yongli@yeslab.com | 1 Dec 07:10 2012

question about bioperl program

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

Gmane