Problem With Awk Printing

Question

[RandManP]

Hi All, I would like to put "N" instead of those numbers which are less than 0.04 but keep 0. so:

0         0.1    9     0.004      98
23        2      89    0.002      9
0.001     0.03   45    9          10

awk '{for(i=1; i<=5; i++) {if ($i==0 || $i>0.04) print $i; else print "N"; }}' in.txt > out.txt

the output is correct but it will be printed in one column not in 5 columns like in.file. Thank you so much

[Neilfws]

Please indicate relevance of this question to a bioinformatics research problem.

[RandManP]

I want to make a cutoff (RNA-seq data). Also it is only an example not real data. I want to know how I can manipulate the data

[Raygozak]

"print" always adds a new line by default

[Anthony Mathelier]

That is why you need to use printf here as I did in my following answer.

Answer 1

[Anthony Mathelier]

With awk, you can do the following (just need to tune up the printf to get what you want):

awk '{for(i=1; i<=4; i++) {if($i==0 || $i>0.04) printf("%f\t", $i); else printf("N\t");} if($5==0 || $5>0.04) print $5; else print "N";}' eggs

Answer 2

[Neilfws]

Can't help you with awk, but here's a solution in R, assuming file is tab-delimited:

# read file
mydata <- read.table("in.txt", sep = "\t", header = F)
# transform values
mydata.t <- as.data.frame(sapply(mydata, function(x) ifelse(x < 0.04 & x > 0, "N", x)))

Result:

  V1  V2 V3 V4 V5
1  0 0.1  9  N 98
2 23   2 89  N  9
3  N   N 45  9 10

Can write back to a tab-delimited file using:

write.table(mydata.t, "out.txt", row.names = F, col.names = F, quote = F, sep = "\t")

[RandManP]

thank you so much :)

Answer 3

[RandManP]

thanks, very helpful