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Full Discussion: Failure using regex with awk in 'while read file' loop
Top Forums Shell Programming and Scripting Failure using regex with awk in 'while read file' loop Post 302940524 by pathunkathunk on Monday 6th of April 2015 11:26:55 PM
Old 04-07-2015
Failure using regex with awk in 'while read file' loop
I have a file1.txt with several 100k lines, each of which has a column 9 containing one of 60 "label" identifiers. Using an labels.txt file containing a list of labels, I'd like to extract 200 random lines from file1.txt for each of the labels in index.txt.

Using a contrived mini-example:
Code:
$ cat file1.txt 
H	0	328	100.0	-	0	0	38D150M140D	M01433:68:000000000-AAT0D:1:1111:13371:3239;barcodelabel=c8;	OTU_1;size=17947;
H	1	325	100.0	+	0	0	150M175D	M01433:68:000000000-AAT0D:1:1105:27659:19941;barcodelabel=c12;	OTU_2;size=101;
H	4	411	99.3	+	0	0	24D150M237D	M01433:68:000000000-AAT0D:1:2107:16393:23698;barcodelabel=g10;	OTU_5;size=64;
H	2	283	98.7	+	0	0	150M133D	M01433:68:000000000-AAT0D:1:2104:21919:3018;barcodelabel=c12;	OTU_3;size=80;
H	1	277	98.5	-	0	0	15I135M142D	M01433:68:000000000-AAT0D:1:2108:12616:12185;barcodelabel=c12;	OTU_2;size=101;
H	0	295	100.0	+	0	0	14D150M131D	M01433:68:000000000-AAT0D:1:1108:4978:15986;barcodelabel=g10;	OTU_1;size=17947;
H	29	312	97.6	-	0	0	25I125M187D	M01433:68:000000000-AAT0D:1:1109:20934:22671;barcodelabel=g15;	OTU_30;size=8;
H	0	315	99.3	-	0	0	88D150M77D	M01433:68:000000000-AAT0D:1:2114:17509:23920;barcodelabel=g10;	OTU_1;size=17947;

$ cat labels.txt
c12
g10

This is what I'm trying, but it results in empty files:
Code:
$ while read file
> do
> awk '/${file}/' file1.txt | gshuf -n 200 > ${file}.txt
> done < labels.txt

Desired output--two random lines for each label in labels.txt (i.e. may vary except for "label=c12" or "label=g12", respectively):
Code:
$ cat c12.txt
H	1	325	100.0	+	0	0	150M175D	M01433:68:000000000-AAT0D:1:1105:27659:19941;barcodelabel=c12;	OTU_2;size=101;
H	2	283	98.7	+	0	0	150M133D	M01433:68:000000000-AAT0D:1:2104:21919:3018;barcodelabel=c12;	OTU_3;size=80;

$ cat g10.txt
H	0	295	100.0	+	0	0	14D150M131D	M01433:68:000000000-AAT0D:1:1108:4978:15986;barcodelabel=g10;	OTU_1;size=17947;
H	0	315	99.3	-	0	0	88D150M77D	M01433:68:000000000-AAT0D:1:2114:17509:23920;barcodelabel=g10;	OTU_1;size=17947;

It seems like the problem is with the " awk '/${file}/' "? I say this because I can extract lines for each label but only if I explicitly specify the label regex (in this case g10.txt also has two random lines with "label=c12" instead of g10):
Code:
$ while read file
> do
> awk '/c12/' file1.txt | gshuf -n 2 > ${file}.txt
> done < labels.txt
$ cat c12.txt 
H	1	277	98.5	-	0	0	15I135M142D	M01433:68:000000000-AAT0D:1:2108:12616:12185;barcodelabel=c12;	OTU_2;size=101;
H	1	325	100.0	+	0	0	150M175D	M01433:68:000000000-AAT0D:1:1105:27659:19941;barcodelabel=c12;	OTU_2;size=101;

Thanks for any pointers.
 

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LEARN ABOUT FREEBSD

random

RANDOM(6)							 BSD Games Manual							 RANDOM(6)

NAME

     random -- random lines from a file or random numbers

SYNOPSIS

     random [-elrUuw] [-f filename] [denominator]

DESCRIPTION

     Random has two distinct modes of operations.  The default is to read in lines from the standard input and randomly write them out to the
     standard output with a probability of 1 / denominator.  The default denominator for this mode of operation is 2, giving each line a 50/50
     chance of being displayed.

     The second mode of operation is to read in a file from filename and randomize the contents of the file and send it back out to standard out-
     put.  The contents can be randomized based off of newlines or based off of space characters as determined by isspace(3).  The default
     denominator for this mode of operation is 1, which gives each line a chance to be displayed, but in a random(3) order.

     The options are as follows:

     -e      If the -e option is specified, random does not read or write anything, and simply exits with a random exit value of 0 to denominator
	     - 1, inclusive.

     -f filename
	     The -f option is used to specify the filename to read from.  Standard input is used if filename is set to '-'.

     -l      Randomize the input via newlines (the default).

     -r      The -r option guarantees that the output is unbuffered.

     -U      Tells random(6) that it is okay for it to reuse any given line or word when creating a randomized output.

     -u      Tells random(6) not to select the same line or word from a file more than once (the default).  This does not guarantee uniqueness if
	     there are two of the same tokens from the input, but it does prevent selecting the same token more than once.

     -w      Randomize words separated by isspace(3) instead of newlines.

SEE ALSO

     random(3), fortune(6)

HISTORY

     The functionality to randomizing lines and words was added in 2003 by Sean Chittenden <seanc@FreeBSD.org>.

BUGS

     No index is used when printing out tokens from the list which makes it rather slow for large files (10MB+).  For smaller files, however, it
     should still be quite fast and efficient.

BSD
								 February 8, 2003							       BSD
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