I'm using BioPerl module to obtain a string from a set of parameters. I followed the HOWTO:Beginners page. The module apparently returns a hash object. How do I get the actual string out of the hash object?
use Bio::DB::GenBank;
use Data::Dumper;
my $gb = Bio::DB::GenBank->new(-format => 'Fasta',
-seq_start => 1,
-seq_stop => 251,
-strand => 1
-complexity => 1);
my $seq = $gb->get_Seq_by_acc('NG_016346');
my $sequence_string = lc($seq->seq());
my $seq_obj = Bio::Seq->new(-seq => $sequence_string,
-alphabet => 'dna' );
my $prot_obj = $seq_obj->translate;
print Dumper($prot_obj);
The data dumper prints the following:
$VAR1 = bless( {
'primary_seq' => bless( {
'length' => 83,
'_root_verbose' => 0,
'_nowarnonempty' => undef,
'seq' => 'RLCVKEGPWPAVEGTWSWG*HRPGSRACPRWGAPNSVQATSYTPSPTHAPFSVSPIPIC*MSLLEASCWPGSREDGARMSAGM',
'alphabet' => 'protein'
}, 'Bio::PrimarySeq' ),
'_root_verbose' => 0
}, 'Bio::Seq' );
How do I obtain 'seq' that is stored in $prot_obj
?
I tried
print $prot_obj{'primary_seq'}{'seq'};
but it doesn't print anything. Data dumper printed the word bless
. Maybe seq
is a field of an object oriented variable.
The correct format for accessing object properties uses ->
:
print $prot_obj->{'primary_seq'}->{'seq'};