Issue 280 #292
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Issue 280 #292
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…ORFs was that the reading process waas **blocking**, due to using a simple queue with a bare put instead of put_nowait. This single change makes the code finally parallel and provides therefore a massive speed-up.
Removing the evaluation of invalidity causes bugs. It's better to recalculate constantly in this case.
Edited Travis to reflect the changes in master
…erably slowed down `serialise`.
…. Also, now using properties to avoid calculating the invalidity of a BED12 object over and over again. This should lead to some more speed improvements.
… Some improvements but currently broken, and it could be better
…er from bioPython is so slow
…as opposed to only XMLs.
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Changes:
invalidproperty (now it is lazily evaluated) and by using NumPy arrays in some critical points of the code.Bio.SearchIO.parserather thanBio.Blast.NCBIXML.parse. The former is actually slower, but is the new standard inBioPython. Switching to it will ensure future compatibility.This should close #269 and #280.