I have two files File1.txt and File2.txt. I need to compare the three columns 1, 2 and 3 from File1 with 4,5 and 6 of File2, respectively and if the match is found, I want to retrieve the corresponding value from the column 2 of File2 and paste it in Output.txt. The sample files are as below:
File1.txt
ASP B 276
ASN B 290
ALA B 294
ALA B 297
ARG B 298
ARG B 303
LYS D 288
File2.txt
ATOM 4770 N ALA A 346 71.417 37.005 4.562 1 0 N
ATOM 4778 C ALA A 346 72.003 34.855 3.476 1 0 C
ATOM 4779 O ALA A 346 72.956 34.2 3.103 1 0 O
ATOM 4859 N SER A 353 78.218 33.415 -2.595 1 0 N
ATOM 4867 HG SER A 353 78.828 31.548 0.899 1 0
ATOM 4868 C SER A 353 79.637 31.351 -2.619 1 0 C
ATOM 4869 O SER A 353 80.669 30.76 -2.372 1 0 O
ATOM 9771 N ASP B 238 52.86 30.061 -7.031 1 0 N
ATOM 9772 H ASP B 238 53.651 30.105 -7.641 1 0
ATOM 9776 HB1 ASP B 238 53.516 32.92 -5.486 1 0
ATOM 10352 H ASP B 276 11.565 35.255 6.968 1 0
ATOM 10356 HB1 ASP B 276 10.084 33.659 6.727 1 0
ATOM 10357 HB2 ASP B 276 10.331 32.059 6.945 1 0
ATOM 10358 CG ASP B 276 9.946 33.07 8.681 1 0 C
ATOM 10453 H ASN B 290 16.73 30.519 13.339 1 0
ATOM 10454 CA ASN B 290 18.755 31.013 13.763 1 0 C
ATOM 10458 HB2 ASN B 290 20.105 29.465 13.891 1 0
ATOM 10459 CG ASN B 290 18.471 28.842 14.99 1 0 C
ATOM 10460 OD1 ASN B 290 18.246 29.429 16.072 1 0 O
ATOM 10512 H ALA B 294 24.099 33.167 8.943 1 0
ATOM 10513 CA ALA B 294 26.095 33.794 9.273 1 0 C
ATOM 10514 HA ALA B 294 26.597 34.261 8.545 1 0
ATOM 10515 CB ALA B 294 25.515 34.817 10.199 1 0 C
ATOM 10556 H ALA B 297 28.288 31.299 7.752 1 0
ATOM 10557 CA ALA B 297 30.202 31.869 7.061 1 0 C
ATOM 10558 HA ALA B 297 30.566 31.457 6.226 1 0
ATOM 10566 H ARG B 298 30.012 32.059 9.568 1 0
ATOM 10567 CA ARG B 298 31.961 32.047 10.392 1 0 C
ATOM 10568 HA ARG B 298 32.532 32.853 10.237 1 0
ATOM 10569 CB ARG B 298 31.251 32.167 11.74 1 0 C
ATOM 10650 HE ARG B 303 36.405 23.564 2.394 1 0
ATOM 10651 CZ ARG B 303 34.807 22.582 3.07 1 0 C
ATOM 10652 NH1 ARG B 303 33.867 22.493 3.991 1 0 N
ATOM 10653 1HH1 ARG B 303 33.829 23.162 4.733 1 0
ATOM 10654 2HH1 ARG B 303 33.192 21.757 3.947 1 0
ATOM 10655 NH2 ARG B 303 34.847 21.706 2.081 1 0 N
ATOM 17143 OE1 GLU C 295 59.322 13.561 -6.631 1 0 O
ATOM 17144 OE2 GLU C 295 57.646 14.02 -7.941 1 0 O
ATOM 17145 C GLU C 295 54.718 13.527 -3.448 1 0 C
ATOM 17146 O GLU C 295 54.509 14.618 -2.982 1 0 O
ATOM 23627 HB1 LYS D 288 32.909 52.854 29.282 1 0
ATOM 23628 HB2 LYS D 288 31.41 53.372 29.672 1 0
ATOM 23629 CG LYS D 288 32.811 53.749 31.138 1 0 C
ATOM 23630 HG1 LYS D 288 32.137 53.82 31.873 1 0
ATOM 23631 HG2 LYS D 288 33.636 53.303 31.484 1 0
ATOM 23632 CD LYS D 288 33.168 55.146 30.656 1 0 C
The output.txt should contain the values of column 2 of second file only if the three columns of File1 matches with the three columns of File2.
Output.txt
10352
10356
10357
10358
10453
10454
10458
10459
10460
10512
10513
10514
10515
10556
10557
10558
10566
10567
10568
10569
10650
10651
10652
10653
10654
10655
23627
23628
23629
23630
23631
23632
I have tried with awk one liner, which is provided below. The script was executed but has retrieved different values of the column 2 of File2. Hence, I need help in resolving this and finding out where am I going wrong.
awk 'FNR==NR{a[$1,$2,$3]=$0;next}{if(b=a[$4,$5,$6]){print $2}}' File1.txt File2.txt > Output.txt
Thanks in advance.
Asha, MBU, IISc, Bangalore, India
