将文件名添加到统计数据中

Question

假设我有类似下面的文件。

文件 1

1,144931087,144931087,T,C  
16,89017167,89017167,C,G  
17,7330235,7330235,G,T  
17,10222478,10222478,C,T

文件 2

1,144931087,144931087,T,C
16,89017167,89017167,C,G
17,10222478,10222478,C,T

文件 3

17,10222478,10222478,C,T

我想找出每个文件中存在多少次重复值，因此理想情况下，输出如下：

输出

2 1,144931087,144931087,T,C  
2 16,89017167,89017167,C,G  
3 17,10222478,10222478,C,T  
1 17,7330235,7330235,G,T

我使用了以下命令来计算重复值。

sort Test1.csv Test2.csv Test3.csv | uniq --count

现在我想为统计输出添加文件名。我想要的输出应该是这样的：

Test1 Test2 2 1,144931087,144931087,T,C  
Test1 Test2 2 16,89017167,89017167,C,G  
Test1 Test2 Test 3 3 17,10222478,10222478,C,T  
Test1 1 17,7330235,7330235,G,T

任何人都可以帮助我获得所需的输出，或者任何人都可以建议我获得所需输出的更好方法吗？

Answer 1

使用 awk。抱歉我聪明的文件命名方案：

$ awk '{
    a[[=10=]]++                   # count hits
    b[[=10=]]=b[[=10=]] FILENAME " "  # store filenames
}
END {
    for(i in a)               
        print b[i] a[i],i     # output them
}' foo bar baz
foo bar 2 1,144931087,144931087,T,C
foo bar 2 16,89017167,89017167,C,G
foo bar baz 3 17,10222478,10222478,C,T
foo 1 17,7330235,7330235,G,T

已更新 每条评论：

$ awk 'BEGIN {
    FS=OFS=","
} 
{
    a[ OFS  OFS  OFS ]++ 
    b[ OFS  OFS  OFS ]=b[ OFS  OFS  OFS ] FILENAME "|"
    c[ OFS  OFS  OFS ]=[=11=]                      # keep the last record with 
}                                                      # specific key combination 
END { 
    for(i in a) 
        print b[i] "," a[i],c[i]  
}' foo  bar baz
foo|bar|,2,16,89017167,89017167,C
foo|,1,17,7330235,7330235,G
foo|bar|,2,1,144931087,144931087,T
foo|bar|baz|,3,17,10222478,10222478,C

Answer 2

输入：

more Test*.csv
::::::::::::::
Test1.csv
::::::::::::::
1,144931087,144931087,T,C
16,89017167,89017167,C,G
17,7330235,7330235,G,T
17,10222478,10222478,C,T
::::::::::::::
Test2.csv
::::::::::::::
1,144931087,144931087,T,C
16,89017167,89017167,C,G
17,10222478,10222478,C,T
::::::::::::::
Test3.csv
::::::::::::::
17,10222478,10222478,C,T

命令：

awk '{tmp[[=11=]]++;if(length(tmp2[[=11=]])==0){tmp2[[=11=]]=FILENAME;next}tmp2[[=11=]]=tmp2[[=11=]] OFS FILENAME}END{for(elem in tmp){print tmp2[elem] OFS tmp[elem] OFS elem}}' Test*.csv

输出：

Test1.csv Test2.csv 2 1,144931087,144931087,T,C
Test1.csv Test2.csv 2 16,89017167,89017167,C,G
Test1.csv Test2.csv Test3.csv 3 17,10222478,10222478,C,T
Test1.csv 1 17,7330235,7330235,G,T

解释：

  # gawk profile, created Mon Dec 17 14:46:47 2018

  # Rule(s)

   {
           tmp[[=13=]]++ #associative array to count the occurrences freq
           if (length(tmp2[[=13=]]) == 0) {  #when you add the first occurrence filename you do not need to add a space
                   tmp2[[=13=]] = FILENAME
                   next
            }
           #append to variable with a space
           tmp2[[=13=]] = tmp2[[=13=]] OFS FILENAME
    }

    # END rule(s)

    END {
           # loop on each element of the associative arrays and print them
           for (elem in tmp) {
                   print tmp2[elem] OFS tmp[elem] OFS elem
            }
    }

可以将if...next...替换为(length(tmp2[[=16=]]) == 0 ? tmp2[[=16=]] = FILENAME : tmp2[[=16=]] = tmp2[[=16=]] OFS FILENAME)，将awk脚本简化为：

  {
       tmp[[=14=]]++
       (length(tmp2[[=14=]]) == 0 ? tmp2[[=14=]] = FILENAME : tmp2[[=14=]] = tmp2[[=14=]] OFS FILENAME)
  }

  END {
         for (elem in tmp) {
              print tmp2[elem] OFS tmp[elem] OFS elem
         }
  }

Answer 3

能否请您尝试以下操作，这应该会让您输出到 Input_file 行的输入事件中。我使用了 gsub(/[[:space:]]+$/,"") 因为你的 Input_file(s) 在最后一行有空格所以在这里删除它们，你可以删除它以防万一不是这种情况。

awk '
{
  gsub(/[[:space:]]+$/,"")
}
!a[[=10=]]++{
  b[++count]=[=10=]
}
{
  c[[=10=]]++
  d[[=10=]]=d[[=10=]]?d[[=10=]] OFS FILENAME:FILENAME
}
END{
  for(i=1;i<=count;i++){
    print d[b[i]]"|"c[b[i]],b[i]
  }
}'  test1 test2 test3

输出如下。

test1 test2|2 1,144931087,144931087,T,C
test1 test2|2 16,89017167,89017167,C,G
test1|1 17,7330235,7330235,G,T
test1 test2 test3|3 17,10222478,10222478,C,T

Answer 4

使用 Perl 的另一个答案。

> cat file1m.csv
1,144931087,144931087,T,C
16,89017167,89017167,C,G
17,7330235,7330235,G,T
17,10222478,10222478,C,T
> cat file2m.csv 
1,144931087,144931087,T,C
16,89017167,89017167,C,G
17,10222478,10222478,C,T
> cat file3m.csv
17,10222478,10222478,C,T
> cat uniq_perl.ksh
perl -lne ' 
@t=@{ $kvf{$_} };
if( not $ARGV ~~ @t ) { push(@t,$ARGV); $kvf{$_}=[ @t ] ;  }
close(ARGV) if eof; 
END { for(keys %kvf) { @x=@{$kvf{$_}};  print join(" ",@x)." ".scalar(@x)." ".$_  } }   
' file*m*csv 
> ./uniq_perl.ksh
file1m.csv file2m.csv file3m.csv 3 17,10222478,10222478,C,T
file1m.csv 1 17,7330235,7330235,G,T
file1m.csv file2m.csv 2 1,144931087,144931087,T,C
file1m.csv file2m.csv 2 16,89017167,89017167,C,G
>

将文件名添加到统计数据中

Adding file name to the counted data

unix

comparison

awk

compare

string-comparison