I would really appreciate some help with manipulating a file.
Here is my input file:
Here is the output I need:
I don't really care about the order. Just need to have two columns where the first one is the columns of SNP_... and the second one is the z-score.
The first problem is that the z-score column is shifted down by one. Every 4th column is empty. Then I don't need every 3rd and 4th column, I need columns 1,2, 5,6, 9,10etc.
So, first I've tried to create 2 files with every 5th and 6th columns:
the file with every 5th column (starting with the 1st):
the file with every 6th column (starting with 2nd):
then outfile1 will look like this:
outfile2 will look like this:
then I am thinking to delete the first line of outfile2:
then I will print all columns in one for each file:
and, finally, I combine the two files:
The problem is that the for loop with cut doesn't work. For some reason it keeps on complaining that there is illegal list value:
Any ideas how to solve this?
Many thanks for your time in advance!
---------- Post updated at 09:21 PM ---------- Previous update was at 06:36 PM ----------
it seems that the for loop with cut should look rather like this:
The problem is that is overwrites the columns and I end up having just the last column in my outfiles. Perhaps I should output into an array?
---------- Post updated at 09:54 PM ---------- Previous update was at 09:21 PM ----------
OK, I was able to make the initial file to work with like this:
and then I can get my output using these commands:
the output looked like this:
Many thanks for your time!
Last edited by Don Cragun; 10-06-2013 at 12:08 AM..
Reason: Changed lots of HTML and ICODE tags to CODE tags.
The immediately obvious problem is that the string i is not a numeric value. Try changing:
to:
I would also guess that you meant to have the single file infile as an input file instead of the two files in and file. If that is correct, what you probably wanted is:
You have a few lines like this with different output files. They all need to be fixed.
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