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Shell Programming and Scripting

Extract Big and continuous regions

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# 1  
Old 03-20-2016
Extract Big and continuous regions
Hi all,
I have a file like this I want to extract only those regions which are big and continous


Code:
chr1    3280000 3440000
chr1    3440000 3920000
chr1    3600000 3920000 # region coming within the 3440000 3920000. so i don't want it to be printed in output
chr1    3920000 4800000 
chr1    4080000 4800000 # region coming within the 3920000 4800000 . so i don't want it to be printed in output
chr1    4160000 4360000 # region coming within the 3920000 4800000 . so i don't want it to be printed in output
chr1    4160000 4760000 # region coming within the 3920000 4800000 . so i don't want it to be printed in output
chr1    4360000 4760000 # region coming within the 3920000 4800000 . so i don't want it to be printed in output
chr1    4800000 4920000 # region coming within the 4800000 6160000 . so i don't want it to be printed in output
chr1    4800000 5200000 # region coming within the 4800000 6160000 . so i don't want it to be printed in output
chr1    4800000 5280000 # region coming within the 4800000 6160000 . so i don't want it to be printed in output
chr1    4800000 6160000 
chr1    4920000 5200000 # region coming within the 4800000 6160000 . so i don't want it to be printed in output
chr1    5280000 6160000 # region coming within the 4800000 6160000 . so i don't want it to be printed in output



Finally the below regions could be printed in output
Code:
chr1    3280000 3440000
chr1    3440000 3920000
chr1    3920000 4800000
chr1    4800000 6160000

So can anyone help me to get that
# 2  
Old 03-20-2016
The following seems to do what you want:
Code:
awk '
$3 > LH {
	D[++c] = $0
	L[c] = $2
	H[c] = LH = $3
}
END {	for(i = c - 1; i > 0; i--)
		if(H[i] > L[i + 1]) {
			for(j = i; j < c; j++) {
				D[j] = D[j + 1]
				L[j] = L[j + 1]
				H[j] = H[j + 1]
			}
			c--
		}
	for(i = 1; i <= c; i++)
		print D[i]
}' file

If you want to try this on a Solaris/SunOS system, change awk to /usr/xpg4/bin/awk or nawk.
# 3  
Old 03-20-2016
Code:
perl -anle 'if($F[2]>$h){ $s{$F[1]} = $_; $h=$F[2] } END{ for(sort keys %s){ print $s{$_} } }' amrutha_sastry.input

Code:
chr1    3280000 3440000
chr1    3440000 3920000
chr1    3920000 4800000
chr1    4800000 6160000

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