[ create a new paste ] login | about

Link: http://codepad.org/sxfvq3GE    [ raw code | fork ]

Perl, pasted on May 10:
use Bio::FeatureIO::gff;
use Bio::SeqFeature::Annotated;
open($fh,"chr01_Canonical.gff3") or die "can't open file $!";

my $featureOut = Bio::FeatureIO->new(
    -format => 'gff',
    -version => 3,
    -fh => $fh,
    -validate_terms => 0, #boolean. validate ontology terms online?  default 0 (false).
  );
#@features= $featureOut->next_feature_group;
my @toplevel_features;
           while (my @fg = $featureOut->next_feature_group) {
               push(@toplevel_features, @fg);
           }
print @toplevel_features;



------------- EXCEPTION: Bio::Root::Exception -------------
MSG: Parent with ID 13101.t00002 not found!
STACK: Error::throw
STACK: Bio::Root::Root::throw /usr/lib/perl5/site_perl/5.10.0/Bio/Root/Root.pm:368
STACK: Bio::FeatureIO::gff::next_feature_group /usr/lib/perl5/site_perl/5.10.0/Bio/FeatureIO/gff.pm:227
STACK: /home/vasilis/workspace/mrnaClean/gffParser.pl:15
-----------------------------------------------------------


Create a new paste based on this one


Comments: