awk to place specific contents filename within text file Post: 302965502

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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

01-29-2016

Registered User

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.

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LEARN ABOUT FREEBSD

expand

EXPAND(1)						    BSD General Commands Manual 						 EXPAND(1)

NAME

     expand, unexpand -- expand tabs to spaces, and vice versa

SYNOPSIS

     expand [-t tab1,tab2,...,tabn] [file ...]
     unexpand [-a | -t tab1,tab2,...,tabn] [file ...]

DESCRIPTION

     The expand utility processes the named files or the standard input writing the standard output with tabs changed into blanks.  Backspace
     characters are preserved into the output and decrement the column count for tab calculations.  The expand utility is useful for pre-process-
     ing character files (before sorting, looking at specific columns, etc.) that contain tabs.

     The unexpand utility puts tabs back into the data from the standard input or the named files and writes the result on the standard output.

     The following options are available:

     -a      (unexpand only.)  By default, only leading blanks and tabs are reconverted to maximal strings of tabs.  If the -a option is given,
	     then tabs are inserted whenever they would compress the resultant file by replacing two or more characters.

     -t tab1,tab2,...,tabn
	     Set tab stops at column positions tab1, tab2, ..., tabn.  If only a single number is given, tab stops are set that number of column
	     positions apart instead of the default number of 8.

ENVIRONMENT

     The LANG, LC_ALL and LC_CTYPE environment variables affect the execution of expand and unexpand as described in environ(7).

EXIT STATUS

     The expand and unexpand utilities exit 0 on success, and >0 if an error occurs.

STANDARDS

     The expand and unexpand utilities conform to IEEE Std 1003.1-2001 (``POSIX.1'').

HISTORY

     The expand command appeared in 3.0BSD.

BSD
								 October 13, 2006							       BSD

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