使用Perl腳本包含R腳本以檢索的accesion數

Question

名單我已經寫了一個Perl腳本來檢索圍棋註釋（分子功能尤其是去ID）轉到註釋。爲了檢索去註釋，我使用了一個R語句，可以在幾行內做到這一點，並使用Perl來格式化輸出。但它不起作用。

我有這個錯誤：

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. 

這是我的代碼：

#! 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; 

任何解決方案使用Perl腳本，R腳本來達到我的目的或合併兩者都應該是有用的。

輸出文件格式是這樣的：

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

謝謝你這麼多。

Answer 1

在雙引號中的字符串，Perl的插值變量。 qq`...`是一個雙引號字符串，所以$lines被解釋爲一個Perl的變量，但它並沒有被聲明爲my任何地方，因此錯誤。

BTW，

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

是錯誤的。它循環只有一次，在列表上下文中使用<>返回的句柄的所有行。在循環中，$_是chomped，但$_尚未填充那裏。相反，也許你想

chomp(my @lines = <ACC>);