[Bioperl-l] Blat wrapper rewrite (and a PSL 'bonus')

Chris Fields cjfields at illinois.edu
Fri Nov 5 11:06:01 EDT 2010


All,

I have a local Blat wrapper refactoring that I had to quickly write up for some local work.  Unfortunately, the original Blat wrapper in BioPerl-Run (Bio::Tools::Run::Alignment::Blat) had parameters that weren't compatible with more recent versions of Blat, and which didn't even use most passed parameters, so it was unfortunately pretty much useless in my hands (one couldn't designate whether the query/db was dna, prot, dnax, etc).

Anyone object to just scrapping the original Blat wrapper in place of this one (which allows all current Blat parameters)?  I plan on having it pass the original tests and adding a bit more.

As a small semi-'bonus', along with this I am also writing up additional code for Bio::SearchIO::psl that allows switching parsing logic to cluster distinct regional hits; basically, same query = Result, each Hit = distinct region, each set of blocks = HSP.  This is in response from some users here to making the bp_search2gff.pl script work with PSL a little better.  Should be added in over the next few weeks.

chris


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