Hi everyone,

I have wrote a perl script to retrieve Go annotations (Molecular Function especially with go id). To retrieve go annotation i use a chunck from R that can do this in few lines, and use Perl to format the output. But it's not working.

I have got this error:

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.

This is my code :

#! 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;

Any solution to reach my purpose using Perl script, R script or merging both should be useful.

The output file format is like :

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

Thanks you so much