[Bioperl-l] question about bioperl program

[Brian Osborne]

Yong Li,

You want to take a look at this HOWTO:

http://www.bioperl.org/wiki/HOWTO:Feature-Annotation

Those genes you see in the file are features in the genome sequence.

Brian O.



On Dec 1, 2012, at 1:10 AM, yongli at yeslab.com wrote:

> 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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