[Bioperl-l] [How to add features in genbank flat file]

[Sebastien Moretti]

Hello,
I saw that Genbank web site have changed:
Now, features like 'SNPs' are no more included in the EST flat files.
At the NCBI web site, we must click on 'features: SNP' to add them in our flat 
file.

With BioPerl, 1.4 or 1.5, it's the same, the variation features are no more 
included in the EST flat files that I upload.

Here is the script I use:
	#!/usr/bin/perl -w
	
	use strict;
	use Bio::DB::GenBank;
	use Bio::DB::Query::GenBank;
	use Bio::SeqIO;
	my $acc=$ARGV[0] or die "\n\tThe accession number you seek for is missing.
\n\tTry something like: $0 NM_178432\n\n";
	
	$acc=$acc."[Accession]";
	
	my $query_string = "$acc";
	my $query = Bio::DB::Query::GenBank->new(-db=>'nucleotide',
	                                                 -query=>$query_string);
	
	my $gb = new Bio::DB::GenBank;
	my $stream = $gb->get_Stream_by_query($query);
	
	my $out=Bio::SeqIO->new(-format=>'genbank');
	my $seq = $stream->next_seq();
	
	my $result=$out->write_seq($seq);
	$result =~ s/^1.*$//;
	#print $out->write_seq($seq);
	print $result;
	
	exit;


How can I add most of features to my nucleotide flat files ?

Thanks

-- 
Sebastien Moretti
CNRS - IGS
31 chemin Joseph Aiguier
13402 Marseille cedex