Match in two files

Shell Programming and Scripting
1

Trying to match $5 of file1.txt to $1 of file2.txt and if there is a match copy $6 of file2.txt and paste it to $7 of file1.txt. My attempt is below but it does not seem to produce the desired output. Thank you :).

 awk 'NR==FNR{A[$5]=$1; next}  A[$6]  {$6=$6 " " A[$7]}1' file2.txt file1.txt > match.txt

File1.txt

RefPrimer	ref	antiref	omosome	PrimerSet	SeqRxn	Link
AntirefPrimer	antiref	ref	omosome			
PXL-A0000005ref	69066	69311	1	PXL-A0000005	SeqRxn4	
PXL-A0000005antiref	69311	69066	1			
PXL-A0000007ref	69700	70033	1	PXL-A0000007	SeqRxn4	
PXL-A0000007antiref	70033	69700	1

File2.txt

PXL-A0000005	chr1	69066	69311	DTE3504500000005 https://www.xxxx.com/add_2_cart.php?catno=PXL-A0000005&storage=lyophilized&rxns=100&num=1&test=mixed&format=tube
PXL-A0000007	chr1	69700	70033	DTE3504500000007 https://www.xxxx.com/add_2_cart.php?catno=PXL-A0000007&storage=lyophilized&rxns=100&num=1&test=mixed&format=tube

Desired output

RefPrimer	ref	antiref	omosome	PrimerSet	SeqRxn	Link
AntirefPrimer	antiref	ref	omosome			
PXL-A0000005ref	69066	69311	1	PXL-A0000005	SeqRxn4	https://www.xxxx.com/add_2_cart.php?catno=PXL-A0000005&storage=lyophilized&rxns=100&num=1&test=mixed&format=tube
PXL-A0000005antiref	69311	69066	1 
PXL-A0000007ref	69700	70033	1	PXL-A0000007	SeqRxn4	https://www.xxxx.com/add_2_cart.php?catno=PXL-A0000007&storage=lyophilized&rxns=100&num=1&test=mixed&format=tube
PXL-A0000007antiref	70033	69700	1
2 
awk 'NR==FNR {A[$1]=$6; next} ($5 in A) {print $0,A[$5]}' file2.txt file1.txt

If you want to print the non-matching lines then omit the ($5 in A) condition.

1 Like
3

Thank you :)... works great.