Linux

Sorry if this is a super simple issue, but am extremely new to this and am trying to teach myself as I go along. But can someone please help me out?

I have a data file similar to this for many samples, for all chromosomes

Code:

Sample      Chr     bp           p       roh
Sample1	1	49598178	0	1
Sample1	1	49598207	0	1
Sample1	1	49598209	0	1
Sample1	2	49974371	0	1
Sample1	2	49974670	0	1
Sample1	2	49974931	0	1
Sample1	2	50003025	0.000001	1
 etc etc

I would like to determine the maximum and minimum bp for each chromosome for each sample, and then output the distance between the min and max bp for each chromosome for each sample.

As I am super new to all this, and I have noone to help me, I was wondering if someone here could help me out?

I have so far written this:

Code:

for sample in `listofsamples.txt`
do
awk 'chr=$2; for (chr=1; chr<=25; chr++) { 
     NR==1 { min=$3; max=$3; length=0; next } 
           { max < $3 {max=$3} min > $3 {min=$3} } 
     END { roh=(max-min)/1000000; print "sample", "chr", "min", "max", "length"; print $sample, chr, min, max, length }}' awktestfile.txt
done

And I keep getting the thi following syntax error message

Code:

'/file: line 2: syntax error near unexpected token `do
'/file: line 2: `do

I have no idea what it means - please help? Any advice would be greatly appreciated.

Best

V