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Match in awk skipping header rows

 
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Old 02-01-2016
Match in awk skipping header rows
I am trying to match $1-$7 between the two files and if a match is found then the contents of $8 in file2 and copied over. The awk I tried is below. There is also a header row in file2 that has the Chr Start End Ref Alt that does not need to be searched. Thank you Smilie.

awk
Code:
awk 'FNR==NR>1{a[$1,$2,$3,$4,$5,$6,$7]=$0;next}{if(b=a[$1,$2,$3,$4,$5,$6,$7]){print b}}' file1.txt file2.txt > output.txt 
-bash: $'\342\200\213awk': command not found

file1
Code:
yyyyy,yyy	Chr	Start	End	Ref	Alt	Func.refGene
yyyyy,yyy	22	40757228	40757228	A	C	intronic
yyyyy,yyy	5	125887715	125887715	T	G	exonic
yyyyy,yyy	5	125880589	125880589	T	C	UTR3
xxxxxxx,xxx	1111111	Chr	Start	End	Ref	Alt	Func.refGene
xxxxxxx,xxx	1111111	1	43394661	43394661	A	G	exonic
xxxxxxx,xxx	1111111	2	166870221	166870221	A	C	intronic

file2
Code:
yyyyy,yyy 	0	22	40757228	40757228	A	C	likely benign
yyyyy,yyy  0	5	125887715	125887715	T	G	likely benign
yyyyy,yyy	0	5	125880589	125880589	T	C	likely benign



desired output
Code:
yyyyy,yyy	Chr	Start	End	Ref	Alt	Func.refGene
yyyyy,yyy	22	40757228	40757228	A	C	intronic likely benign
yyyyy,yyy	5	125887715	125887715	T	G	exonic likely benign
yyyyy,yyy	5	125880589	125880589	T	C	UTR3 likely benign

Last edited by cmccabe; 02-02-2016 at 11:54 AM.. Reason: added details
 
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