使用Perl脚本（包括R脚本）检索访问编号列表的Go注释

我已经编写了一个Perl脚本来检索Go注释（分子函数，特别是带有Go id的函数）。为了检索go注释，我使用了一个来自R的chunck，它可以在几行中完成这项工作，并使用Perl格式化输出。但它不起作用

我有一个错误：

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;

---

非常感谢。

在双引号字符串中，Perl插入变量

qq```

是一个双引号字符串，因此

$lines

被解释为一个Perl变量，但它没有在任何地方用

my

声明，因此出现了错误

顺便说一句

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

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

chomp( my @lines = <ACC> );