[Bioperl-l] extracting ORGANISM line from genbank file

[Hilmar Lapp]

Hi Anna,

sequence formats all have some varying amount of information that must  
be present or otherwise the syntax is invalid. If what you need is a  
two-column table of display_id and species name, then I would simply  
write that, and not squeeze it into a standard sequence format.  
(Unless you actually do want the sequence too, in which case you need  
to add it as a wanted slot; even in that case though, writing a three- 
column table might serve you better.)

	-hilmar

On Aug 24, 2009, at 5:20 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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-- 
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: Hilmar Lapp  -:-  Durham, NC  -:-  hlapp at gmx dot net :
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