Downloading sequence file with perl - perl

Question

I am trying to download the sequence file from the gene bank database using perl but it shows error. I don't have any guide to correct my program.
Can any one help me with this? The error is in line 6 (use Bio::DB::GenBank;)
File accnumber.txt is on my desktop and I am running the program from desktop itself. I am using CentOS.
#!usr/bin/perl -w
use strict;
use warnings;
use Bio::DB::GenBank;
open (INPUT_FILE, 'accnumber.txt');
open (OUTPUT_FILE, 'sequence_dwnl.fa');
while()
{
chomp;
my $line = $_;
my #acc_no = split(",", $line);
my $counter = 0;
while ($acc_no[$counter])
{
$acc_no[$counter] =~ s/\s//g;
if ($acc_no[$counter] =~ /^$/)
{
exit;
}
my $db_obj = Bio::DB::GenBank->new;
my $seq_obj = $db_obj->get_Seq_by_acc($acc_no[$counter]);
my $sequence1 = $seq_obj->seq;
print OUTPUT_FILE ">"."$acc_no[$counter]","\n";
print OUTPUT_FILE $sequence1,"\n";
print "Sequence Downloaded:", "\t", $acc_no[$counter], "\n";
$counter++;
}
}
close OUTPUT_FILE;
close INPUT_FILE;
These are errors I get:
Bareword "Bio::DB::GenBank" not allowed while "strict subs" in use at db.pl line 6.
Bareword "new" not allowed while "strict subs" in use at db.pl line 27.
Bareword "seq" not allowed while "strict subs" in use at db.pl line 29.
Execution of db.pl aborted due to compilation errors.

Answer 1

Since line you mention loads external Perl module Bio::DB::GenBank from CPAN, first thing that came to my mind: Is the module installed on your system?
Try running command cpan Bio::DB::GenBank as root (e.g. by prepending it with sudo). This should not hurt even if the module is installed, in that case it will check CPAN for updates.

Answer 2

In addition to the above answer,
Please use die function to check whether the files are opened.
open (INPUT_FILE, 'accnumber.txt');
open (OUTPUT_FILE, 'sequence_dwnl.fa');
Like this:
open (my $input_file, '<', 'accnumber.txt') or die "Could not open because $!\n";
open (my $output_file, '<', 'sequence_dwnl.fa') or die "Could not open because $!\n";
Also, please specify the purpose of opening each file with these operators:
< to open file in read only mode.
> to overwrite the file content.
>> to append the file content.
Also please check whether you have Bio::DB::GenBank module installed or not.
You can do that by running this in command line:
perldoc -l Bio::DB::GenBank or perl -MBio::DB::GenBank -e 1