(( 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
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.
- "reciprocal blast" functions (see
- 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 (
- 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
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)