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Operating Systems Linux Problem with my loop and awk script Post 302913533 by vuvuzelo on Monday 18th of August 2014 09:30:54 AM
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
 

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mlib_ImageExtrema2(3MLIB)				    mediaLib Library Functions					 mlib_ImageExtrema2(3MLIB)

NAME
mlib_ImageExtrema2, mlib_ImageExtrema2_Fp - image extrema SYNOPSIS
cc [ flag... ] file... -lmlib [ library... ] #include <mlib.h> mlib_status mlib_ImageExtrema2(mlib_s32 *min, mlib_s32 *max, const mlib_image *img, mlib_s32 xStart, mlib_s32 yStart, mlib_s32 xPeriod, mlib_s32 yPeriod); mlib_status mlib_ImageExtrema2_Fp(mlib_d64 *min, mlib_d64 *max, const mlib_image *img, mlib_s32 xStart, mlib_s32 yStart, mlib_s32 xPeriod, mlib_s32 yPeriod); DESCRIPTION
Each of the functions determines the extrema values for each channel in an image, possibly with subsampling. It uses the following equation: min[i] = MIN{ img[x][y][i] } max[i] = MAX{ img[x][y][i] } where x = xStart + p*xPeriod; 0 <= p < (w - xStart)/xPeriod y = yStart + q*yPeriod; 0 <= q < (h - yStart)/yPeriod PARAMETERS
Each of the functions takes the following arguments: min Pointer to minimum vector, where length is the number of channels in the image. min[i] contains the minimum of channel i. max Pointer to maximum vector, where length is the number of channels in the image. max[i] contains the maximum of channel i. img Pointer to a source image. xStart Initial X sample coordinate. yStart Initial Y sample coordinate. xPeriod X sample rate. xPeriod >= 1. yPeriod Y sample rate. yPeriod >= 1. RETURN VALUES
The function returns MLIB_SUCCESS if successful. Otherwise it returns MLIB_FAILURE. ATTRIBUTES
See attributes(5) for descriptions of the following attributes: +-----------------------------+-----------------------------+ | ATTRIBUTE TYPE | ATTRIBUTE VALUE | +-----------------------------+-----------------------------+ |Interface Stability |Committed | +-----------------------------+-----------------------------+ |MT-Level |MT-Safe | +-----------------------------+-----------------------------+ SEE ALSO
mlib_ImageExtremaLocations(3MLIB), mlib_ImageMaximum(3MLIB), mlib_ImageMaximum_Fp(3MLIB), mlib_ImageMinimum(3MLIB), mlib_ImageMini- mum_Fp(3MLIB), attributes(5) SunOS 5.11 2 Mar 2007 mlib_ImageExtrema2(3MLIB)
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