macos - 为什么 fgrep 表现得很奇怪？

Question

我正在尝试使用 grep 从 file2 中的 file1 中提取匹配的单词并定向到输出文件。

我有文件1

Acetoanaerobium sticklandii
Acetobacter pasteurianus

喜欢 >1000 个物种。

文件2

>WP_013360383.1 ATP-dependent Clp protease ATP-binding subunit [Acetoanaerobium sticklandii]
>WP_013360396.1 ATP-dependent Clp protease ATP-binding subunit [Acetoanaerobium sticklandii]
>WP_003623694.1 multidrug efflux RND transporter permease subunit [Acetobacter pasteurianus]
>WP_003624003.1 superoxide dismutase [Acetobacter pasteurianus]
>WP_003624029.1 UDP-galactopyranose mutase [Acetobacter pasteurianus]
>WP_003624540.1 mannose-1-phosphate guanylyltransferase/mannose-6-phosphate isomerase [Acetobacter pasteurianus]
>WP_077905956.1 effector protein [Salmonella enterica]
>WP_077905962.1 type III secretion system YopJ family effector AvrA [Salmonella enterica]
>WP_005544680.1 3-deoxy-8-phosphooctulonate synthase [Aggregatibacter actinomycetemcomitans]
>WP_005545812.1 MFS transporter [Aggregatibacter actinomycetemcomitans]
>WP_005546163.1 UTP--glucose-1-phosphate uridylyltransferase GalU [Aggregatibacter actinomycetemcomitans]

等等..

当我使用代码时

grep -f file1 file2 > output 

或

fgrep -f file1 file2 > output

结果输出是包含 file1 最后一行的列表，其余输入列表将被 grep 忽略。即使使用 -w 选项，输出也是相同的。

为什么 grep 会这样？难道是我的外壳有问题？我使用的是 Mojave 操作系统版本的 MacBook。

请建议我等效的 awk 命令。

我试过了

awk 'NR==FNR{a[$0];next}$NF in a{print}' file1 file2 > output

但结果是空文件。

Answer 1

第一个解决方案:比我的第二个解决方案通用且更快的解决方案。这将在 Input_file2 中查找从 [ 到 ] 的字符串，而不管此处的字段硬编码如何。

awk '
{ gsub(/\r/,"") }
FNR==NR{
  array[$0]
  next
}
match($0,/\[[^]]*/){
  val=substr($0,RSTART+1,RLENGTH-1)
}
(val in array)
' file1 file2

说明:为上述内容添加了详细说明。

awk '                                     ##Starting awk program from here.
{ gsub(/\r/,"") }
FNR==NR{                                  ##Checkiing condition FNR==NR which will be TRUE hen file1 is being read.
  array[$0]                               ##Creating array with index of current line.
  next                                    ##next will skip all statements from here.
}
match($0,/\[[^]]*/){                      ##Using match to match from [ to till ] in line.
  val=substr($0,RSTART+1,RLENGTH-1)       ##Creating val which has sub-string from RSTART  to RLENGH here.
}
(val in array)                            ##Checking condition if val is present in array then print that line.
' file1 file2                             ##Mentioning Input_file names here.

---

---

第二个解决方案:您能否尝试按照所示示例进行编写和测试。这是更通用的解决方案，因为字段编号没有硬编码在解决方案中，但无论此处的字段编号如何，此代码都将起作用。

awk '{ gsub(/\r/,"") } FNR==NR{array[$0];next} {for(i in array){if(match($0,i)){print;next}}}' file1 file2

说明:为上述内容添加详细说明。

awk '                    ##Starting awk program from here.
{ gsub(/\r/,"") }
FNR==NR{                 ##Checking condition FNR==NR if that's true then do following.
  array[$0]              ##Creating an array with index of current line.
  next                   ##next will skip further statements from here.
}
{
  for(i in array){       ##Looping through array here.
    if(match($0,i)){     ##Checking if current key is present  in current line then do following.
      print              ##Printing current line here.
      next               ##next will skip further statements from here.
    }
  }
}
'  file1 file2           ##Mentioning Input_file names here.