[Bioperl-l] extracting ORGANISM line from genbank file

[Anna Kostikova]

hello Chris,

Well, my final aim is to get 2 files: first one is a fasta file with all 
the sequences, and the seconds one is simply a list of species names 
extracted from the same Genbank file. So that's why I though it would be 
a good thing to put all together into one script with bioperl objects.
Is there a better way to do it?

Thanks,
Anna

* Chris Fields <cjfields at illinois.edu> [Mon, 24 Aug 2009 07:55:56 
-0500]:
> Anna,
>
> It's stored in the Bio::Species object.  I have to say, though, I
> think you're using a stick of dynamite for a scalpel here; if you only
> need ORGANISM parse it out directly (it's much faster).  Or am I
> missing something?
>
> chris
>
> On Aug 24, 2009, at 4:20 AM, Anna Kostikova wrote:
>
> > Dear all,
> >
> > I am trying to extract species taxonomy from ORGANISM line. In fact
> > I only need a first line under ORGANISM tag (e.i. genus + species).
> > I though that it would be possible to do with the SeqBuilder object
> > by stating
> >
> > $builder->add_wanted_slot('display_id','species');
> >
> > the problem is, however, that I've got an empty file as a result.
> > What might be wrong with the script (see below)?
> > Thanks a lot in advance for any ideas,
> >
> > -------------------------------------------
> >
> > #!/usr/bin/perl
> > use strict;
> > use Bio::SeqIO;
> > use Bio::Seq::SeqBuilder;
> >
> > my $usage = "genbank_to_fasta_cleaning.pl infile outfile \n";
> >        my $infile = shift or die $usage;
> >        my $infileformat = 'Genbank' ;
> >        my $outfile = shift or die $usage;
> >        my $outfileformat = 'raw';
> > 		 my $i = 0;
> >
> >        my $seq_in = Bio::SeqIO->new('-file' => "<$infile",
> >                                     '-format' => $infileformat);
> >
> > 	     my $seq_out = Bio::SeqIO->new('-file' => ">$outfile",
> >                                      '-format' => $outfileformat);
> >
> > 		my $builder = $seq_in->sequence_builder();
> >
> >  $builder->want_none();
> >  $builder->add_wanted_slot('display_id','species');
> >
> >  while(my $seq = $seq_in->next_seq()) {
> >      $seq_out->write_seq($seq);
> >  }
> >
> >    exit;
> >
> > ----------------------------------------------------
> >
> > Anna
> > _______________________________________________
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>