使用Perl脚本包含R脚本以检索的accesion数

Question

名单我已经写了一个Perl脚本来检索围棋注释（分子功能尤其是去ID）转到注释。为了检索去注释，我使用了一个R语句，可以在几行内做到这一点，并使用Perl来格式化输出。但它不起作用。

我有这个错误：

Global symbol "$lines" requires explicit package name (did you forget to declare "my $lines"?) at GO_Perl_R line 21. Global symbol "$lines" requires explicit package name (did you forget to declare "my $lines"?) at GO_Perl_R line 22. Global symbol "$hits" requires explicit package name (did you forget to declare "my $hits"?) at GO_Perl_R line 22. Global symbol "$go" requires explicit package name (did you forget to declare "my $go"?) at GO_Perl_R line 24. Global symbol "@MF" requires explicit package name (did you forget to declare "my @MF"?) at GO_Perl_R line 24. Global symbol "$id" requires explicit package name (did you forget to declare "my $id"?) at GO_Perl_R line 
24. Global symbol "$lines" requires explicit package name (did you forget to declare "my $lines"?) at GO_Perl_R line 25. Global symbol "$go" requires explicit package name (did you forget to declare "my $go"?) at GO_Perl_R line 25. Global symbol "@MF" requires explicit package name (did you forget to declare "my @MF"?) at GO_Perl_R line 
25. Global symbol "@id" requires explicit package name (did you forget to declare "my @id"?) at GO_Perl_R line 25. Global symbol "$go" requires explicit package name (did you forget to declare "my $go"?) at GO_Perl_R line 25. Global symbol "@MF" requires explicit package name (did you forget to declare "my @MF"?) at GO_Perl_R line 25. Global symbol "@term" requires explicit package name (did you forget to declare "my @term"?) at GO_Perl_R line 25. Execution of GO_Perl_R aborted due to compilation errors. 

这是我的代码：

#! usr/bin/perl 

use warnings; 
use strict; 
use Statistics::R; 

my $R = Statistics::R->new(); 
my $i = 1; 
# open the file containing uniprot accession numbers 
open (ACC, "acc_numbers.txt") or die "Can't open acc_numbers.txt: $!\n"; 

while (my @lines=<ACC>) { 
    chomp($_); 
} 

$R -> startR; 
$R -> send('library(mygene);'); 
$R -> run (q`sink('GO_MF.txt')`); 
$R -> run (q`sink()`); 
$R -> run (
    qq`while($lines){ 
     res<-query($lines,fields='go')$hits, 
     sink('GO_MF.txt', append=TRUE), 
     while($i <= length(res$go$MF[[1]]$id) { 
      print(paste($lines,"\n",res$go$MF[[1]]$id[$i],"\t",res$go$MF[[1]]$term[$i],"\n"), 
     sink(), 
     } 
    }` 
); 

exit 0; 

任何解决方案使用Perl脚本，R脚本来达到我的目的或合并两者都应该是有用的。

输出文件格式是这样的：

P10214 
    GO:xxxxxxx     "aaaaaaaaaaaaaaaaaaaaa" 
    GO:zzzzzzzz     "bbbbbbbbbbbbbbbbbbbbb" 
    ...................     
Q34F56 
    GO:fffffffffff      "ccccccccccccccccccccccc" 
    GO:gggggg      "hhhhhhhhhhhhhhhhhhhh" 
    ................... 

谢谢你这么多。

Answer 1

在双引号中的字符串，Perl的插值变量。 qq`...`是一个双引号字符串，所以$lines被解释为一个Perl的变量，但它并没有被声明为my任何地方，因此错误。

BTW，

while (my @lines=<ACC>) { 
    chomp($_); 
} 

是错误的。它循环只有一次，在列表上下文中使用<>返回的句柄的所有行。在循环中，$_是chomped，但$_尚未填充那里。相反，也许你想

chomp(my @lines = <ACC>);