How can I save BioPerl sequence nested features in genbank or embl format?

Posted by Ryan Thompson on Stack Overflow See other posts from Stack Overflow or by Ryan Thompson
Published on 2010-04-27T18:36:14Z Indexed on 2010/04/27 21:13 UTC
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bioperl

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bioinformatics

In BioPerl, a sequence object can have any number of features, and each of these can have subfeatures nested within them. For example, a feature may be a complete coding sequence of a gene, and its subfeatures might be individual exons that are concatenated to form the full coding sequence.

However, when I use BioPerl to write a sequence object to a file in genbank or embl format, only the top-level features are written to the file, not the sub-features nested within the top-level features. How can I store my subfeatures in sequence files? Should I just convert all my subfeatures into top-level features, and then reconstruct the tree structure next time I read in the sequence?

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