如何基于多列中的数据合并两个文件? [英] How to merge two files based on data in multiple columns?

问题描述

我有两个单独的文件，每个文件包含不同数量的列，我想根据多个列中的数据进行合并.

I have two separate files, each containing a different number of columns which I want to merge based on data in multiple columns.

file1

VMNF01000015.1  1769465 1769675 .   .   -   Focub_II5_mimp_1
VMNF01000014.1  3225875 3226081 .   .   +   Focub_II5_mimp_1
VMNF01000014.1  3226046 3226081 .   .   -   Focub_II5_mimp_1
VMNF01000014.1  3585246 3585281 .   .   -   Focub_II5_mimp_1
VMNF01000014.1  3692468 3692503 .   .   -   Focub_II5_mimp_1
VMNF01000014.1  3715380 3715415 .   .   +   Focub_II5_mimp_1
VMNF01000014.1  2872478 2872511 .   .   -   Focub_II5_mimp_1

file2

VMNF01000014.1  3225875-3226081(+)  gtacttcagcctggattcaaacttattgcatcccactgta
VMNF01000014.1  3226046-3226081(-)  tacacacctgcgaatactttttgcatcccactgta
VMNF01000015.1  1769465-1769675(-)  gtacttcagcctggattcaaacttattgcatcccactgta
VMNF01000014.1  3692468-3692503(-)  tacagtgggatgcaaaaagtattcgcaggtgt
VMNF01000014.1  3715380-3715415(+)  gtacttcagcctggattcaaacttattgcatcccactgta
VMNF01000014.1  3585246-3585281(-)  tacagtgggatgcaaaaagtattcgcaggtgt
VMNF01000014.1  2872478-2872511(-)  gtacttcagcctggattcaaacttattgcatcccactgta

首先，我想我需要在file2中创建另外2列，用-"分隔数字，并为(*)"创建新列，但是我不知道如何在不替换((- )"也.到目前为止，我一直在使用以下命令:

First, I think I need to create another 2 columns in file2, separating numbers by "-" and creating a new column for "(*)", but I cannot work out how to separate the numbers without replacing "(-)" too. So far I have been using this command:

awk '{gsub("-","\t",$2);print;}'

完成此操作后，我想将file2中的最后一列添加到file1中.我已经可以使用以下命令执行此操作:

Once this has been done, I would like to add the last column in file2 to file1. I have been able to do this using the following command:

awk 'NR==FNR {a[$1]=$3; next} {print $1,$2,$3,$4,$5,$6,$7,a[$1];}' file2 file1 > file3. 

但是，数据不匹配.它是根据第1列中的条目进行匹配的.在许多情况下，第1列中的数据是相同的，因此file3的第8列中的数据仅与其中一项匹配，而与第2或3列中的数据不匹配在文件1中

However, the data does not match. It is matched based on the entry in column 1. The data in column 1 is the same in many instances, so the data in column 8 of file3 only matches one of the entries, and doesn't match the data in column 2 or 3 in file1 e.g.

file3:

VMNF01000015.1  1769465 1769675 .   .   -   Focub_II5_mimp_1    gtacttcagcctggattcaaacttattgcatcccactgta
VMNF01000014.1  3225875 3226081 .   .   +   Focub_II5_mimp_1    gtacttcagcctggattcaaacttattgcatcccactgta
VMNF01000014.1  3226046 3226081 .   .   -   Focub_II5_mimp_1    gtacttcagcctggattcaaacttattgcatcccactgta
VMNF01000014.1  3585246 3585281 .   .   -   Focub_II5_mimp_1    gtacttcagcctggattcaaacttattgcatcccactgta
VMNF01000014.1  3692468 3692503 .   .   -   Focub_II5_mimp_1    gtacttcagcctggattcaaacttattgcatcccactgta
VMNF01000014.1  3715380 3715415 .   .   +   Focub_II5_mimp_1    gtacttcagcctggattcaaacttattgcatcccactgta
VMNF01000014.1  2872478 2872511 .   .   -   Focub_II5_mimp_1    gtacttcagcctggattcaaacttattgcatcccactgta

即使我能够分离file2的第2列中的数据，我仍然会遇到相同的问题，因为在某些情况下，第2列中的数据是相同的.我需要的是这样的代码，其内容大致如下:对第2列中的数据进行分类(请参见下文)；

Even if I was able to separate the data in column 2 of file2, I would still have the same problem as the data in column 2 is the same in some instances. What I need is code that says something along the lines of: sperate the data in column 2 (see below);

VMNF01000014.1  3225875    3226081    (+)   gtacttcagcctggattcaaacttattgcatcccactgta

然后:

如果文件1中的$ 1，$ 2，$ 3与文件2中的$ 1，$ 2，$ 3相匹配，则从文件1中打印$ 1，$ 2，$ 3，$ 4，$ 5，$ 6，$ 7，并从文件2中添加$ 5.

if $1,$2,$3 in file1 match $1,$2,$3 in file2, print $1,$2,$3,$4,$5,$6,$7 from file1 and add $5 from file2.

我该怎么做?我知道awk可以使用if语句，但是我不知道如何在awk中使用它们.

How can I do this? I know that awk can use if statements, but I don't know how to use them in awk.

有什么建议吗?

推荐答案

能否请您尝试以下操作.

Could you please try following.

awk '
FNR==NR{
  split($2,array,"[-(]")
  mainarray[$1,array[1],array[2]]=$NF
  next
}
(($1,$2,$3) in mainarray){
  print $0,mainarray[$1,$2,$3]
}
'  Input_file2  Input_file1

第二种解决方案: 由于OP在上述代码中出现错误，因此在上面进行了一些更改.

2nd solution: Since OP is getting an error in above code so made a little change in above.

awk '
FNR==NR{
  split($2,array,"[-(]")
  key=$1 OFS array[1] OFS array[2]
  mainarray[key]=$NF
  next
}
{ key = $1 OFS $2 OFS $3 }
(key in mainarray){
  print $0,mainarray[key]
}
'  Input_file2  Input_file1

说明: :添加了上述代码的详细说明.

Explanation: Adding detailed explanation for above code.

awk '                                       ##Starting awk program from here.
FNR==NR{                                    ##Checking condition FNR==NR when  Input_file2 is being read.
  split($2,array,"[-(]")                    ##Splitting 2nd field into an array named array where delimiter is - OR (
  mainarray[$1,array[1],array[2]]=$NF       ##Creating mainarray index of $1,array[1],array[2] and value is current line is last field.
  next                                      ##next will skip all further statements from here.
}
(($1,$2,$3) in mainarray){                  ##Checking condition if $1,$2,$3 of current line is present in mainaarray.
  print $0,mainarray[$1,$2,$3]              ##Printing current line with value of mainarray with index of $1,$2,$3
}
'  Input_file2  Input_file1                 ##Mentioning Input_file names here.

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