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Top Forums Shell Programming and Scripting Sum specified values (columns) per row Post 302898126 by pathunkathunk on Friday 18th of April 2014 09:48:21 PM
Old 04-18-2014
This works for the example file, but when I try it with my larger file there are some issues. For example if these lines are the input:
Code:
comp51820_c1_seq1	405	N	0:29:0:0:0:0	0:51:0:0:0:0	0:57:0:0:0:0	0:6:0:0:0:0	0:37:0:0:0:0
comp51820_c1_seq1	406	N	0:0:0:29:0:0	0:0:0:51:0:0	0:0:0:57:0:0	0:0:0:6:0:0	0:0:0:37:0:0
comp51820_c1_seq1	407	N	0:0:0:31:0:0	0:0:0:48:0:0	0:0:0:59:0:0	0:0:0:8:0:0	0:0:0:45:0:0
comp51820_c1_seq1	408	N	0:31:0:0:0:0	0:51:0:0:0:0	0:60:0:0:0:0	0:9:0:0:0:0	0:48:0:0:0:0
comp51820_c1_seq1	409	N	0:1:0:0:0:0	0:51:0:0:0:0	0:60:0:0:0:0	0:9:0:0:0:0	0:48:0:0:0:0

The output I get is:
Code:
-bash-4.1$ cat path.awk 
{   
	f=0   
	for(i=4;i<=NF;i++) {     
		n=split($i,a,":")     
		s=0     
		for(j=1;j<=n;j++) s+=a[j]     
		if (s>=8)        
		f++   } 
} 
f==(NF-4)
-bash-4.1$ 
-bash-4.1$ awk -f path.awk file.txt
comp51820_c1_seq1	405	N	0:29:0:0:0:0	0:51:0:0:0:0	0:57:0:0:0:0	0:6:0:0:0:0	0:37:0:0:0:0
comp51820_c1_seq1	406	N	0:0:0:29:0:0	0:0:0:51:0:0	0:0:0:57:0:0	0:0:0:6:0:0	0:0:0:37:0:0
comp51820_c1_seq1	409	N	0:1:0:0:0:0	0:51:0:0:0:0	0:60:0:0:0:0	0:9:0:0:0:0	0:48:0:0:0:0

This output is incorrect because the sum of $7 is < 8 in the first two lines, and the sum of $4 < 8 in the third line.

Expected output is:
Code:
comp51820_c1_seq1	407	N	0:0:0:31:0:0	0:0:0:48:0:0	0:0:0:59:0:0	0:0:0:8:0:0	0:0:0:45:0:0
comp51820_c1_seq1	408	N	0:31:0:0:0:0	0:51:0:0:0:0	0:60:0:0:0:0	0:9:0:0:0:0	0:48:0:0:0:0

The latest version also don't seem to work with the original example file:
Code:
-bash-4.1$ cat file2.txt 
comp51820_c1_seq1	42	N	0:0:0:0:0:0	1:0:0:0:0:0	0:0:0:0:0:0	3:0:0:0:0:0	0:0:0:0:0:0
comp51820_c1_seq1	43	N	0:0:0:0:0:0	0:1:0:0:0:0	0:0:0:0:0:0	0:3:0:0:0:0	0:0:0:0:0:0
comp51820_c1_seq1	44	N	0:0:4:0:3:1	0:0:1:9:0:0	10:0:0:0:0:0	0:3:3:2:2:6	2:2:2:5:60:3
comp51820_c1_seq1	45	N	0:4:0:0:5:0	0:1:8:0:0:0	0:0:0:0:9:0	0:3:0:0:6:0	0:0:0:0:13:0
-bash-4.1$ 
-bash-4.1$ awk -f path.awk file2.txt
-bash-4.1$ awk -f path2.awk file2.txt
comp51820_c1_seq1	44	N	0:0:4:0:3:1	0:0:1:9:0:0	10:0:0:0:0:0	0:3:3:2:2:6	2:2:2:5:60:3
-bash-4.1$ 
-bash-4.1$ cat path2.awk 
{   
	f=0   
	for(i=4;i<=NF;i++) {     
		n=split($i,a,":")     
		s=0     
		for(j=1;j<n;j++) s+=a[j]     
		if (s>=8)        
		f++   } 
} 
f==(NF-4)
-bash-4.1$ 
-bash-4.1$ cat path.awk 
{   
	f=0   
	for(i=4;i<=NF;i++) {     
		n=split($i,a,":")     
		s=0     
		for(j=1;j<=n;j++) s+=a[j]     
		if (s>=8)        
		f++   } 
} 
f==(NF-4)

 

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bup-margin(1)						      General Commands Manual						     bup-margin(1)

NAME
bup-margin - figure out your deduplication safety margin SYNOPSIS
bup margin [options...] DESCRIPTION
bup margin iterates through all objects in your bup repository, calculating the largest number of prefix bits shared between any two entries. This number, n, identifies the longest subset of SHA-1 you could use and still encounter a collision between your object ids. For example, one system that was tested had a collection of 11 million objects (70 GB), and bup margin returned 45. That means a 46-bit hash would be sufficient to avoid all collisions among that set of objects; each object in that repository could be uniquely identified by its first 46 bits. The number of bits needed seems to increase by about 1 or 2 for every doubling of the number of objects. Since SHA-1 hashes have 160 bits, that leaves 115 bits of margin. Of course, because SHA-1 hashes are essentially random, it's theoretically possible to use many more bits with far fewer objects. If you're paranoid about the possibility of SHA-1 collisions, you can monitor your repository by running bup margin occasionally to see if you're getting dangerously close to 160 bits. OPTIONS
--predict Guess the offset into each index file where a particular object will appear, and report the maximum deviation of the correct answer from the guess. This is potentially useful for tuning an interpolation search algorithm. --ignore-midx don't use .midx files, use only .idx files. This is only really useful when used with --predict. EXAMPLE
$ bup margin Reading indexes: 100.00% (1612581/1612581), done. 40 40 matching prefix bits 1.94 bits per doubling 120 bits (61.86 doublings) remaining 4.19338e+18 times larger is possible Everyone on earth could have 625878182 data sets like yours, all in one repository, and we would expect 1 object collision. $ bup margin --predict PackIdxList: using 1 index. Reading indexes: 100.00% (1612581/1612581), done. 915 of 1612581 (0.057%) SEE ALSO
bup-midx(1), bup-save(1) BUP
Part of the bup(1) suite. AUTHORS
Avery Pennarun <apenwarr@gmail.com>. Bup unknown- bup-margin(1)
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