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I have two files: File1

ARS-BFGL-BAC-10975 0.9303 688423261 1 01/04/2015 0.9983763305
ARS-BFGL-BAC-11025 0.9092 688423261 1 01/04/2015 0.9983763305
ARS-BFGL-BAC-11044 0.9626 688423261 2 01/04/2015 0.9983763305
ARS-BFGL-BAC-11193 0.9544 688423261 1 01/04/2015 0.9983763305
ARS-BFGL-BAC-10975 0.9303 688423263 1 01/04/2015 0.9983763305
ARS-BFGL-BAC-11025 0.9092 688423263 1 01/04/2015 0.9983763305
ARS-BFGL-BAC-11044 0.9626 688423263 2 01/04/2015 0.9983763305
ARS-BFGL-BAC-11193 0.9544 688423263 1 01/04/2015 0.9983763305

File2:

ARS-BFGL-BAC-10975 10 21225382
ARS-BFGL-BAC-11025 10 84516867
ARS-BFGL-BAC-11193 1 29303546

Desired output

ARS-BFGL-BAC-10975 0.9303 688423261 1 01/04/2015 0.9983763305 10 21225382
ARS-BFGL-BAC-11025 0.9092 688423261 1 01/04/2015 0.9983763305 10 84516867
ARS-BFGL-BAC-11193 0.9544 688423261 1 01/04/2015 0.9983763305 1 29303546
ARS-BFGL-BAC-10975 0.9303 688423263 1 01/04/2015 0.9983763305 10 21225382
ARS-BFGL-BAC-11025 0.9092 688423263 1 01/04/2015 0.9983763305 10 84516867
ARS-BFGL-BAC-11193 0.9544 688423263 1 01/04/2015 0.9983763305 1 29303546

So file 1 has many more rows than file 2. I only want to keep rows in the output that are in file 2 based on column1.

I have tried join but I cant get it to work right-it will tell me my files are not sorted

join -j 1 -o 1.1,1.2,1.3,1.4,1.5,1.6,2.2,2.3 <(sort -k1 file1) <(sort -k1 file2)

Preferably I would prefer an awk command. File 1 will be very large. I have tried

awk 'FNR==NR{a[$1]=$2 FS $3;next}{ print $0, a[$1]}' file2 file1 > output

Any help would be much appreciated. Thanks

Sorry I cant comment below but just to clarify file not all rows in column1 in file 1 will be in file2.

The awk command

awk 'FNR==NR{a[$1]=$2 FS $3;next} $1 in a {print $0, a[$1]}' 

will only keep the amount of rows there is in file 2. But ideally what I want is were for expample ARS-BFGL-10975 is repeated twice (realistically way more) to appear twice in my output.

Thanks for the help so far

  • Please edit your question and fix the examples you show. Every single 1st column in file1 is also present in file2. – terdon Mar 13 '16 at 16:53
  • glenn’s answer works for me (i.e., for your example data, it produces the six lines of output that you say you want). I notice that, when you quote it (when you say it doesn’t work), you quote it incompletely.  Are you maybe passing the file arguments as file1 file2 rather than file2 file1, as is required for it to work correctly? – Scott Aug 26 '17 at 19:41
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For your awk command, you're only missing the check to see if the key from file1 has been seen in file2

awk 'FNR==NR{a[$1]=$2 FS $3;next} $1 in a {print $0, a[$1]}' file2 file1 > output
# ................................^^^^^^^
1

Using your example data:

$ join <(sort file1) <(sort file2)
ARS-BFGL-BAC-10975 0.9303 688423261 1 01/04/2015 0.9983763305 10 21225382
ARS-BFGL-BAC-10975 0.9303 688423263 1 01/04/2015 0.9983763305 10 21225382
ARS-BFGL-BAC-11025 0.9092 688423261 1 01/04/2015 0.9983763305 10 84516867
ARS-BFGL-BAC-11025 0.9092 688423263 1 01/04/2015 0.9983763305 10 84516867
ARS-BFGL-BAC-11193 0.9544 688423261 1 01/04/2015 0.9983763305 1 29303546
ARS-BFGL-BAC-11193 0.9544 688423263 1 01/04/2015 0.9983763305 1 29303546

This appears to do what you would want it to do, apart from the ordering of the lines in the output (which is sorted here, and I don't know if that's significant to you or not).

The default join field is the first field, so -j 1 is not needed (this is a GNU join extension).

The default output of join: "Each output line consists of the join field, the remaining fields from file1 and then the remaining fields from file2" (from the OpenBSD manual). This means that the output field specification that you used isn't needed either as it matches the default behaviour.

For sort, -k1 is likewise equivalent to the default.

I don't know what caused the error message that you got other than accidentally using sort -c.

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