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Problem with my loop and awk script

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Operating Systems Linux Problem with my loop and awk script
# 1  
Old 08-18-2014
Problem with my loop and awk script
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
Last edited by Franklin52; 08-18-2014 at 11:08 AM.. Reason: Please use code tags
# 2  
Old 08-18-2014
This line seems wrong
Code:
for sample in `listofsamples.txt`

The back ticks imply that listofsamples.txt is a command. It seems you want
to process the contents of listofsamples.txt. This would make more sense
Code:
for sample in `cat listofsamples.txt`

but I am not sure that is what you really need. What is in the file awktestfile.txt?
# 3  
Old 08-18-2014
Thanks blackrageous. The awktestfile.txt is the data file I am trying to analyse.
Last edited by rbatte1; 08-19-2014 at 01:39 PM..
# 4  
Old 08-18-2014
For the sample input shown, what output are you hoping to produce?

Are all lines for a given Sample/Chr pair on adjacent lines in your input file? And, if not, how big are your input files?
# 5  
Old 08-19-2014
Thanks Don, I have a single data file which simply lists all base pairs for all chromosomes for the samples one under the other, so the file is quite large (there are over 3000 samples). Ideally I would like to output for each sample, the max and min bp for each chromosome eg.
Code:
Sample1	1	49598178	49598209
Sample1	2	49974371	50003025

From this I think I should be able to continue my analysis.

Thanks
Last edited by Franklin52; 08-19-2014 at 05:58 AM.. Reason: Fixed code tags
# 6  
Old 08-19-2014
Try
Code:
awk     'NR==1          {next}
                        {samchr=$1" "$2}
         samchr != osc  {print osc, MIN, MAX, (MAX-MIN)/10000; osc=samchr; MIN=1E24; MAX=-1E24}
         $3 > MAX       {MAX = $3}
         $3 < MIN       {MIN = $3}
         END            {print samchr, MIN, MAX, (MAX-MIN)/10000}
        ' file
Sample1 1 49598178 49598209 0.0031
Sample1 2 49974371 50003025 2.8654

# 7  
Old 08-19-2014
Thanks RudiC, that's amazing. I seem to always over complicate it.
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