在awk中打​​印用户定义函数的输出会产生意外的令牌错误 [英] print output of user-defined function in awk gives unexpected token error

问题描述

我想灵活地将两个小awk的输出打印到bash管道，这些管道使用了变量（他们最初的工作原理）。我最初以为我可以将整个命令存储为变量本身，但对于一个它不起作用，显然（存储awk命令在bash脚本的变量中）这不是一个好主意。所以我写了两个函数，但我在完成附近获得了一个意外标记，但它的格式与上面的链接相同。

我的错误在哪里？

 覆盖范围内的文件* / *。cov 
 do 
 #gene_count = $（awk'{print $ 5}'$ coverage_file | sort | uniq -c | wc -l）#this显然不是一个好主意
 #contig_count = $（awk'{print $ 1}'$ coverage_file | sort | uniq -c | wc -l）＃这显然不是一个好主意
 cmd_gene（）{awk'{print $ 5}'$ coverage_file | sort | uniq -c | wc -l} 
 cmd_contig（）{awk'{print $ 1}'$ coverage_file | sort | uniq -c | wc -l} 
 cmd_gene $ coverage_file 
 cmd_contig $ coverage_file 
 #printwe found，$ gene_count，genes on，$ contig_countcontigs 
 done 
  

cov文件看起来像这样：

  k141_85332.3 4119 19 A5 phnM_031 
 k141_85332.3 4119 19 A5 phnM_031 
 k141_85332.3 4119 28 A1 phnM_031 
 k141_85332.3 4119 28 A1 phnM_031 
 k141_85332.3 4119 8 A2 phnM_031 
 k141_85332.3 4119 8 A2 phnM_031 
 k141_88684 267 5 B10 phnM_032 
 k141_88684 268 5 B10 phnM_032 
 k141_88684 269 5 B10 phnM_032 
 k141_88684 270 5 B10 phnM_032 
 k141_88684 271 5 B10 phnM_032 
 k141_88684 272 5 B10 phnM_032 
  

编辑：这包括被接受的答案+一种可能的方式来清楚地打印它：

 ＃！/ bin / bash 
 
 #define变量
基因=phnM
阈值=5
 
 #define函数
 cmd_gene（）{awk'{print $ 5 }'$ 1 | sort | uniq -c | wc -l;}＃分号在这里很重要！ 
 cmd_contig（）{awk'{print $ 1}'$ 1 | sort | uniq -c | wc -l; } #semicolon在这里很重要！ 
 
 #loop覆盖文件和打印结果（printf会更漂亮）
覆盖文件* / *。cov 
 do 
 echo $ genewas found $（cmd_gene$ coverage_file）timeson$（cmd_contig$ coverage_file）覆盖范围最小覆盖范围$ coverage_file 
完成
  pre> 
 
 
输出：
  phnM在65个contig上被找到67次phnm / test.cov 
 phnM的最小覆盖率为5，在2个contig上发现了3次，test / test.cov中的最小覆盖率为5，
  
 
 
解决方案
意外的令牌错误即将到来，因为当您定义函数时，}必须位于它自己的行或前面;。  
 
 
另外，因为您在函数的定义中使用 $ coverage_file ，所以您不必通过它。
  for coverage_file in * / *。cov 
 do 
 cmd_gene（）{awk' {print $ 5}'$ coverage_file | sort | uniq -c | wc -l; } 
 cmd_contig（）{awk'{print $ 1}'$ coverage_file | sort | uniq -c | wc -l; } 
 cmd_gene 
 cmd_contig 
 #printwe found，$ gene_count，genes on，$ contig_countcontigs 
 done 
  
如果你想在for循环之外定义函数，你可以使用 $ 1 与awk的$ 1混淆）并且像  
 
 编辑那样传递 $ coverage_file  strong>：上面的示例
  $ cat a.sh 
 cmd_gene（）{awk'{print $ 5}' $ 1 | sort | uniq -c | wc -l;} 
 cmd_contig（）{awk'{print $ 1}'$ 1 | sort | uniq -c | wc -l;} 
 
 for coverage_file in * / *。cov 
 do 
 cmd_gene $ coverage_file 
 cmd_contig $ coverage_file 
完成
 
 $ ls * / *。cov 
 bf / a.cov 
 
 $ cat * / *。cov 
 k141_85332.3 4119 19 A5 phnM_031 
 k141_85332.3 4119 19 A5 phnM_031 
 k141_85332.3 4119 28 A1 phnM_031 
 k141_85332.3 4119 28 A1 phnM_031 
 k141_85332.3 4119 8 A2 phnM_031 
 k141_85332.3 4119 8 A2 phnM_0 31 
 k141_88684 267 5 B10 phnM_032 
 k141_88684 268 5 B10 phnM_032 
 k141_88684 269 5 B10 phnM_032 
 k141_88684 270 5 B10 phnM_032 
 k141_88684 271 5 B10 phnM_032 
 k141_88684 272 5 B10 phnM_032 
 
 $ sh a.sh 
 2 
 2 
  
 
I wanted to flexibly print the output of two small awk to bash pipes, which are using variables (they worked originally). I initially thought I could store the whole command as variable itself, but for one it did not work and apparently (store awk command in a variable of bash script) it is not a good idea. So I wrote two functions, but I'm getting an "unexpected token" near "done", but it is formatted as in the link above. 


Where is my mistake? 
for coverage_file in */*.cov
do
    #gene_count=$(awk '{print $5}' $coverage_file |sort | uniq -c | wc -l) #this is apparently not a good idea
    #contig_count=$(awk '{print $1}' $coverage_file |sort | uniq -c | wc -l) #this is apparently not a good idea
    cmd_gene() { awk '{print $5}' $coverage_file |sort | uniq -c | wc -l }
    cmd_contig() { awk '{print $1}' $coverage_file |sort | uniq -c | wc -l }
    cmd_gene $coverage_file
    cmd_contig $coverage_file
    #print "we found", $gene_count, "genes on ",$contig_count" contigs
done
the cov files look like this:
k141_85332.3 4119 19 A5 phnM_031
k141_85332.3 4119 19 A5 phnM_031
k141_85332.3 4119 28 A1 phnM_031
k141_85332.3 4119 28 A1 phnM_031
k141_85332.3 4119 8 A2 phnM_031
k141_85332.3 4119 8 A2 phnM_031
k141_88684 267 5 B10 phnM_032
k141_88684 268 5 B10 phnM_032
k141_88684 269 5 B10 phnM_032
k141_88684 270 5 B10 phnM_032
k141_88684 271 5 B10 phnM_032
k141_88684 272 5 B10 phnM_032
EDIT: this includes the accepted answer + a possible way to print it plainly:
#!/bin/bash

#define variables
gene="phnM"
threshold="5"

#define functions
cmd_gene() { awk '{print $5}' $1 |sort | uniq -c | wc -l ; } #semicolon is important here!
cmd_contig() { awk '{print $1}' $1 |sort | uniq -c | wc -l ; } #semicolon is important here!

#loop over files and print results (would be prettier with printf)
for coverage_file in */*.cov
do
    echo $gene" was found" $(cmd_gene "$coverage_file") "times on" $(cmd_contig "$coverage_file")" contigs with minimum coverage of" $threshold in $coverage_file
done
OUTPUT:
phnM was found 67 times on 65 contigs with minimum coverage of 5 in phnm/test.cov
phnM was found 3 times on 2 contigs with minimum coverage of 5 in test/test.cov

解决方案
The unexpected token error is coming because when you define a function, the } has to be on it's own line or preceded by ;. 

Also, since you're using $coverage_file in the definition of the function, you don't have to pass it.
for coverage_file in */*.cov
do
    cmd_gene() { awk '{print $5}' $coverage_file |sort | uniq -c | wc -l; }
    cmd_contig() { awk '{print $1}' $coverage_file |sort | uniq -c | wc -l; }
    cmd_gene 
    cmd_contig 
    #print "we found", $gene_count, "genes on ",$contig_count" contigs
done
If you want to define the functions outside the for loop, you would use $1 (not to be confused with awk's $1) and pass $coverage_file like you were doing before.

EDIT: Example of above
$ cat a.sh
cmd_gene() { awk '{print $5}' $1 |sort | uniq -c | wc -l; }
cmd_contig() { awk '{print $1}' $1 |sort | uniq -c | wc -l; }

for coverage_file in */*.cov
do
    cmd_gene $coverage_file
    cmd_contig $coverage_file
done

$ ls */*.cov
bf/a.cov

$ cat */*.cov
k141_85332.3 4119 19 A5 phnM_031
k141_85332.3 4119 19 A5 phnM_031
k141_85332.3 4119 28 A1 phnM_031
k141_85332.3 4119 28 A1 phnM_031
k141_85332.3 4119 8 A2 phnM_031
k141_85332.3 4119 8 A2 phnM_031
k141_88684 267 5 B10 phnM_032
k141_88684 268 5 B10 phnM_032
k141_88684 269 5 B10 phnM_032
k141_88684 270 5 B10 phnM_032
k141_88684 271 5 B10 phnM_032
k141_88684 272 5 B10 phnM_032

$ sh a.sh
       2
       2


                        
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