Help with sort only column 2 data separately Post: 302966923

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Top Forums Shell Programming and Scripting Help with sort only column 2 data separately Post 302966923 by Don Cragun on Thursday 18th of February 2016 04:05:20 AM

02-18-2016

Registered User

If you really want to keep column 1 as it is and sort the 2nd and 3rd columns by increasing numeric value of the 2nd column (instead of sorting column 2 values with column 1 values, you could try:

Code:

#!/bin/ksh
tmpfn=${0##*/}.$$

trap 'rm -rf "$tmpfn"' EXIT

awk -v tmpfn="$tmpfn" '
BEGIN {	OFS = "\t"
	cmd = "sort -k1n > " tmpfn
}
{	f1[++lc] = $1
	print $2, $3 | cmd
}
END {	close(cmd)
	for(i = 1; i <= lc; i++) {
		getline < tmpfn
		print f1[i], $1, $2
	}
	close(tmpfn)
}' Input_File

which, with your sample input (without the .... lines) produces the output:

Code:

Contig_1_294435nt	39664	39742
Contig_1_294435nt	39666	39743
Contig_1_294435nt	41610	41684
Contig_1_294435nt	41617	41684
Contig_2_242278nt	75910	76271
Contig_2_242278nt	76036	76316
Contig_2_242278nt	76036	76316
Contig_3_206988nt	100775	100835
Contig_3_206988nt	100775	100835
Contig_3_206988nt	156143	157111
Contig_3_206988nt	156147	157111
Contig_3_206988nt	178412	178537
Contig_3_206988nt	178729	178896
Contig_3_206988nt	179269	179510
Contig_3_206988nt	179269	179517
Contig_3_206988nt	179269	180441
Contig_3_206988nt	180033	180441
Contig_3_206988nt	180043	180441
Contig_3_206988nt	242231	242751
Contig_3_206988nt	242390	242782
Contig_3_206988nt	242390	242782
Contig_3_206988nt	291578	291668

Of course, a lot of error checking should be added in the END clause, but this seems to work as a proof of concept.

As always, if you want to try this on a Solaris/SunOS system, change awk to /usr/xpg4/bin/awk or nawk.

This was written and tested using a 1993+ version of the Korn shell, but will work with any POSIX-conforming shell.

Last edited by Don Cragun; 02-18-2016 at 05:06 AM.. Reason: Remove the debugging sleep.

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trace-cmd-options

TRACE-CMD-OPTIONS(1)													      TRACE-CMD-OPTIONS(1)

NAME

       trace-cmd-options - list available options from trace-cmd plugins

SYNOPSIS

       trace-cmd options

DESCRIPTION

       The trace-cmd(1) options command will examine all the trace-cmd plugins that are used by trace-cmd report(1) and list them.

SEE ALSO

       trace-cmd(1), trace-cmd-record(1), trace-cmd-start(1), trace-cmd-stop(1), trace-cmd-extract(1), trace-cmd-reset(1), trace-cmd-split(1),
       trace-cmd-list(1), trace-cmd-listen(1)

AUTHOR

       Written by Steven Rostedt, <rostedt@goodmis.org[1]>

RESOURCES

       git://git.kernel.org/pub/scm/linux/kernel/git/rostedt/trace-cmd.git

COPYING

       Copyright (C) 2011 Red Hat, Inc. Free use of this software is granted under the terms of the GNU Public License (GPL).

NOTES

	1. rostedt@goodmis.org
	   mailto:rostedt@goodmis.org

								    06/11/2014						      TRACE-CMD-OPTIONS(1)