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sed to add field heards to specific fields

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# 1  
Old 07-07-2016
sed to add field headers to specific fields
I have tab delimited input that prints out in the format below:

I am trying to add field headers to $5 and $6. Not sure if sed is the best tool but my attempt is below. Thank you Smilie.

Code:
$5 = REF
$6 = ALT

file
Code:
ID     CHR    START        STOP
123    1         100            200        A     C
456    1         201            300        T     G

desired output
Code:
ID     CHR    START           STOP      REF    ALT
123    1         100          200         A         C
456    1         201          300         T         G

Code:
  
sed -i '1iREF, ALT' file

Code:
awk 'NR==1{print $1" "$2" "$3" "$4 REF ALT ;next}{print}' inputfile

Might also work in this case, but my actual input has 53 fields and only $50-$53 need headers added to them.
Last edited by cmccabe; 07-07-2016 at 07:50 PM.. Reason: fixed format, added awk
# 2  
Old 07-07-2016
The sample input you provided is not tab delimited. If your real input is tab delimited and you just want to set the headers for certain fields, the easy way would be something like:
Code:
awk '
BEGIN {	FS = OFS = "\t"
}
NR == 1 {
	$5 = "REF"
	$6 = "ALT"
}
1' file

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
# 3  
Old 07-07-2016
So does the NR == 1 store the header that is already there? Thank you Smilie.
# 4  
Old 07-07-2016
Quote:
Originally Posted by cmccabe
So does the NR == 1 store the header that is already there? Thank you Smilie.
What happened when you tried it?

It doesn't store anything. The NR==1 section of the code replaces the header for the specified fields on the 1st input line it reads. Then, the condition 1 with the default action ({print}) prints the updated header line and all following unmodified lines to standard output.
This User Gave Thanks to Don Cragun For This Post:
cmccabe
# 5  
Old 07-07-2016
Please, try:
Code:
perl -ple '$_.="\tREF\tALT" if $. == 1' inputfile

This User Gave Thanks to Aia For This Post:
cmccabe
# 6  
Old 07-08-2016
Code:
sed '1s/$/\tREF\tALT/' file
ID	CHR	START	STOP	REF	ALT
123	1	100	200	A	C
456	1	201	300	T	G

This User Gave Thanks to RudiC For This Post:
cmccabe
# 7  
Old 07-08-2016
Thank you all for your help and explanations Smilie
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