Hi,
I used to usethis code to download sequence from genabnk ,now bioperl complains about sequence is empty, do yiu know if gen bank structure has been changed?
use Bio::SeqIO;
use Bio::Seq;
use Bio:B::EUtilities;
@refSeqIDs=qw(NC_000915.1 NC_017379.1 NC_017371.1 NC_017354.1);
foreach my $refSeqIDs (@refSeqIDs){
my $factory = Bio:B::EUtilities->new(-eutil => 'efetch',-db=> 'protein',- rettype => 'gb',
-email => '[email protected]',-id=> $refSeqIDs);
my $rawfile = "$refSeqIDs.gbk";
$factory->get_Response(-file =>"$refSeqIDs.gbk");
my $seqio_object = Bio::SeqIO->new(-format=>"Genbank",-file =>"$refSeqIDs.gbk");
while ( my $seq_object=$seqio_object->next_seq){
$sequence=$seq_object->seq;
print ("$sequence\n");
}
}
I used to usethis code to download sequence from genabnk ,now bioperl complains about sequence is empty, do yiu know if gen bank structure has been changed?
use Bio::SeqIO;
use Bio::Seq;
use Bio:B::EUtilities;
@refSeqIDs=qw(NC_000915.1 NC_017379.1 NC_017371.1 NC_017354.1);
foreach my $refSeqIDs (@refSeqIDs){
my $factory = Bio:B::EUtilities->new(-eutil => 'efetch',-db=> 'protein',- rettype => 'gb',
-email => '[email protected]',-id=> $refSeqIDs);
my $rawfile = "$refSeqIDs.gbk";
$factory->get_Response(-file =>"$refSeqIDs.gbk");
my $seqio_object = Bio::SeqIO->new(-format=>"Genbank",-file =>"$refSeqIDs.gbk");
while ( my $seq_object=$seqio_object->next_seq){
$sequence=$seq_object->seq;
print ("$sequence\n");
}
}
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