Bio::SeqFeature::Tools::Unflattener Bio::SeqFeature::Tools::Unflattener is a Perl module that turns flat list of genbank-sourced features.
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Perl module hierarchy bioperl SeqFeature hierarchy SeqFeature tools SeqFeature

Bio::SeqFeature::Tools::Unflattener Description

Bio::SeqFeature::Tools::Unflattener is a Perl module that turns flat list of genbank-sourced features. Bio::SeqFeature::Tools::Unflattener is a Perl module that turns flat list of genbank-sourced features into a nested SeqFeatureI hierarchy.SYNOPSIS # standard / generic use - unflatten a genbank record use Bio::SeqIO; use Bio::SeqFeature::Tools::Unflattener; # generate an Unflattener object $unflattener = Bio::SeqFeature::Tools::Unflattener->new; # first fetch a genbank SeqI object $seqio = Bio::SeqIO->new(-file=>'AE003644.gbk', -format=>'GenBank'); my $out = Bio::SeqIO->new(-format=>'asciitree'); while ($seq = $seqio->next_seq()) { # get top level unflattended SeqFeatureI objects $unflattener->unflatten_seq(-seq=>$seq, -use_magic=>1); $out->write_seq($seq); @top_sfs = $seq->get_SeqFeatures; foreach my $sf (@top_sfs) { # do something with top-level features (eg genes) } }Most GenBank entries for annotated genomic DNA contain a flat list of features. These features can be parsed into an equivalent flat list of Bio::SeqFeatureI objects using the standard Bio::SeqIO classes. However, it is often desirable to unflatten this list into something resembling actual gene models, in which genes, mRNAs and CDSs are nested according to the nature of the gene model.The BioPerl object model allows us to store these kind of associations between SeqFeatures in containment hierarchies -- any SeqFeatureI object can contain nested SeqFeatureI objects. The Bio::SeqFeature::Tools::Unflattener object facilitates construction of these hierarchies from the underlying GenBank flat-feature-list representation. Requirements: · Perl

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