sort a file based on a column in another file

Question

I have two files both in the format of: ``` loc1 num1 num2 loc2 num3 num4 ``` The first column is the location and I want to use the order of the locations in the first file to sort the second file so that I can put the two files together where the numbers are right for the location. I can write a perl script to do this but I felt there might be some quick/easy shell/awk command to achieve this. Do you have any ideas? Thanks. Edits: Here is the input, now I actually want to use column 2 in file 1 to sort file2. File1: ``` GID location NAME GWEIGHT C1SI M1CO M1SI C1LY M1LY C1CO C1LI M1LI AID ARRY2X ARRY1X ARRY3X ARRY4X ARRY5X ARRY0X ARRY6X ARRY7X EWEIGHT 1.000000 1.000000 1.000000 1.000000 1.000000 1.000000 1.000000 1.000000 GENE735X chr17:66199278-66199496 chr17:66199278-66199496 1.000000 0.211785 -0.853890 1.071875 0.544136 0.703871 0.371880 0.218960 -2.268618 GENE1562X chr10:80097054-80097298 chr10:80097054-80097298 1.000000 0.533673 -0.397202 0.783363 0.109824 -0.436342 0.158667 0.…

Accepted Answer

An awk solution: store the 2nd file in memory, then loop over the first file, emitting matching lines from the 2nd file:

```
awk 'FNR==NR {x2[$1] = $0; next} $1 in x2 {print x2[$1]}' second first
```

Implementing @Barmar's comment

```
join -1 2 -o "1.1 1.2 2.2 2.3" <(cat -n first | sort -k2) <(sort second) | 
sort -n | 
cut -d ' ' -f 2-
```

note to other answerers, I tested with these files:

```
$ cat first
foo x y
bar x y
baz x y
$ cat second
bar x1 y1
baz x2 y2
foo x3 y3
```

Explanation of

```
awk 'FNR==NR {x2[$1] = $0; next} $1 in x2 {print x2[$1]}' second first
```

This part reads the 1st file in the command line paramters (here, "second"):

```
FNR==NR {x2[$1] = $0; next}
```

The condition `FNR == NR` will be true only for the first named file. `FNR` is awk's "File Record Number" variable, `NR` is the current record number from all input sources. The current line is stored in an associative array named `x2` (not a great variable name) indexed by the first field of the record.

The next condition, `$1 in x2`, will only start after the file "second" has been completely read. It will look at the first field of the line in file named "first", and the action prints the corresponding line from file "second", which has been stored in the array.

Note that the order of the files in the awk command is important. Since you control the output based on the file named "first", it must be the last file processed by awk.

sort a file based on a column in another file

Solution

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