[Bioperl-guts-l] [Bug 1664] New: Bio::SeqIO::genbank didn't output ORIGIN Annotation::SimpleValue correctly

bugzilla-daemon at portal.open-bio.org bugzilla-daemon at portal.open-bio.org
Thu Jul 8 05:13:04 EDT 2004


http://bugzilla.open-bio.org/show_bug.cgi?id=1664

           Summary: Bio::SeqIO::genbank didn't output ORIGIN
                    Annotation::SimpleValue correctly
           Product: Bioperl
           Version: unspecified
          Platform: PC
        OS/Version: Windows XP
            Status: NEW
          Severity: normal
          Priority: P2
         Component: Bio::SeqIO
        AssignedTo: bioperl-guts-l at bioperl.org
        ReportedBy: jr at imb-jena.de


#!perl
use Bio::Seq::RichSeq;
use Bio::SeqIO::genbank;

my $col = Bio::Annotation::Collection->new();
my $sv = new Bio::Annotation::SimpleValue(-value => '5\' of gene
(Annotation::SimpleValue)');   
   $col->add_Annotation('origin', $sv);

my $seq    = Bio::Seq::RichSeq->new( -seq => 'ATG',
                                             -id  => 'start',
				             -accession_number => 'A001',
                                             -annotation => $col
				            );

my $stream = Bio::SeqIO->new(-format => 'GenBank');
   $stream->write_seq($seq);

output without space formating:
...
ORIGIN5' of gene (Annotation::SimpleValue)
        1 atg
//



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