[Bioperl-l] progress on Bio::Search::Tiling

Sendu Bala bix at sendu.me.uk
Wed May 27 21:46:04 UTC 2009

Mark A. Jensen wrote:
> With the current bioperl-dev revision of MapTiling (r15712), I get
> 6/1095 "failures", which you may judge below. The results indicate to
> me that the algorithm is working, and that the translated dna
> coordinate transformations (which kick in based on study of the
> algorithm name) are correct, at least in this limited set.
> Comments *highly* appreciated-- many thanks for any time you spend
> considering this.
> not ok 389 - tricky.wublast(1)
> #   Failed test 'tricky.wublast(1)'
> #   at blast-MapTiling.t line 571.
> #     '0.222'
> #         >
> #     '0.9'
> # Not sure why frac_identical should be > 0.9, when no reported 'Identities' value is greater than 24% /maj

That's almost certainly my mistake. For those two cmp tests I just 
didn't know what the answer was supposed to be, so probably picked a 
figure out of thin air based on the subsequent 2 answers.

You should manually (or by some other independent method) check what the 
correct answers are for those two cmp tests and change them to 'is' tests.

Thanks for your work on this. I'd be interested in seeing a summary of 
what you've achieved at the end. Especially if you point out areas where 
the old system was getting things wrong - people may want to recheck 
their results with the new modules.

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