Using Perl script including R script to retrive Go annotations for list of accesion number -

i have wrote perl script retrieve go annotations (molecular function go id). retrieve go annotation use chunck r can in few lines, , use perl format output. it's not working.

i have got error:

global symbol "$lines" requires explicit package name (did forget declare "my $lines"?) @ go_perl_r line 21. global symbol "$lines" requires explicit package name (did forget declare "my $lines"?) @ go_perl_r line 22. global symbol "$hits" requires explicit package name (did forget declare "my $hits"?) @ go_perl_r line 22. global symbol "$go" requires explicit package name (did forget declare "my $go"?) @ go_perl_r line 24. global symbol "@mf" requires explicit package name (did forget declare "my @mf"?) @ go_perl_r line 24. global symbol "$id" requires explicit package name (did forget declare "my $id"?) @ go_perl_r line 24. global symbol "$lines" requires explicit package name (did forget declare "my $lines"?) @ go_perl_r line 25. global symbol "$go" requires explicit package name (did forget declare "my $go"?) @ go_perl_r line 25. global symbol "@mf" requires explicit package name (did forget declare "my @mf"?) @ go_perl_r line 25. global symbol "@id" requires explicit package name (did forget declare "my @id"?) @ go_perl_r line 25. global symbol "$go" requires explicit package name (did forget declare "my $go"?) @ go_perl_r line 25. global symbol "@mf" requires explicit package name (did forget declare "my @mf"?) @ go_perl_r line 25. global symbol "@term" requires explicit package name (did forget declare "my @term"?) @ go_perl_r line 25. execution of go_perl_r aborted due compilation errors. 

this code :

#! usr/bin/perl  use warnings; use strict; use statistics::r;  $r = statistics::r->new(); $i = 1; # open 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 reach purpose using perl script, r script or merging both should useful.

the output file format :

p10214     go:xxxxxxx                    "aaaaaaaaaaaaaaaaaaaaa"     go:zzzzzzzz                    "bbbbbbbbbbbbbbbbbbbbb"     ...................                    q34f56     go:fffffffffff                       "ccccccccccccccccccccccc"     go:gggggg                        "hhhhhhhhhhhhhhhhhhhh"     ................... 

thanks much.

in double quoted strings, perl interpolates variables. qq`...` double-quoted string, $lines interpreted perl variable, hasn't been declared my anywhere, hence error.

btw,

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

is wrong. iterates once, <> used in list context returns lines of filehandle. inside loop, $_ chomped, $_ hasn't been populated there. instead, maybe wanted

chomp( @lines = <acc> );