1 Dec 2012 07:10
question about bioperl program
yongli <at> yeslab.com <yongli <at> yeslab.com>
2012-12-01 06:10:15 GMT
2012-12-01 06:10:15 GMT
Dear Sir or Madam,
I just begin to learn bioperl and am using a bioperl program to extract a kind of bacterial genes sequences
from genome genbank file. I download NC_003450.gbk, ppt, ffn files. NC_003450 is a kind of bacterial
genome genbank file. My bioperl code as follows:
use Bio::Seq;
use Bio::SeqIO;
$seqio_obj=Bio::SeqIO->new (-file=>'NC_003450.gbk',-format=>'genbank');
# $seq_obj=$seqio_obj->next_seq;
while($seq_obj=$seqio_obj->next_seq)
{
$display_name=$seq_obj->display_name;
$desc=$seq_obj->desc;
$seq=$seq_obj->seq;
$acc = $seq_obj->accession_number;
$seqio_obj = Bio::SeqIO->new(-file => '>sequence.fasta', -format => 'fasta' );
$seqio_obj->write_seq($seq_obj);
}
After the program runned I just gain a genome complete sequence without a file including every gene
sequence one by one. I want to get the genes sequences one by one in a fasta files. So I write you for help.
Yong Li
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