 0 28 0
,,.$.,..,....,.G,g,T.gG..Gg.,,,........,g,.....,g...,^F. 0 0 3 1 0 0 5 0
,,.$.,..,....,.G,g,T.gG..Gg.,,,........,g,.....,g...,^F. 0 0 3 1 0 0 5 0
,,.$.,..,....,.G,g,T.gG..Gg.,,,........,g,.....,g...,^F. 0 0 3 1 0 0 5 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,...$..,,...,.cgA,,.GG,...........,,,,.G,,.Ng,,.G.,. 1 0 4 0 0 2 2 0
...,.,,,..,c,...$..,,...,.cgA,,.GG,...........,,,,.G,,.Ng,,.G.,. 1 0 4 0 0 2 2 0

If I replaced line 2 of the above example with an empty line, I still got a + but the following lines were then correct:

Code:
ccCCcc$c$cCC$CC$ccccCc$CCCccccCcccccCCCcCCcCccCccCCCCCCCcCcCCcCCCcccCCCCCC 0 37 0 0 0 32 0 0 +
ggGGgGGgggGGGGggggGgggggGGGgGGgGggGggGGGGGGGgGgGGgGGGgggGGGGGGg 0 0 35 0 0 0 28 0 +
 +
,,.$.,..,....,.G,g,T.gG..Gg.,,,........,g,.....,g...,^F. 0 0 3 1 0 0 5 0 -
,,.$.,..,....,.G,g,T.gG..Gg.,,,........,g,.....,g...,^F. 0 0 3 1 0 0 5 0 +
,,.$.,..,....,.G,g,T.gG..Gg.,,,........,g,.....,g...,^F. 0 0 3 1 0 0 5 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,...$..,,...,.cgA,,.GG,...........,,,,.G,,.Ng,,.G.,. 1 0 4 0 0 2 2 0 +
...,.,,,..,c,...$..,,...,.cgA,,.GG,...........,,,,.G,,.Ng,,.G.,. 1 0 4 0 0 2 2 0 +

# 10  
Old 01-07-2010
Code:
$ cat dna.awk 
old0!=$0 { old0=$0; i=2 }

i<=5 {
    while (!($i || $(i+4)) && i<=5)
        i++
    if (i<=5) {
        print $0, ($i>$(i+4) ? "+" : "-")
        i++
        next
    }
}

i==6 && /\.|,/ {
    print $0, (split($0, a, /\./) > split($0, a, /,/) ? "+" : "-")
}

$ cat data
.......GGGG,.G,,G...G.,.T...G.,..,.,,^F, 0 0 8 1 0 0 0 0
.......GGGG,.G,,G...G.,.T...G.,..,.,,^F, 0 0 8 1 0 0 0 0
.......GGGG,.G,,G...G.,.T...G.,..,.,,^F, 0 0 8 1 0 0 0 0
,gc,,cga,g,c,,,,,,, 0 0 0 0 1 3 3 0
,gc,,cga,g,c,,,,,,, 0 0 0 0 1 3 3 0
,gc,,cga,g,c,,,,,,, 0 0 0 0 1 3 3 0
,gc,,cga,g,c,,,,,,, 0 0 0 0 1 3 3 0
ccCCcc$c$cCC$CC$ccccCc$CCCccccCcccccCCCcCCcCccCccCCCCCCCcCcCCcCCCcccCCCCCC 0 37 0 0 0 32 0 0
ggGGgGGgggGGGGggggGgggggGGGgGGgGggGggGGGGGGGgGgGGgGGGgggGGGGGGg 0 0 35 0 0 0 28 0
.....,,..,,...,,......,...cA.c,cC. 1 1 0 0 0 3 0 0
.....,,..,,...,,......,...cA.c,cC. 1 1 0 0 0 3 0 0
.....,,..,,...,,......,...cA.c,cC. 1 1 0 0 0 3 0 0

$ awk -f dna.awk data
.......GGGG,.G,,G...G.,.T...G.,..,.,,^F, 0 0 8 1 0 0 0 0 +
.......GGGG,.G,,G...G.,.T...G.,..,.,,^F, 0 0 8 1 0 0 0 0 +
.......GGGG,.G,,G...G.,.T...G.,..,.,,^F, 0 0 8 1 0 0 0 0 +
,gc,,cga,g,c,,,,,,, 0 0 0 0 1 3 3 0 -
,gc,,cga,g,c,,,,,,, 0 0 0 0 1 3 3 0 -
,gc,,cga,g,c,,,,,,, 0 0 0 0 1 3 3 0 -
,gc,,cga,g,c,,,,,,, 0 0 0 0 1 3 3 0 -
ccCCcc$c$cCC$CC$ccccCc$CCCccccCcccccCCCcCCcCccCccCCCCCCCcCcCCcCCCcccCCCCCC 0 37 0 0 0 32 0 0 +
ggGGgGGgggGGGGggggGgggggGGGgGGgGggGggGGGGGGGgGgGGgGGGgggGGGGGGg 0 0 35 0 0 0 28 0 +
.....,,..,,...,,......,...cA.c,cC. 1 1 0 0 0 3 0 0 +
.....,,..,,...,,......,...cA.c,cC. 1 1 0 0 0 3 0 0 -
.....,,..,,...,,......,...cA.c,cC. 1 1 0 0 0 3 0 0 +

# 11  
Old 01-08-2010
Hi Alister,

Thanks for the modified script. The errors are not corrected but some of the lines got deleted. When I ran it on my data of about 4.5million lines, nearly 3000 got deleted. However, I managed to correct the bug by removing the back slash in the last 2 lines and everything looks fine now:

Code:
i==6 && /\.|,/ {
    print $0, (split($0, a, /\./) > split($0, a, /,/) ? "+" : "-")

to:

Code:
i==6 && /.|,/ {
    print $0, (split($0, a, /./) > split($0, a, /,/) ? "+" : "-")

Once again, thank you for your help. Took me nearly a week to get this done.
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