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Full Discussion: awk to place specific contents filename within text file
Top Forums Shell Programming and Scripting awk to place specific contents filename within text file Post 302965502 by Don Cragun on Friday 29th of January 2016 07:58:38 PM
Old 01-29-2016
If I understand what you're trying to do (and I am not at all sure that I do), the following seems to do what you want:
Code:
awk '
FNR == 1 {
	if((n = split(FILENAME, name, "_")) < 2) {
		print "********************************"
		printf("Filename (%s) does not fit expected pattern.\n",
		    FILENAME)
		print "********************************"
		exit 1
	}
	split(name[2], number, ".")
}
{	print name[1], number[1], $0
}' OFS='\t' *multianno

which, with your attached sample data (stored in a file named LastName,FirstName_123456.txt.hg19_multianno) produces the following as the 1st five lines of its output:
Code:
LastName,FirstName	123456	Chr	Start	End	Ref	Alt	Func.refGene	Gene.refGene	GeneDetail.refGene	ExonicFunc.refGene	AAChange.refGene	PopFreqMax	1000G2012APR_ALL	1000G2012APR_AFR	1000G2012APR_AMR	1000G2012APR_ASN	1000G2012APR_EUR	ESP6500si_ALL	ESP6500si_AA	ESP6500si_EA	CG46	common	clinvar	clinvarsubmit	clinvarreference
LastName,FirstName	123456	1	43394661	43394661	A	exonic	SLC2A1		nonsynonymous SNV	SLC2A1:NM_006516.2:exon8:c.T1016C:p.I339T	0.0002	.	.	.	.	.	0.0001	0.0002	unknown	.	.
LastName,FirstName	123456	2	166870221	166870221	A	intronic	SCN1A				0.01	0.01	.	0.0028	.	0.01	0.0072	0.002	0.0099	.	Common			
LastName,FirstName	123456	9	135802555	135802555	C	intronic	TSC1				0.01	0.0046	.	0.01	.	0.01	0.0075	0.002	0.01	.	Common	untested	Tuberous_sclerosis_database_(TSC1)	TSC1_00008
LastName,FirstName	123456	22	40745898	40745898	C	exonic	ADSL		synonymous SNV	ADSL:NM_000026.3:exon2:c.C216T:p.I72I,ADSL:NM_001123378:exon2:c.C216T:p.I72I	0.01	0.0027	0.002	0.01	.	0.0006	0.0011	0.0003	.

Is this what you're trying to do?

Note, as always, if you want to try this on a Solaris/SunOS system, change awk to /usr/xpg4/bin/awk or nawk.
This User Gave Thanks to Don Cragun For This Post:
cmccabe
 

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LEARN ABOUT REDHAT

adsl-connect

ADSL-CONNECT(8) 					      System Manager's Manual						   ADSL-CONNECT(8)

NAME

       adsl-connect - Shell script to manage a PPPoE link

SYNOPSIS

       adsl-connect [config_file]

       adsl-connect interface user [config_file]

DESCRIPTION

       adsl-connect  is  a  shell  script  which  manages  an ADSL connection using the Roaring Penguin user-space PPPoE client.  If you omit con-
       fig_file, the default file /etc/sysconfig/network-scripts/ifcfg-ppp0 is used.  If you supply interface and user,  then  they  override  the
       Ethernet interface and user-name settings in the configuration file.

       Note that normally, you should not invoke adsl-connect directly.  Instead, use adsl-start to bring up the ADSL connection.

       adsl-connect first reads a configuration file.  It then brings up a PPPoE connection.  If the connection ever drops, a message is logged to
       syslog, and adsl-connect re-establishes the connection.	In addition, each time the connection is dropped or cannot be  established,  adsl-
       connect executes the script /etc/ppp/adsl-lost if it exists and is executable.

       The shell script adsl-stop causes adsl-connect to break out of its loop, bring the connection down, and exit.

TECHNICAL DETAILS

       adsl-connect uses the following shell variables from the configuration file:

       ETH    The Ethernet interface connected to the ADSL modem (for example, eth0).

       USER   The ADSL user-id (for example, b1xxnxnx@sympatico.ca).

       PIDFILE
	      A  file in which to write the process-ID of the adsl-connect process (for example, /var/run/pppoe.pid).  Two additional files ($PID-
	      FILE.pppd and $PIDFILE.pppoe) hold the process-ID's of the pppd and pppoe processes, respectively.

       By using different configuration files with different PIDFILE settings, you can manage multiple PPPoE connections.  Just specify  the  con-
       figuration file as an argument to adsl-start and adsl-stop.

AUTHOR

       adsl-connect was written by David F. Skoll <dfs@roaringpenguin.com>.

       The pppoe home page is http://www.roaringpenguin.com/pppoe/.

SEE ALSO

       pppoe(8),  adsl-start(8),  adsl-stop(8),  pppd(8),  pppoe.conf(5),  adsl-setup(8),  adsl-status(8), pppoe-sniff(8), pppoe-server(8), pppoe-
       relay(8)

4th Berkeley Distribution					 21 February 2000						   ADSL-CONNECT(8)
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