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I am looking for something similar to the bash command comm, that I can use to select entries both unique to my 2 files and common to them. Comm worked great when I had just one column per file, eg. 

 comm -13 FILE1.txt FILE2.txt > Entries_only_in_file1.txt

But now I have multiple columns of info I wish to keep. I want to select column 2 as the one to filter rows for unique and common entries between my two files. If the entry in column two appears in both files I also want to record the info in columns 3,4,and 5 (if possible, this is not as important). Here is an example of input and output. 

FILE1.txt
NM_023928   AACS    2   2   1
NM_182662   AADAT   2   2   1
NM_153698   AAED1   1   5   3
NM_001271   AAGAB   2   2   1


FILE2.txt
NM_153698   AAED1   2   5   3
NM_001271   AAGAB   2   2   1
NM_001605   AARS    3   40  37
NM_212533   ABCA2   3   4   2

Output wanted:

COMMON.txt
NM_153698   AAED1   1   5   3   2   5   3
NM_001271   AAGAB   2   2   1   2   2   1

UNIQUE_TO_1.txt
NM_023928   AACS    2   2   1
NM_182662   AADAT   2   2   1

UNIQUE_TO_2.txt
NM_001605   AARS    3   40  37
NM_212533   ABCA2   3   4   2

I know there has been similar questions before but I can't quite find what I'm looking for. Any ideas greatly appreciated, thank you.

4

2 回答 2

3

join具有以下对您的任务有用的选项：

  • -j FIELD: 加入现场FIELD
  • -o FORMAT：指定输出格式，以逗号分隔的 FILENUM.FIELD 列表。
  • -v FILENUM: 仅在 . 上输出行FILENUM。

两个文件共有：

$ join -j2 -o 1.1,1.2,1.3,1.4,1.5,2.3,2.4,2.5 FILE1.txt FILE2.txt 
NM_153698 AAED1 1 5 3 2 5 3
NM_001271 AAGAB 2 2 1 2 2 1

FILE1 独有：

$ join -j2 -v1 FILE1.txt FILE2.txt 
AACS NM_023928 2 2 1
AADAT NM_182662 2 2 1

FILE2 独有：

$ join -j2 -v2 FILE1.txt FILE2.txt 
AARS NM_001605 3 40 37
ABCA2 NM_212533 3 4 2
于 2016-05-11T19:33:21.220 回答
0

您可以使用 gnu awk 进行归档，这是一个脚本：

脚本.awk

function unique(filename, line) {
    split( line , tmp, FS)
    print tmp[1], tmpp[2], tmp[3], tmp[4], tmp[5] >> filename
}

NR == FNR { # in case we are reading the first file: store line under key
        file1[ $2 ] = $0
        next
    }

    {
        if( $2 in file1 ) { # key from file2 was in also in file1:
            split( file1[ $2 ], tmp, FS)
            print $1, $2, tmp[3], tmp[4], tmp[5], $3, $4, $5 >> "COMMON.txt"
   # remove common key, thus we can later find unique keys from file1
            delete file1[ $2 ] 
        }
        else { # unique key from file2 
            unique("UNIQUE_TO_2.txt", $0)
        }
    }

END {
  # remaining keys are unique in file1
        for( k in file1 ) {
            unique("UNIQUE_TO_1.txt", file1[ k ])
        }
    }

像这样使用它：

# erase the output files if present
rm -f COMMON.txt UNIQUE_TO_1.txt UNIQUE_TO_2.txt
# run script, create the file
awk -f script.awk FILE1.txt FILE2.txt
# output the files
for f in COMMON.txt UNIQUE_TO_1.txt UNIQUE_TO_2.txt; do echo "$f"; cat "$f"; done

将printf ... >> filename文本附加到文件名。这在rm第二次运行脚本时需要输出文件。

于 2016-05-11T19:22:11.890 回答