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Gmane
From: =?utf-8?B?eW9uZ2xpQHllc2xhYi5jb20=?= <yongli <at> yeslab.com>
Subject: =?utf-8?q?question_about_bioperl_program?=
Newsgroups: gmane.comp.lang.perl.bio.general
Date: Saturday 1st December 2012 06:10:15 UTC (over 3 years ago)
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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