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# 1  
Old 10-05-2013
Loop question
Hi,

I would really appreciate some help with manipulating a file.
Here is my input file:

Code:
SNP_1	:	        1		SNP_11	:	        1
SNP_2	-0.12	        1		SNP_12	-0.3472	1
SNP_3	-0.708	1		SNP_13	0.5037	1
SNP_4	1.492	        0.5		SNP_14	-0.0685	1
SNP_5	1.27	        0.5		SNP_15	0.547	        1
SNP_6	1.832	        1		SNP_16	0.538	        0.5
SNP_7	-0.882	0.5		SNP_17	-1.0781	1
SNP_8	1.047	        0.5		SNP_18	-0.1406	1
SNP_9	1.201	        0.5		SNP_19	-0.3987	1
SNP_10	0.877	        1		SNP_20	0.2784	1
	        0.683				                0.4642

Here is the output I need:

Code:
SNP_1 -0.12
SNP_2 -0.708
SNP_3 1.492
SNP_4 1.27
etc
SNP_11 -0.3472
SNP_12 0.5037
etc

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):
Code:
for((i=1;i<=7;i+4));
do
cut -f i in file > outfile1
done

the file with every 6th column (starting with 2nd):
Code:
for((i=2;i<=7;i+4));
do
cut -f i in file > outfile2
done

then outfile1 will look like this:

Code:
SNP_1	SNP_11
SNP_2	SNP_12
SNP_3	SNP_13
SNP_4	SNP_14
SNP_5	SNP_15
SNP_6	SNP_16
SNP_7	SNP_17
SNP_8	SNP_18
SNP_9	SNP_19
SNP_10	SNP_20

outfile2 will look like this:
Code:
:	         :
-0.12  	-0.3472
-0.708	0.5037
1.492 	-0.0685
1.27	        0.547
1.832	        0.538
-0.882	-1.0781
1.047	        -0.1406
1.201  	-0.3987
0.877	         0.2784
0.683	         0.4642

then I am thinking to delete the first line of outfile2:

Code:
sed '1d' outfile2 > outfile3

then I will print all columns in one for each file:

Code:
(cat outfile1) | xargs -n 1 > outfile4

(cat outfile3) | xargs -n 1 > outfile5

and, finally, I combine the two files:

Code:
paste outfile4 outfile5 > result

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:

Code:
cut: [-cf] list: 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:

Code:
for((i=1;i<=11;i+=4)); do cut -f$i infile > outfile1; done
for((i=2;i<=11;i+=4)); do cut -f$i infile > outfile2; done

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:

Code:
SNP_4981	-0.682	1		SNP_4991	0.688	1
SNP_4982	-1.884	0.5		SNP_4992	-0.242	0.5
SNP_4983	-0.151	0.5		SNP_4993	0.768	0.5
SNP_4984	-2.069	0.5		SNP_4994	0.992	1
SNP_4985	0.596	1		SNP_4995	0.646	0.5
SNP_4986	-1.654	0.5		SNP_4996	-1.663	0.5
SNP_4987	1.718	0.5		SNP_4997	-0.367	0.5
SNP_4988	-2.137	0.5		SNP_4998	-1.328	0.5
SNP_4989	-1.573	0.5		SNP_4999	0.509	1
SNP_4990	-2.563	0.5		SNP_5000	-1.231	0.5

and then I can get my output using these commands:

Code:
awk '{for(i=2;i<=NF;i+=3){print $i}}' test > test2
awk '{for(i=1;i<=NF;i+=3){print $i}}' test > test1
paste test1 test2 > result

the output looked like this:

Code:
SNP_4981        -0.682
SNP_4991        0.688
SNP_4982        -1.884
SNP_4992        -0.242
SNP_4983        -0.151
SNP_4993        0.768
SNP_4984        -2.069
SNP_4994        0.992
SNP_4985        0.596
SNP_4995        0.646
SNP_4986        -1.654
SNP_4996        -1.663
SNP_4987        1.718
SNP_4997        -0.367
SNP_4988        -2.137
SNP_4998        -1.328
SNP_4989        -1.573
SNP_4999        0.509
SNP_4990        -2.563
SNP_5000        -1.231

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.
# 2  
Old 10-06-2013
The immediately obvious problem is that the string i is not a numeric value. Try changing:
Code:
cut -f i in file > outfile2

to:
Code:
cut -f $i in file > outfile2

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:
Code:
cut -f $i infile > outfile2

You have a few lines like this with different output files. They all need to be fixed.
# 3  
Old 10-06-2013
Code:
awk '{
	if (NR==1) F=NF;
	else { n=0;
		for (i=1;i<=NF;i++)
			if (NF!=F) print a[++n] " " $i;
			else if ((i-2)%3==0) print  a[++n] " " $i;
	} n=0;
	for (i=1;i<=NF;i++)
		if ((i-1)%3==0) a[++n]=$i;
}' file

# 4  
Old 10-06-2013
Thank you for the comments and suggestions!
 
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