SeqLab (Perl)

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(( Disambiguation: See other uses of SeqLab. ))

SeqLab is the name of a ball of Perl written by Jay Hannah, mainly late in 2006. It makes heavy use of BioPerl, BLAST, and many CPAN packages. The project was hosted as seqlab.net for a couple of years.

Download the entire project:

svn checkout https://clabsvn.ist.unomaha.edu/anonsvn/user/jhannah/UNO/seqlab

Documentation

Apologies for the formatting. This all made sense when I had my own domain attached -- the HTML was actually rendered as HTML, etc. Now you're just seeing the raw code.  :) --Jhannah 11:54, 9 March 2008 (CDT)

  • seqlab/tutorial.pod - A tutorial I barely started writing.
  • htdocs/lib/install - An install document that works pretty well.

Highlights

  • "reciprocal blast" functions (see cross_blast())
    • formatdb, etc., all automated. Sequences de-duping built in.
    • blasts an arbitrary number of sequences against each other and gathers stats across all results based on arbitrary hit "tiers." Tracks all relationships inside these different "tiers" of hits (Pools.pm).
    • creates Affymetrix microarray definition files from results.
  • Logging via Log::Log4perl, test suite included (mediocre coverage?).
jhannah@cac-dev:~/src/seqlab> find ./ -name "*pm"
./seqlab/SeqLab/GeneChip/InstructionFileDetail.pm
./seqlab/SeqLab/t/HashTest.pm
./seqlab/SeqLab/SequenceSet/DeDupe.pm
./seqlab/SeqLab/DB/LocalFiles.pm
./seqlab/SeqLab/BlastStats.pm
./seqlab/SeqLab/SequenceSet.pm
./seqlab/SeqLab/DB.pm
./seqlab/SeqLab/Dictionary.pm
./seqlab/SeqLab/BlastResults.pm
./seqlab/SeqLab/Registry.pm
./seqlab/SeqLab/Base.pm
./seqlab/SeqLab/Pools.pm
./seqlab/SeqLab/PrimersAndSeq.pm
./seqlab/SeqLab/H_Pools.pm
./seqlab/SeqLab/Hash.pm
./seqlab/SeqLab.pm

Status

I abandoned my maiden voyage into bioinformatics, called "SeqLab," as a stand-alone entity when the subsequent thousand tasks I worked turned out to be unrelated to all the software I had built so far. My naive grand unification vision for all of bioinformatics didn't quite work out as I had planned. -laugh- Nowadays I just cherry-pick solutions out of its guts on demand.  :)

I'm happy to field any questions you have about that code, if it helps you any.

--Jhannah 13:19, 7 March 2008 (CST)

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