Xargs, awk, match, if greater - as a one-liner Post: 302979192

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Top Forums Shell Programming and Scripting Xargs, awk, match, if greater - as a one-liner Post 302979192 by Don Cragun on Wednesday 10th of August 2016 03:06:48 PM

08-10-2016

Registered User

Quote:

Originally Posted by ts89490

thanks Don
Parallel processing is not an issue here as I am doing it on a cluster.

The string to match appears invariably in third column but the order of variables NRHITS and PVALUE in third column might vary.

While the code does not write separate output files, I am wondering if a combination of xargs and sed can help. If so, how ?
Thanks

OK. I completely misunderstood your example. I thought your field separator was <semicolon>, but now I'm guessing that <tab> is your field separator, and <semicolon> is a subfield separator in your third field.

And you are wrong. The code I suggested produces a separate output file for each input file that contains lines that meet your criteria.

Using your updated description (but assuming that no <semicolon> characters appear anywhere in the 1st two fields in your input files AND assuming that a single <tab> character separates the first three fields), my code adjusted for your new description of the problem is:

Code:

awk -F'[\t;]' '
FNR == 1 {
	if(of != "")
		close(of)
	of = FILENAME ".fail"
}
{	for(i = 3; i <= NF; i++)
		if($i ~ /^PVALUE=/ && (substr($i, 8) + 0) > .05) {
			print > of
			next
		}
}' *.txt

And, with the following input files:
file1.txt:

Code:

#row1	
#row2	
#row3	
#row4	
#row5	
CHR	POS	INFO
chrX	10000	NRHITS=35;PVALUE=0.04
chrX	109000	NRHITS=6;PVALUE=
chrX	110000	NRHITS=10;PVALUE=0.6
chrX	120000	NRHITS=18;PVALUE=0.2
chrX	130000	NRHITS=39;PVALUE=0.035

file2.txt:

Code:

#row1	
#row2	
#row3	
#row4	
#row5	
CHR	POS	INFO
chrX	10000	PVALUE=0.04;NRHITS=35
chrX	109000	PVALUE=;NRHITS=6
chrX	110000	PVALUE=0.6;NRHITS=10
chrX	120000	PVALUE=0.2;NRHITS=18
chrX	130000	PVALUE=0.035;NRHITS=39

file3.txt:

Code:

#row1	
#row2	
#row3	
#row4	
#row5	
CHR	POS	INFO
chrX	10000	EXTRA=1;NRHITS=35;PVALUE=0.04
chrX	109000	NRHITS=6;PVALUE=;EXTRA=2
chrX	110000	NRHITS=10;EXTRA=3;PVALUE=0.6
chrX	120000	EXTRA=4;NRHITS=18;PVALUE=0.2
chrX	130000	NRHITS=39;PVALUE=0.035;EXTRA=5

file4.txt:

Code:

#row1	
#row2	
#row3	
#row4	
#row5	
CHR	POS	INFO
chrX	10000	NRHITS=35;PVALUE=0.04
chrX	109000	NRHITS=6;PVALUE=
chrX	110000	NRHITS=10;PVALUE=0.006
chrX	120000	NRHITS=18;PVALUE=0.02
chrX	130000	NRHITS=39;PVALUE=0.035

It produces the output files:
file1.txt.fail:

Code:

chrX	110000	NRHITS=10;PVALUE=0.6
chrX	120000	NRHITS=18;PVALUE=0.2

file2.txt.fail:

Code:

chrX	110000	PVALUE=0.6;NRHITS=10
chrX	120000	PVALUE=0.2;NRHITS=18

file3.txt.fail:

Code:

chrX	110000	NRHITS=10;EXTRA=3;PVALUE=0.6
chrX	120000	EXTRA=4;NRHITS=18;PVALUE=0.2

Note that there is no file4.txt.fail file because no line in file4.txt meets your criteria.

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