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I want to compare two files:

For example:

file 1:

1:10471 A/C/G   rs1309260800
1:10472 G/T rs1238646298
1:10473 A/G rs1408062762
1:10474 A/T rs1326069208
1:10475 A/T rs1404283754
1:10475 G/T rs1321149898
X:59363536  A/T rs868821995
Y:59363566  G/T rs865996778

file 2:

1:10473 1:10473_G/A
1:13380 1:13380_C/G
1:13380 1:13380_G/C
1:52152 1:52152_ATAAT/A
X:5936355   X:5936355_A/T

when I tried

awk 'FNR==NR{seen[$1]=$0; next} ($1 in seen) {$1=seen[$1]}1'  file2 file1

It gives me

1:10471 A/C/G   rs1309260800
1:10472 G/T rs1238646298
1:10473 1:10473_G/A A/G rs1408062762
1:10474 A/T rs1326069208
1:10475 A/T rs1404283754
1:10475 G/T rs1321149898
X:59363536  A/T rs868821995
Y:59363566  G/T rs865996778

But I want to get all the matched row and unmacthed rows from file 2. So I change the position of files and tried

awk 'FNR==NR{seen[$1]=$0; next} ($1 in seen) {$1=seen[$1]}1'  file1 file2

to get

1:10473 1:10473_G/A A/G rs1408062762
1:13380 1:13380_C/G
1:13380 1:13380_G/C
1:52152 1:52152_ATAAT/A
X:5936355   X:5936355_A/T

But I am not getting this and giving me 0 rows

Can anyone please suggest to me, why is this error happening when I change the position of files in the awk command line

laxmi
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    You want to research the `join` command, I think. Start with `man join`. – underscore_d Jun 24 '20 at 12:20
  • Does this answer your question? [How to merge two files using AWK?](https://stackoverflow.com/questions/5467690/how-to-merge-two-files-using-awk) – underscore_d Jun 24 '20 at 12:22
  • @underscore_d That is not giving me the desired output. I have done some edits on the problem after doing some workaround. Could you please suggest on that. – laxmi Jun 25 '20 at 11:25

0 Answers0