[Bioperl-l] [How to add features in genbank flat file]
moretti at igs.cnrs-mrs.fr
Tue Feb 15 09:25:38 EST 2005
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
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:
my $acc=$ARGV or die "\n\tThe accession number you seek for is missing.
\n\tTry something like: $0 NM_178432\n\n";
my $query_string = "$acc";
my $query = Bio::DB::Query::GenBank->new(-db=>'nucleotide',
my $gb = new Bio::DB::GenBank;
my $stream = $gb->get_Stream_by_query($query);
my $seq = $stream->next_seq();
$result =~ s/^1.*$//;
How can I add most of features to my nucleotide flat files ?
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