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What is the Deobfuscator?

The Deobfuscator was written to make it easier to determine the methods that are available from a given BioPerl module (a common BioPerl FAQ).

BioPerl is a highly object-oriented software package, with often multiple levels of inheritance. Although each individual module is usually well-documented for the methods specific to it, identifying the inherited methods is less straightforward.

The Deobfuscator indexes all of the BioPerl POD documentation, taking account of the inheritance tree (thanks to Class::Inspector), and then presents all of the methods available to each module through a searchable web interface.

Where can I find the Deobfuscator?

The Deobfuscator is currently available here, indexing bioperl-live.

We are currently working on a Deobfuscator interface capable of browsing the bioperl-run and bioperl-ext packages.

Have a suggestion?

By all means, put it here! Or better yet, ask for the source and contribute your code...

Feature requests

  • option to view search results in separate window (Amir Karger). Added in v0.0.3.
  • sort classes alphabetically (Amir Karger). Added in v0.0.3.
  • indicate that search is class names only (Amir Karger). Added in v0.0.3.
  • make "no match" search error more prominent (Amir Karger). Added in v0.0.3.
  • change title to "BioPerl Deobfuscator" (Amir Karger). Added in v0.0.3.
  • more cell padding -- too cramped (Sendu Bala). Added in v0.0.3.
  • Show which version of BioPerl is indexed on the the deob_interface.cgi page (Phillip SanMiguel). Added 10/6/2006.
  • allow search of function names -- e.g., which module has the revcom method? (Amir Karger)
  • clicking on method name causes in-place reveal via css/javascript rather than opening a separate window (Sendu Bala)
  • Have column headings for the methods table in the fixed part of the page, rather than the scroll box. (Phillip SanMiguel)
  • Be able to handle multiple packages in a single file. (Chris Fields)


  • Bio::Ontology modules are missing prefix in browsable list, and when clicked the lower table of methods fails to open (Hilmar Lapp). Fixed in v0.0.3.
  • methods listed as "not documented" for "Returns" and "Usage" when in fact they are. e.g. Bio::Seq::SeqWithQuality. (Phillip SanMiguel)
  • Non-BioPerl modules in the inheritance tree link to Pdoc, not their real docs. e.g. Exporter inherited by Bio::Root::RootI (Dave Messina)
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