I made an executable file in terminal and it looks like this.
Code:
echo Enter the name of the file without the .wig extension
read NAME
echo Enter the ratio
read RATIO
awk '{$2*=$RATIO;{print $0}}' ${NAME}.wig > ${NAME}normalized.wig
I have a file with several million lines that look like this
What I am trying to do is ask for a file name, then ask for a ratio to normalize my data by, just a number like 0.5, by multiplying the second column of each line (not including headers) by 0.5 and replace that column with the new value and output that line into the normalized file. At the same time I do not want to do calculations on the headers (variableStep chrom=Uextra span=25), but I still want the headers in the output file. There are several headers which appear on lines much further into the files.
When I run the program it isn't giving me the values I expect, but it is making the new file. When I run the program removing the
echo Enter the ratio
read RATIO
and replacing $RATIO with the actual value I want, like 0.5, I get the values I expect.... but it is doing math on the headers and is removing the tabs and replacing them with spaces. So there are a few problems with my program.
Thanks!
---------- Post updated at 06:16 PM ---------- Previous update was at 05:54 PM ----------
!*!*!UPDATE!*!*!
I was able to fix the problem with the headers being calculated, using this
Code:
echo Enter the name of the file without the .wig extension
read NAME
awk '{if($1 == "variableStep") {print $0} else {$2*=.5952;{print $0}}}' ${NAME}.wig > ${NAME}normalized.wig
but I still can't seem to specify the RATIO variable to get it to multiply the second column by RATIO. I have to edit the program each time with the number I want (.5952)
Here is the final program looking to code anything like this.
Code:
echo Enter the name of the file without the .wig
read NAME
echo the ratio?
read ratio
awk -v ratio=$ratio '{if($1 == "variableStep") {print $0} else {$2*=ratio;{print $0}}}' ${NAME}.wig > ${NAME}normalized.wig
Last edited by Franklin52; 12-01-2011 at 05:30 AM..
Reason: Please use code tags for code and data samples, thank you
You can simplify that a lot by knowing what statements before and after a code block do in awk.
Code:
awk -v ratio=$ratio '$1=="variableStep" { $2 *= ratio } 1
The $1=="variableStep" before the code block tells it to run { $2 *= ratio } only when $1=="variableStep".
The 1 after the code block tells it to print every single line (even when $2 *= ratio isn't run). You could put any logical statement there but we put '1' so it's always true.
I also noticed a problem with my previous program. The data it outputs is correct, but for some reason the new file has fields separated by spaces, not tab. I'm trying to figure out how to take this code.
Code:
echo Enter the name of the file without the .wig
read NAME
echo the ratio?
read ratio
awk -v ratio=$ratio '{if($1 == "variableStep") {print $0} else {$2*=ratio;{print $0}}}' ${NAME}.wig > ${NAME}normalized.wig
and have it make a new file with fields that are tab separated, not space.
---------- Post updated at 02:45 PM ---------- Previous update was at 02:40 PM ----------
@Corona668 I changed the == to != and it seems to be computing everything correctly now, but again its giving me a space separated set of fields and I need them to be tab separated.
I fixed the problem with the space separated fields.
Code:
echo Enter the name of the file without the .wig
read NAME
echo the ratio?
read ratio
awk -v ratio=$ratio '{if($1 == "variableStep") {print $0} else { $2 *= ratio;{print $1 "\t" $2}}}' ${NAME}.wig > ${NAME}normalized.wig
OSX 10.9
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11-29-2011
